Disease resistant plants

Abstract

NOT VISIBLE DUE TO STATUS OF PATENT

Description

DISEASE RESISTANT PLANTSCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to United States Provisional Application No. 63 / 617,712, filed January 4, 2024, the entire contents of which is incorporated by reference herein.REFERENCE TO SEQUENCE LISTING

[0002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled SOILC.002WO_ST26.XML, created and last saved on January 2, 2025 which is 341,401 bytes in size. The information in the electronic Sequence Listing is incorporated herein by reference in its entirety.STATEMENT REGARDING FEDERALLY SPONSORED R&D

[0003] This invention was made with government support under Grant No. 2126741 awarded by the National Science Foundation and Grant No. 2020-33610-31993 awarded by the United States Department of Agriculture, National Institute of Food and Agriculture. The government has certain rights in the invention.FIELD

[0004] The present disclosure relates to disease resistant plants. More specifically, the disclosure relates to plants that are resistant to Ca. Liberibacter infection and / or its associated diseases, such as Huanglongbing (HLB), also known as citrus greening disease, and Zebra Chip (ZC) disease.BACKGROUND OF THE INVENTION

[0005] Huanglongbing (HLB) is a disease caused by species of the phloem-limited, gram-negative bacteria of genus Ca. Liberibacter. In the U.S., the predominant pathogenic species is Ca. Liberibacter asiaticus (Las); whereas Ca. Liberibacter africanus (Laf) and Ca. Liberibacter americanus (Lam) are the predominant pathogenic species in South Africa and Brazil, respectively. Ca. Liberibacter is a vector-transmitted pathogen. All commercial citrus plants aresusceptible to HLB, and infected citrus plants will irrevocably decline. Similarly, Zebra Chip (ZC) disease occurs in commercial potato fields in the United States, Mexico, Central America, and New Zealand and is caused by fastidious alpha-proteobacterium belonging to the ‘ Candidatus' genus Liberibacter, Candidatus Liberibacter solanacearum' (CLso). Due to the rapid spread of these diseases in commercial crops, there remains a strong need for development of plants that are tolerant or resistant to HLB and / or ZC disease.SUMMARY OF THE INVENTION

[0006] In one aspect a plant, a plant part or a plant seed comprising plant cells is provided which comprises a modification to two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Putative F-box protein (PP2-B12), Cysteine Protease (CP), and Lethal Leaf Spot 1 (List).

[0007] In some embodiments, the modification confers resistance or tolerance to Ca. Liberibacter infection in the plant, plant part or the plant seed relative to the plant, plant part or the plant seed of the same variety lacking the modification. In some embodiments, resistance encompasses tolerance to Ca. Liberibacter infection. In some embodiments, the modification confers resistance or tolerance to infection by one or more bacterial species from the genus Ca. Liberibacter. In some embodiments, resistance encompasses a reduction of bacterial load or bacterial titer upon infection or reduction of ability to be infected by a Ca. Liberibacter species. In some embodiments, the bacterial titer is reduced by at least 50% in the modified plant, plant part or the plant seed relative to the plant, plant part or the plant seed of the same variety lacking the modification. In some embodiments, the Ca. Liberibacter species include Candidatus Liberibacter asiaticus (CLas), Candidatus Liberibacter solanacearum (CLso), or a combination thereof.

[0008] In some embodiments, the plant, plant part or the plant seed comprises a modification to both ACD2 and Llsl genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to both CP and Llsl genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to ACD2, Llsl and CP genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to ACD2, Llsl, PP2- B12 and CP genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to both ACD2 and PP2-B12 genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to both ACD2 and CP genes. In some embodiments, the plant,plant part or the plant seed comprises a modification to both CP and PP2-B 12 genes. In some embodiments, the plant, plant part or the plant seed comprises a modification to both PP2-B 12 and Llsl genes.

[0009] In some embodiments, a plant, plant part or a plant seed is provided that comprises plant cells comprising a modification at two or more wild-type genomic loci. In some embodiments, the two or more wild-type genomic loci are independently selected from the genetic loci of SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or any sequence comprising at least 95% identity therewith.

[0010] In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or the plant seed is provided that comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith.

[0011] In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8 and 30 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID Nos: 25 and 28 or a sequence comprising at least 95% identity therewith. In other embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant pail or the plant seed comprises a genetic modification to a wildtype genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8 and 30 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomiclocus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25 and 28 or a sequence comprising at least 95% identity therewith. In other embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8 and 30 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25 and 28 or a sequence comprising at least 95% identity therewith.

[0012] In some embodiments, a plant, plant part or a plant seed is provided that comprises plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith. In some embodiments, a plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111,120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith. In some embodiments, a plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.

[0013] In other embodiments, a plant, plant part or a plant seed is provided that comprises plant cells comprising a modification to one or more wild-type genomic loci comprising SEQ ID NOs: 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76,87, 94, 106, 116, 96, 108, 1 18, 99, 1 11 , 121 , 122, 123, 124,120 or a sequence comprising at least 95% identity therewith.

[0014] In some embodiments, the plant, plant part or the plant seed of interest is of a citrus variety. In some embodiments, the citrus is a Carrizo, Hamlin, Sour Orange, US-812, Swingle, Flying Dragon, Grapefruit or a Valencia variety. In some embodiments, the citrus is a rootstock variety. In some embodiments, the rootstock variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, pomelo, citron, grapefruit, or a hybrid derived from those varieties. In some embodiments, the citrus is a scion variety. In some embodiments, the scion variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, pomelo, citron, grapefruit, or a hybrid derived from those varieties. In some embodiments, the citrus is an interstock variety. In some embodiments, the interstock variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, pomelo, citron, grapefruit, or a hybrid derived from those varieties.

[0015] In some embodiments, the modification is a deletion. In some embodiments, the modification is a substitution. In some embodiments, the modification is an insertion. In some embodiments, the modification comprises an indel. In some embodiments, the indel results in a frameshift mutation. In some embodiments, the indel results in a missense mutation. In some embodiments, the indel results in a nonsense mutation. In some embodiments, the indel results in a neutral mutation. In some embodiments, the indel results in a silent mutation.

[0016] In some embodiments, the plant, plant part, plant seed, scion, interstock and / or rootstock are transgenic. In some embodiments, the plant, plant part, plant seed, scion, interstock and / or rootstock are non-transgenic.

[0017] In some embodiments, a plant, plant part or a plant seed is provided that comprises a modification to two or more endogenous genes or regulatory elements thereof, selected from the group consisting of Accelerated Cell Death 2 (ACD2), Putative F-box protein (PP2-B12), Cysteine Protease (CP), and Lethal Leaf Spot 1, (Lis 1). In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0018] In some embodiments, a plant, plant part or a plant seed is provided that comprises a modification to two or more wild-type genomic loci selected from SEQ ID Nos: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0019] In some embodiments, the plant, plant part or a plant seed comprises a plant seed comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of the SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith. In some embodiments, plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0020] In some embodiments, the plant, plant part or a plant seed comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122,118 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121,116 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0021] In some embodiments, the plant, plant part or a plant seed comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or a plant seed is provided that comprises a plant seed comprising plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a modificationto a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61 , 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0022] In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 8 and 30 or a sequence comprising at least 95% identity therewith. In other embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising the SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 25, 28 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part or the plant seed is provided that comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 8 and 30 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID Nos: 25, 28 or a sequence comprising at least 95% identity therewith. In other embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0023] In some embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID Nos: 8, 30 or a sequence comprising at least 95% identity therewith. In other embodiments, the plant, plant part or the plant seed comprises a genetic modification to a wildtype genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 25,28 or a sequence comprising at least 95% identity therewith. In some embodiments, the plant, plant part, plant seed is non-transgenic.

[0024] In another aspect, a Valencia plant, plant part or a plant seed is provided that comprises plant cells comprising a modification to one or more of wild-type genomic locicomprising any one of SEQ ID Nos: 8, 30, 25, 28, 15 or a sequence comprising at least 95% identity therewith.

[0025] In some embodiments, the Valencia plant, plant part or a plant seed comprises a modification to wild-type genomic loci comprising any one of SEQ ID Nos: 8, 30 or a sequence comprising at least 95% identity therewith and any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith. In some embodiments, the Valencia plant, plant part or a plant seed comprises a modification to a wild-type genomic loci comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a genomic loci comprising any one of SEQ ID Nos: 8, 30 or a sequence comprising at least 95% identity therewith and a wild-type genomic loci comprising any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith. In some embodiments, the Valencia plant, plant part or a plant seed is non- transgenic. In some embodiments, the Valencia plant, plant part or a plant seed is transgenic.

[0026] In another aspect, a method of generating a modified citrus plant having resistance or tolerance to infection by a bacterial species from the genus Ca. Liberibacter is provided. The method comprises the steps of (a) modifying two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot 1 (Llsl) gene of a citrus plant cell such that expression of the said genes is knocked down. In some embodiments, the expression of the said genes is reduced. In some embodiments, the interaction of the polypeptide encoded by said genes with at least one effector protein secreted by one or more bacterial species from the genus Ca. Liberibacter is reduced; and (b) regenerating the modified plant from said plant cell or a progenitor cell thereof. In some embodiments, the modified citrus plant is resistant to Ca. Liberibacter infection relative to a citrus plant lacking the modification.

[0027] In some embodiments, the modified citrus plant that is resistant to Ca. Liberibacter infection has a reduced bacterial titer relative to a citrus plant lacking the modification. In some embodiments, the bacterial titer is reduced by at least 50% in the modified plant relative to a citrus plant lacking the modification.

[0028] In some embodiments, a Carrizo plant, plant part or a plant seed, is provided comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84,65, 76, 87, 94, 106, 116, 96, 108, 1 18, 99, 1 11 , 121 , 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

[0029] In some embodiments, the Carrizo plant, plant part or a plant seed is provided that comprises plant cells comprising a genetic modification to two or more of wild-type genomic loci comprising SEQ ID NO: 39 or a sequence comprising at least 95% identity therewith, SEQ ID NO:41 or a sequence comprising at least 95% identity therewith, SEQ ID NO:43 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 63 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 73 or a sequence comprising at least 95% identity therewith and SEQ ID NO:84 or a sequence comprising at least 95% identity therewith.

[0030] In some embodiments, the Carrizo plant, plant part or plant seed comprises plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith. In some embodiments, the Carrizo plant, plant part or plant seed comprises plant cells comprising a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith and a modification to a genomic locus comprising any one of SEQ ID NOs: 43, 65, 76, 87 or a sequence comprising at least 95% identity therewith.

[0031] In some embodiments, a Carrizo plant, plant part or plant seed comprises plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 40, 62, 71, 72, 83, 42, 64, 74, 75, 85, 86, 44, 66, 77, 78 and 88 is provided.

[0032] In some embodiments, the Carrizo plant, plant part or a plant seed is non- transgenic. In some embodiments, the Carrizo plant, plant part or a plant seed is transgenic.

[0033] In some embodiments, a Hamlin plant, plant part or a plant seed, is provided comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

[0034] In some embodiments, the Hamlin plant, plant part or a plant seed is provided that comprises plant cells comprising a modification to one or more of wild-type genomic loci comprising the SEQ ID NO: 50 or a sequence comprising at least 95% identity therewith, SEQ ID NO:52 or a sequence comprising at least 95% identity therewith, SEQ ID NO:55 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 94 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 106 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 116 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 96 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 108 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 118 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 99 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 111 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 120 or a sequence comprising at least 95% identity therewith.

[0035] In some embodiments, the Hamlin plant, plant part or plant seed comprises plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin plant, plant part or plant seed comprises plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 55, 99, 111, 120 or a sequence comprising at least 95% identity therewith.

[0036] In some embodiments, the Hamlin plant, plant part or plant seed comprises plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 51, 53, 54, 56, 57, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112 and 32 is provided.

[0037] In some embodiments, a Hamlin plant, plant pail or a plant seed is provided comprising plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 51, 53, 54, 56, 57, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112 and 32.

[0038] In some embodiments, a Hamlin plant, plant part or a plant seed is provided that comprises plant cells comprising a modified genomic locus comprising any one of SEQ ID NOs:40, 62, 71 , 72, 83 or a sequence comprising at least 95% identity therewith, any one of SEQ ID NOs: 42, 64, 74, 75, 85, 86 or a sequence comprising at least 95% identity therewith and any one of SEQ ID NOs: 44, 66, 77, 78, 88 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin plant, plant part or plant seed comprises plant cells comprising a modified genomic locus comprising SEQ ID NO: 51 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 53 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 54 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 56 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 57 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 95 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 107 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 117 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 97 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 98 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 109 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 110 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 119 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 100 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 101 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 112 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 32 or a sequence comprising at least 95% identity therewith.

[0039] In some embodiments, the Hamlin plant, plant part or a plant seed is non- transgenic. In some embodiments, the Hamlin plant, plant part or a plant seed is transgenic.

[0040] In some embodiments, a Valencia plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith is provided. In some embodiments, the Valencia plant, plant part or a plant seed is non-transgenic. In some embodiments, the Valencia plant, plant part or a plant seed is transgenic.BRIEF DESCRIPTION OF THE DRAWINGS

[0041] FIG. 1A illustrates the average weeks the edited and non-edited tomato plants were alive after inoculation with CLso-infected psyllids.

[0042] FIG. IB illustrates the 12- week-old PTC-C edited tomato plant after inoculation with Clso-infcctcd psyllids.

[0043] FIG. 1C illustrates the 12-week-old Cyp edited tomato plant after inoculation with Clso-infected psyllids.

[0044] FIG. 2 illustrates the Valencia protoplasts that were transfected using Polyethylene glycol (PEG)-mediated transfection method.

[0045] FIGS. 3A and 3B illustrate the callus regeneration and plants regenerated from protoplasts and FIG. 3C illustrates double edited Valencia protoplasts to develop into non- transgenic Valencia plants targeting ACD2 and Llsl genes.

[0046] FIGS. 4A and 4B illustrate single edited non-transgenic Valencia plants and FIGS. 4C and 4D illustrate double edited non-transgenic Valencia plants.

[0047] FIGS. 5A-5E illustrate Valencia plants with no edits (FIG. 5A), edits to CPgC (FIG. 5B), edits to ACD2gE (FIG. 5C and FIG. 5D) and edits to LLSlgB (FIG. 5E) that were that were inoculated by traditionally grafting them with HLB-infected budwood.

[0048] FIGS. 6A, 6B and 6C illustrate Carrizo plant cultured in a dish (FIG. 6A), field trial of CRISPR-edited Carrizo plant with single edit to ACD2 (FIG. 6B) and Carrizo plants with triple edits to ACD2gD, LlslgB, and CPgC (FIG. 6C).

[0049] FIGS. 7A and 7B illustrate acclimated micrografted plants of non-transgenic Valencia plants; back row: CPgC, LlslgB, ACD2gD, ACD2gD / LlslgB, ACD2gD; front row: ACD2gD / LlslgB, ACD2gD / LlslgB, CPgC, LlslgB, LlslgB(FIG. 7A), and a non-transgenic Valencia plant ACD2gD / LlslgB (FIG. 7B).

[0050] FIGS. 8A-8D illustrate non-transgenic, CRISPR-edited Hamlin plants with single edits to ACD2gD, LlslgB, and CPgC, double edits to ACD2gD / LlslgB, and triple edit plants to ACD2gD, LlslgB, and CPgC (FIG. 8A), and three triple-edited plants to ACD2gD, LlslgB, and CPgC (FIG. 8B), FIG.8C illustrates field trial of CRISPR-edited Hamlin plants with single edits to LlslbG and FIG.8D CRISPR-edited Hamlin plants with triple edit plants to ACD2gD, LlslgB, and CPgC.

[0051] FIGS. 9A-9D illustrate CRISPR-edited Valencia plants edits, with double edits to ACD2gD / LlslGb (FIG. 9A, 9B), FIG. 9C illustrates CRISPR-edited Carrizo plants to combinations of ACD2gD, ACD2gB, ACD2gE, LlslgB, LlslgA, CPgC, CPgA, PP2B12, ACD2gD / LlslgB, ACD2gB / LlslgA in hoop house trial and FIG.9D illustrates Field trials ofCarrizo plants and CRTSPR-edited Hamlin plants targeting ACD2gD, ACD2gB, ACD2gE, LlslgB, LlslgA, CPgC, CPgA, PP2B12, ACD2gD / LlslgB, ACD2gB / LlslgA.

[0052] FIG. 10A illustrates the CLas bacterial titer level from single edits to ACD2gB, ACD2gD, ACD2gE, LlslgA, LlslgB, CPgA, CPgC, and PP2B12 and double edits to ACD2gD / LlslgB, and ACD2gB / LlslgA Citrus plants two years post HLB inoculation as compared to wildtype control and FIG. 10B illustrates phenotype resistance of single and double edited citrus plants to HLB two years post HLB inoculation as compared to wildtype control.

[0053] FIGS. 11A and 11B illustrate grafting of wild-type Hamlin plant on wild-type Carrizo (FIG. 11 A) and wild-type Hamlin plant on wild-type Carrizo (FIG. 1 IB).

[0054] FIGS. 12A-G illustrate CRISPR-edited Carrizo rootstock with single edits to ACD2 (FIG, 12A), ACD2 (FIG. 12B), CP (FIG. 12C), ACD2 (FIG. 12D), PP2-B12 (FIG. 12E), double edits to ACD2 and Llsl (FIG. 12F) and triple edits to ACD2, Llsl and CP genes (FIG. 12G).

[0055] FIGS.13A-B illustrates grafting of edited plants with edited or wild-type rootstock varieties. FIG. 13A illustrates grafting of CRISPR-edited Hamlin plant targeting Llsl on wild-type US-942 rootstock and FIG. 13B illustrates grafting of wild-type Hamlin on CRISPR- edited rootstock targeting Llsl gene.

[0056] FIGS. 14A -C illustrate resistance of citrus plants grafted with edited Carrizo rootstocks to HLB infection. FIG. 14A illustrates grafting of HLB-infected Valencia scion onto control wild-type Carrizo rootstock. FIG. 14B illustrates grafting of HLB-infected Rangpur Lime scion onto control wild-type Carrizo rootstock. FIG. 14C illustrates disease resistance of HLB- infected Rangpur Lime scion onto Carrizo rootstock edited at gene PP2-B12 as compared with control wild-type Carrizo rootstock.

[0057] FIG.15A illustrates the CLas bacterial titer level from Carizzo rootstock trees with single edits to ACD2, Llsl, CP, and PP2B12 and double edits to ACD2 / Llsl three years post HLB inoculation as compared to wildtype control and FIG. 15B illustrates phenotype resistance of single and double edited Carizzo rootstock trees to HLB three years post HLB inoculation as compared to wildtype control.DETAILED DESCRIPTION

[0058] Currently available commercial citrus plants and solanaccous crops lack tolerance or resistance to Huanglongbing (HLB) and Zebra Chip (ZC) disease. Due to the rapid spread of bacteria of genus Ca. Liberibacter, new methods to prevent infections are required. One of the ways Candidatus Liberibacter species may elicit the physiological symptoms of HLB and other diseases, such as Zebra Chip, is by secretion of proteins into the plant. Candidatus Liberibacter species use the general secretion pathway (Sec-pathway) to deliver effector proteins (Sec Dependent Effectors, SDEs) into plant cells. The SDEs interact with host susceptibility proteins (S-proteins) and alter their function or abundance. Therefore, genetically modifying the genes encoding S-proteins in citrus and solanaccous plants is a viable alternative to conventional plant breeding for producing varieties that are resistant to Ca. Liberibacter infection and / or its associated diseases. It is a relatively rapid process, and some techniques allow for targeted modification of genetic loci without significant off-target effects.

[0059] In some embodiments, genetic modifications to at least two S-proteins are employed in order to generate citrus plants and solanaccous plants that are resistant to HLB and ZC, respectively. In some embodiments, the modified plants are less likely to suffer from physiological symptoms of HLB or ZC than native plants without modification. In specific embodiments, the citrus plants and solanaccous plants are tolerant to Ca. Liberibacter. Therefore, in some embodiments, the modified plants are less likely to develop undesirable physiological symptoms from Ca. Liberibacter infection and in some embodiments, the modified plants are less likely to be infected by Ca. Liberibacter than native plants or will have a lower copy number after infection. The use of modified S-proteins as disclosed herein to generate disease resistant citrus and solanaccous plants provides a significant improvement over the art due to the prior lack of agronomically acceptable plants with resistance to Ca. Liberibacter infection and to HLB and / or ZC disease. In some embodiments, additional modifications may be made to other genes that render resistance to Ca. Liberibacter infection and to HLB and / or ZC disease.

[0060] Also provided herein are citrus plants and solanaccous plants with one or more modifications to S-proteins that render the citrus plant tolerant to pathogenic Ca. Liberibacter species. In some embodiments, citrus plants with modifications to two or more S-proteins are provided, where the modifications provide the citrus plants with resistance to HLB infection. In some embodiments, solanaceous plants with modifications to two or more S-proteins are provided,where the modifications provide resistance to ZC disease. In some embodiments, the plants are non-transgcnic. In some embodiments, the plants arc transgenic. In specific embodiments, Valencia orange plants that are resistant to HLB are provided. In some embodiments, the Valencia orange plants comprise modifications to two or more S-proteins, such as ACD2 and List. In some embodiments, Hamlin plants comprising modifications to two or more S-proteins, such as ACD2, CP and Llsl are provided. In some embodiments, Carrizo plants comprising modifications to two or more S-proteins, such as ACD2, CP and Llsl are provided. In some embodiments, a citrus plant comprising a modification to Putative F-box protein (PP2-B 12) is provided. In some embodiments, a citrus plant comprising a modification to PP2-B12 in addition to a modification to at least one endogenous S-protein gene or regulatory element thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Lethal Leaf Spot 1 (Llsl) and Accelerated Cell Death Like 1 is provided. As will be understood to those of skill in the art, once a genetic modification conferring resistance to HLB or ZC is generated, this modification can readily be introduced into other cultivars by, for example, crossing.

[0061] In some embodiments one or more additional modifications may be included in order to provide a desired physiological characteristic.Definitions

[0062] The illustrative embodiments described in the detailed description, drawings, and claims are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the spirit or scope of the subject matter presented herein. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the Figures, can be arranged, substituted, combined, separated, and designed in a wide variety of different configurations, all of which are explicitly contemplated herein.

[0063] Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood when read in light of the instant disclosure by one of ordinary skill in the art to which the present disclosure belongs. For purposes of the present disclosure, the following terms are explained below.

[0064] As used herein, “a” or “an” may mean one or more than one.

[0065] As used herein, the term “about” or “approximately” has its usual meaning as understood by those skilled in the art and thus indicates that a value includes the inherent variationof error for the method being employed to determine a value, or the variation that exists among multiple determinations.

[0066] Throughout this specification, unless the context requires otherwise, the words “comprise,” “comprises,” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of’ indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of’ is meant including any elements listed after the phrase and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they materially affect the activity or action of the listed elements.

[0067] As used herein, “nucleic acid”, “nucleic acid molecule”, or “nucleotide” refers to polynucleotides or oligonucleotides such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, fragments generated by the polymerase chain reaction (PCR), and fragments generated by any of ligation, scission, endonuclease action, exonuclease action, and by synthetic generation. Nucleic acid molecules can be composed of monomers that are naturally- occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g., enantiomeric forms of naturally-occurring nucleotides), or a combination of both. Modified nucleotides can have alterations in sugar moieties and / or in pyrimidine or purine base moieties. Nucleic acids can be either single stranded or double stranded.

[0068] The term “homology” refers to nucleic acid sequences that have a sequence identity in at least about 50% of the nucleotide bases, usually at least about 60%, more usually at least about 80%, preferably at least about 90%, and more preferably at least about 95-98% of the nucleotide bases. When referring to polypeptides, the term “homology” indicates that the polypeptide or protein in question exhibits at least about 30% identity with an entire naturally occurring protein or a portion thereof, usually at least about 70% identity, and preferably at least about 95% identity.

[0069] “Percentage of sequence identity” can be determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotidesequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (c.g., a polypeptide of the constructs provided herein), which docs not comprise additions or deletions, for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.

[0070] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same sequences. Two sequences are “substantially identical” if two sequences have a specified percentage of amino acid residues or nucleotides that are the same (for example, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity over a specified region, or, when not specified, over the entire sequence of a reference sequence), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Some embodiments provided herein provide polypeptides or polynucleotides that are substantially identical to the polypeptides or polynucleotides, respectively, exemplified herein. Optionally, the identity exists over a region that is at least about 15, 25 or 50 nucleotides in length, or more preferably over a region that is 100 to 500 or 1000 or more nucleotides in length, or over the full length of the reference sequence. With respect to amino acid sequences, identity or substantial identity can exist over a region that is at least 5, 10, 15 or 20 amino acids in length, optionally at least about 25, 30, 35, 40, 50, 75 or 100 amino acids in length, optionally at least about 150, 200 or 250 amino acids in length, or over the full length of the reference sequence. With respect to shorter amino acid sequences, e.g., amino acid sequences of 20 or fewer amino acids, in some embodiments, substantial identity exists when one or two amino acid residues are conservatively substituted, according to the conservative substitutions defined herein.

[0071] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters arc designated. Default program parameters can be used, or embodiment parameters can be designated. The sequence comparisonalgorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

[0072] The term “gene” as used herein have their plain and ordinary meaning as understood in light of the specification, and generally refers to a portion of a nucleic acid that encodes a protein or functional RNA; however, the term may optionally encompass regulatory sequences. It will be appreciated by those of ordinary skill in the art that the term “gene” may include gene regulatory sequences (e.g., promoters, enhancers, etc.) and / or intron sequences. It will further be appreciated that definitions of gene include references to nucleic acids that do not encode proteins but rather encode functional RNA molecules such as tRNAs and miRNAs. In some cases, the gene includes regulatory sequences involved in transcription, or message production or composition. In other embodiments, the gene comprises transcribed sequences that encode for a protein, polypeptide or peptide. In keeping with the terminology described herein, an “isolated gene” may comprise transcribed nucleic acid(s), regulatory sequences, coding sequences, or the like, isolated substantially away from other such sequences, such as other naturally occurring genes, regulatory sequences, polypeptide or peptide encoding sequences, etc. In this respect, the term “gene” is used for simplicity to refer to a nucleic acid comprising a nucleotide sequence that is transcribed, and the complement thereof. As will be understood by those in the art, this functional term “gene” includes both genomic sequences, RNA or cDNA sequences, or smaller engineered nucleic acid segments, including nucleic acid segments of a non-transcribed pail of a gene, including but not limited to the non-transcribed promoter or enhancer regions of a gene. Smaller engineered gene nucleic acid segments may express, or may be adapted to express using nucleic acid manipulation technology, proteins, polypeptides, domains, peptides, fusion proteins, mutants and / or such like.

[0073] As used herein, the term “wild-type” has its plain and ordinary meaning as understood in light of the specification, and generally refers to a gene, a gene locus, a polynucleotide sequence, a nucleotide sequence or a protein that does not comprise any edits or modifications. A “wild type” gene, gene locus, a polynucleotide, a nucleotide sequence or a protein means that the gene, gene locus, polynucleotide, nucleotide sequence or protein will be active at a level of activity found in nature and / or will comprise the nucleotide or amino acid sequence found in nature. Unless specified otherwise, a “genomic locus” or a “genomic loci” as used herein refers to a genomic locus or a genomic loci that does not comprise any edits or modifications.

[0074] An “expression vector” or a “vector,” as described herein, is a nucleic acid molecule encoding a gene that is expressed in a host-cell. Typically, an expression vector comprises a transcription promoter, a gene, and a transcription terminator. Gene expression is usually placed under the control of a promoter, and such a gene is said to be “operably linked to” the promoter. Similarly, a regulatory element and a core promoter are operably linked if the regulatory element modulates the activity of the core promoter.

[0075] As used herein, modifying a genome is carried out with techniques that employ targeted mutagenesis. These techniques include, but are not limited to, those that utilize endonucleases to generate single-strand and double-strand DNA breaks that activate DNA repair pathways. Genome editing techniques may also comprise systems that enable targeted editing at any genomic locus. These targeting systems include, but are not limited to, polypeptides, such as, Transcription Activator-Like Effectors (TALEs) and zinc fingers (ZFs), or nucleic acids, such as, Clustered Regularly Interspaced Short Palindromic Repeats / Cas (CRISPR / CAS) single guide RNAs or NgAgo (Argonaute) single strand DNAs. As used herein, “genome editing” and “genome-engineering” are interchangeable.

[0076] As used herein, genetic modification refers to a DNA sequence difference, epigenetic difference, or combination thereof between two genomes of the same species in which one genome is identified as the modified genome and the other is identified as the unmodified genome and the DNA sequence or epigenetic difference is the result of applying genome modifying techniques to the unmodified genome to yield the modified genome. A genetic modification, as used herein, encompasses any insertion, deletion, or substitution of a nucleotide sequence of any size and nucleotide content, any epigenetic modification to any number of nucleotides, or a combination thereof. A genetic modification, as used herein, may also encompass introduction of one or more exogenous coding nucleic acids that do not integrate into the unmodified genome, yet are capable of autonomous replication. In certain embodiments, a modification to an endogenous gene or regulatory element thereof may be a deletion, a substitution, or an insertion that reduces expression of the endogenous gene or the polypeptide for which it encodes. In some specific embodiments, the modification may be an indel, wherein the indel may cause a frameshift mutation, a missense mutation, a nonsense mutation, a neutral mutation, or a silent mutation. In specific embodiments, a modification to a regulatory element of an endogenous gene may alter or eliminate a function of the regulatory element. In furthercontemplated embodiments, the modification may comprise a nucleic acid sequence that provides exogenous control of endogenous gene, mRNA, or polypeptide expression levels. In specific embodiments, the modification may also disrupt a post-translational process of a polypeptide encoded by an endogenous gene. Post-translational processes in certain embodiments may be post- translational modifications, protein sorting, or proteasomal degradation.

[0077] As used herein, a genetically modified cell is a cell in which the endogenous genome has been genetically modified; a cell in which one or more exogenous, coding nucleic acids have been introduced that do not integrate into the genome, yet are capable of autonomous replication; or a combination thereof.

[0078] As used herein, a genetically modified plant is a plant comprising at least one genetically modified cell. A genetically modified plant may be regenerated from a genetically modified cell or plant part comprising genetically modified cells, and thus the genetic modification may be heritable and inherited by progeny thereof. The progeny thereof that inherit the genetic modification are also considered genetically modified plants. A genetically modified plant, as used herein, also refers to a plant in which at least one genetically modified cell is introduced to a plant or arises as a result of genetic modification techniques directly applied to the plant.

[0079] As used herein, a genetic modification technique is a technique that is known to those in the art that can modify the genome of a cell including, but not limited to, genome editing, site-specific genetic recombination, epigenetic modifications, and genetic transformation.

[0080] As used herein, a genetic transformation is a process of introducing a DNA sequence or construct (e.g., a vector or expression cassette) into a cell or protoplast in which that exogenous DNA is incorporated into a chromosome or is capable of autonomous replication.

[0081] As used herein, the term transgenic refers to a cell or a plant that expresses nucleic acids at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids. Alternatively, as used herein, a non-transgenic plant or cell comprises modified nucleic acids expressed at their natural locus in the genome.

[0082] As used herein, a heterologous sequence is a sequence which is not normally present in a given host genome in the genetic context in which the sequence is currently found. In this respect, the sequence may be from another species, organism, plant, tree, or variety, or may be native to the host genome, but be rearranged with respect to other genetic sequences within the host sequence. For example, a regulatory sequence may be heterologous in that it is linked to adifferent coding sequence relative to the native regulatory sequence. In addition, a particular recombinant DNA molecule may be heterologous with respect to a cell or organism into which it is inserted when it would not naturally occur in that particular cell or organism.

[0083] As used herein, “regeneration” is the process of growing a plant from a plant cell (e.g., plant protoplast, callus, or explant).

[0084] As used herein, the term “plant” refers to citrus or solanaceous plant, or any other plant that can be infected by a Ca Liberibacter species.

[0085] As used herein, the term “plant part” refer to cells, tissues, organs, seeds, rootstock, scion, interstock and severed parts (e.g., roots, leaves, and flowers) that retain the distinguishing characteristics of the parent plant. “Seed” refers to any plant structure that is formed by continued differentiation of the ovule of the plant, following its normal maturation point at flower opening, irrespective of whether it is formed in the presence or absence of fertilization and irrespective of whether or not the seed structure is fertile or infertile. A plant part may be any part of the plant from which another plant may arise. “Rootstock” refers to a lower portion of a plant which includes the root system of the plant and may include a stem portion of the plant. As used herein, a rootstock may be used to grow a different variety through asexual propagation or reproduction such as grafting or through seeds. “Scion” refers to an upper portion of the plant which includes shoot or a stem which may have flowers, fruit or leaves. A scion may be from the same or a different plant type or variety. “Interstock” refers to an intermediate portion of a plant that is grafted between a rootstock and a scion.

[0086] As used herein, a promoter is a recognition site on a DNA sequence or group of DNA sequences that provides an expression control element for a structural gene and to which RNA polymerase specifically binds and initiates RNA synthesis (transcription) of that gene.

[0087] As used herein, “tolerance” encompasses any relief from, reduced presentation of, improvement of, or any combination thereof of any symptom of an infection by a Ca. Liberibacter species. As used herein, “resistance” encompasses tolerance as well as a reduction of bacterial load upon infection or reduction of ability to be infected by a Ca. Liberibacter species. Resistance to the bacterial infection can be determined by quantifying the copy number of the bacteria or bacterial titer in a given amount of plant genomic DNA. In specific embodiments, an unmodified plant or a plant pail exhibits bacterial copy number or bacterial titer that is at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 500% or any integer that isbetween 10 and 500%, more than the modified, resistant plant. In some embodiments, a modified resistant plant exhibits reduced symptoms of a disease relative to an unmodified plant. Some nonlimiting examples of the symptoms of the disease include decline in the fruit quality, decline in fruit quantity or reduced life span. In specific embodiments of the disclosure, citrus plants or solanaceous plants are provided that are tolerant or resistant to infection by a Ca. Liberibacter species and to HLB and / or ZC disease. This may be assessed, for example, relative to a citrus plant or a solanaceous plant of the same variety not comprising a corresponding genetic modification.

[0088] As used herein, the term “citrus” plant is used in its ordinary manner to refer to members of the family Rutacae, including, for example, sweet orange, bitter orange, blood orange, grapefruit, pomelo, citron, clementine, naval orange, lemon, lime, mandarin, tangerine, tangelo, and the like.

[0089] As used herein, the terms “solanaceous crop” or “solanaceous plant” are used interchangeably and are directed plants of the Solanacea family including, for example, tomato (Solanum lycopersicum and Solanum pennelli); potato (Solanum tuberosum); eggplant (Solatium melongena), bell / chili peppers (Capsicum annuum, Capsicum baccatum, and Capsicum chinense).Sec-Dependent Effector Proteins

[0090] Sec-dependent effector (SDE), as used herein, refers to any bacterial effector protein secreted from a bacterium via the Sec-dependent pathway. In specific embodiments, an SDE is secreted the Ca. Liberibacter species selected from the group consisting of Las, Laf, and Lam. In some specific embodiments, SDEs are CLIBASIA_04025 (Las4025) and CLIBASIA_05150 (Las5150) as described in Pang et al (Plant Physiol. 184(2):792-805, 2020) which is incorporated herein by reference in its entirety.Susceptibility Proteins (S-protein) Associated with Disease Resistance

[0091] A susceptibility protein or S-protein, as used herein, refers to an endogenous host polypeptide targeted by an SDE. A susceptibility gene or S-gene, as used herein, refers to an endogenous host gene encoding an S-protein. An S-protein-SDE complex, as used herein refers to an S-protein interacting with an SDE. An S-protein-SDE interaction is a protein-protein interaction between an S-protein and an SDE. In some embodiments, an S-gene is modified such that the encoded S-protein is no longer capable of interacting with an SDE. In some embodiments, an S- gene is modified such that the encoded S-protein may interact with an SDE, but not disrupt normalphysiology to an extent that a deleterious mechanism of action is triggered. As a non-limiting example, a modified S-gcnc may promote protcasomal degradation of an SDE-S-protcin complex before the complex activates a deleterious mechanism of action.

[0092] In some embodiments, one, two or more citrus S-proteins are modified. The S- proteins may be selected from the group consisting of accelerated cell death 2 (ACD2) protein, Cysteine protease (CP), and Lethal Leaf Spot 1 (List). In some embodiments one, two or more corresponding S-proteins from solanaceous plants are modified.Genetic Modifications Providing Disease Resistance in Citrus and Solanaceous Plants

[0093] In some embodiments, genetic modification to one, two or more S-proteins are employed to generate citrus plants and solanaceous plants that are resistant to HLB and ZC diseases, respectively. In some embodiments, additional modifications may be made to other genes that render resistance to other diseases, such as canker disease.

[0094] In some embodiments, a citrus plant, a citrus plant part or a citrus plant seed is provided comprising one or more plant cells that in turn comprise a modification to at least one endogenous S-protein gene or regulatory element thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Lethal Leaf Spot 1 (Llsl) and Accelerated Cell Death Like 1. In some embodiments, a citrus plant, a citrus plant part or a citrus plant seed is provided comprising one or more plant cells that comprise a modification to Putative F-box protein (PP2-B12). In some embodiments, a citrus plant, a citrus plant part or a citrus plant seed is provided comprising one or more plant cells that comprise a modification to PP2-B12 in addition to a modification to at least one endogenous S-protein gene or regulatory element thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Lethal Leaf Spot 1 (Llsl) and Accelerated Cell Death Like 1. In some embodiments, any of the modifications disclosed herein are made to corresponding homologs of these genes in solanaceous crops. In some embodiments, the modification to at least one endogenous gene or regulatory element thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Lethal Leaf Spot 1 (Llsl), Accelerated Cell Death Like 1 and Putative F-box protein (PP2-B12) is made to a citrus rootstock, citrus interstock and / or citrus scion.

[0095] As used herein, Accelerated Cell Death 2 (ACD2) refers to any ACD2 gene from a citrus variety. In some embodiments, the ACD2 gene is identified by accession number Cslg22670. In some embodiments, the ACD2 gene comprises SEQ ID NO:1, SEQ ID NO:37,SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity to at least one of these sequences. As used herein, Cysteine Protease (CP) refers to any CP gene from a citrus variety. In some embodiments, the CP gene is identified by accession number Cs4g07410. In some embodiments, the CP gene comprises SEQ ID NO:2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123, or a sequence comprising at least 95% identity to at least one of these sequences. As used herein, Lethal Leaf Spot 1 (Llsl) refers to any Llsl gene from a citrus variety. In some embodiments, the Llsl gene is identified by accession number Cs9g02990. In some embodiments, the Llsl gene comprises SEQ ID NO:3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 58, SEQ ID NO: 67, SEQ ID NO: 79, SEQ ID NO: 89, SEQ ID NO: 102, SEQ ID NO: 113, SEQ ID NO: 121, or a sequence comprising at least 95% identity to at least one of these sequences. As used herein, PP2-B 12 refers to any PP2-B 12 gene from a citrus variety. In some embodiments, the PP2- B12 gene is identified by accession number Orangel.lt04174. In some embodiments, the PP2- B12 gene comprises SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith.

[0096] In some embodiments, a modification is made to the Accelerated Cell Death 2 (ACD2) gene. In several embodiments, a modification is made to the Cysteine Protease (CP) gene. In some embodiments, a modification is made to the Lethal Leaf Spot 1 (Llsl) gene. In some embodiments, a modification is made to PP2-B12 gene.

[0097] In some embodiments, the modification is made to at least one of SEQ ID NOS: 1, 2, 3, 36, 37, 38, 45, 46, 47, 48, 49, 58, 67, 79, 60, 69, 81, 59, 68, 80, 89, 102, 113, 92, 93, 105, 115, 90, 91, 103 104, 114, 121, 122, 123 or 124, or a sequence comprising at least 95% identity to at least one of these sequences. In some embodiments, any of the modifications disclosed herein are made to corresponding homologs of these genes in solanaceous crops.

[0098] In some embodiments, the modification(s) disclosed herein confers resistance to Ca. Liberibacler infections. In some embodiments, the modification(s) disclosed herein disrupts the interaction of the modified gene with a bacterial effector protein. In some embodiments, the bacterial load in the modified plant, plant part or plant seed is lower relative to the same variety of plant, plant part or plant seed lacking the said modification. In some embodiments, the bacterial load in the modified rootstock, interstock and / or scion is lower relative to the same variety of plant,plant part or plant seed lacking the said modification. In some embodiments, the modification(s) disclosed herein confers resistance to HLB or citrus greening diseases in citrus plants or ZC disease in solanaceous crops.

[0099] In some embodiments, the modification is made to one or more genomic target loci within a gene. In some embodiments the target loci is selected from a group consisting of LlslgA, LlslgB, ACD2gB ACD2gD, ACD2gE, CPgA, CPgC, PP2 B12gA and PP2B12gB. In some embodiments, the endogenous genomic target locus comprises a coding region. In some embodiments, the endogenous genomic target comprises an intron. As used herein, the ACD2gB locus comprises SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith. As used herein, the ACD2gD locus comprises any one of SEQ ID Nos: 8, 30, 41, 52, 63, 73, 84, 96, 108 or 118 or a sequence comprising at least 95% identity therewith. As used herein, the ACD2gE locus comprises SEQ ID NO: 33 or a sequence comprising at least 95% identity therewith. As used herein, the CPgA locus comprises SEQ ID NO: 13 or a sequence comprising at least 95% identity therewith. As used herein, the CPgC locus comprises SEQ ID Nos: 15, 43, 55, 65, 76, 87, 99, 111 or 120 or a sequence comprising at least 95% identity therewith. As used herein, the LlslgA locus comprises SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith. As used herein, the LlslgB locus comprises any one of SEQ ID Nos: 25, 28, 39, 50, 61, 70, 82, 94, 106 or 116 or a sequence comprising at least 95% identity therewith. As used herein, the PP2B12gA locus comprises SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. As used herein, the PP2B12gB locus comprises SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. In some embodiments, the endogenous genomic target locus comprises a modification in both the alleles. In some embodiments, the endogenous genomic target locus comprises a modification in one allele. In some embodiments, both alleles of the endogenous genomic target locus comprise the same modification. In some embodiments, both alleles of the endogenous genomic target locus comprise different modifications.

[0100] In some embodiments, the modified ACD2gB locus comprises any one of the SEQ ID Nos: 5-7. In some embodiments, the modified ACD2gD locus comprises any one of the SEQ ID Nos: 9-12, 31,35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 119, 126, 127, 130, 131, 133, 134, 143, 144, 145, 146, 149, 150 and 138. In some embodiments, the modified CPgA locus comprises SEQ ID NO: 14. In some embodiments, the modified CPgC locus comprises any one of the SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 112, 135, 136, 153, 154 and 32.In some embodiments, the modified Lis IgA locus comprises any one of the SEQ ID Nos: 22-24. In some embodiments, the modified LlslgB locus comprises any one of the SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the modified PP2 B12gA locus comprises any one of the SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the modified PP2 B12gB locus comprises any one of the SEQ ID NOs: 142 and 156. In some embodiments, a modification to a genomic target loci comprising one or more of SEQ ID Nos: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 124 and 120 results in a modified gene loci comprising one or more of SEQ ID Nos: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147,148,151, 152, 153, 154 and 32.

[0101] In some embodiments, one nucleotide is inserted in the target locus. In some embodiments, one nucleotide is deleted from the target locus. In some embodiments described herein, the inserted or deleted nucleotide is A, T, G, C, or a combination thereof. In some embodiments, the modification to a target locus comprises insertion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25, 50, 100, 200, 300, 400, or 500 nucleotides, or ranges in between. In some embodiments, the modification to the target locus comprises insertion of about 30 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 40 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 50 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 100 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 200 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 250 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 300 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 350 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 400 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 450 nucleotides. In some embodiments, the modification to the target locus comprises insertion of about 500 nucleotides.

[0102] In some embodiments, the modification to a target locus comprises deletion of about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25, 50, 100, 200, 300, 400, or 500 nucleotides, or ranges in between. In some embodiments, the modification to the target locus comprises deletion of about 30 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 40 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 50 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 100 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 200 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 250 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 300 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 350 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 400 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 450 nucleotides. In some embodiments, the modification to the target locus comprises deletion of about 500 nucleotides.

[0103] In some embodiments, the modification comprises a genetic modification to one or more endogenous nucleic acids of the gene. In some embodiments, the modification is an insertion of one or more nucleic acids to the nucleotide sequence of the endogenous gene. In some embodiments, the modification is a deletion of one or more nucleic acids from the nucleotide sequence of the endogenous gene. In some embodiments, the modification is a substitution of one or more nucleic acids in the nucleotide sequence of the endogenous gene. In specific embodiments, the modification may be an indel, wherein the indel may cause a frameshift mutation, a mis sense mutation, a nonsense mutation, a neutral mutation, or a silent mutation. In some embodiments, the modification is an epigenetic modification to any number of nucleotides in the nucleotide sequence of the endogenous gene. In some embodiments, the modification comprises an insertion, deletion, inversion, substitution, epigenetic modification or a combination thereof.

[0104] In some embodiments, a citrus plant, a citrus plant part or a citrus plant seed is provided that comprises one or more plant cells that in turn comprise a modification to two or more endogenous genes or regulatory elements thereof. In some embodiments the two or more endogenous genes are selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl). In some embodiments, themodification is made to two or more of SEQ ID NOS: 1 , 2, 3, 36, 37, 38, 45, 46, 47, 48, 49, 58, 67, 79, 60, 69, 81, 59, 68, 80, 89, 102, 113, 92, 93, 105, 115, 90, 91, 103, 104, 121, 122, 123, 124 or 114, or sequences comprising at least 95% identity therewith. In some embodiments, any of the modifications disclosed herein are made to corresponding homologs of these genes in solanaceous crops. In some embodiments, the modification to at least to two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Lethal Leaf Spot 1, Accelerated Cell Death Like 1 (Llsl) and PP2-B12 is made to a citrus rootstock, citrus interstock and / or citrus scion. In some embodiments, the modification is made to two or more of SEQ ID NOS: 1, 2, 3, 36, 37, 38, 45, 46, 47, 48, 49, 58, 67, 79, 60, 69, 81, 59, 68, 80, 89, 102, 113, 92, 93, 105, 115, 90, 91, 103, 104, 121, 122, 123, 124 or 114, or sequences comprising at least 95% identity therewith.

[0105] In some embodiments, a modification is made to both an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith, and a Lethal Leaf Spot 1 (Llsl) gene, for example comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 58, SEQ ID NO: 67, SEQ ID NO: 79, SEQ ID NO: 89, SEQ ID NO: 102, SEQ ID NO: 113, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith.

[0106] In some embodiments, a modification is made to both an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith, and a PP2-B12 gene, for example comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith.

[0107] In some embodiments, a modification is made to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and a Lethal Leaf Spot 1 (Llsl) gene, for example comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 58, SEQ ID NO: 67, SEQ ID NO: 79, SEQ ID NO: 89, SEQID NO: 102, SEQ ID NO: 113, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith.

[0108] In some embodiments, a modification is made to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and a PP2-B12 gene, for example comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith.

[0109] In some embodiments, a modification is made to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith.

[0110] In some embodiments, the modification is made to two or more genomic target loci from within the desired gene. In some embodiments the target loci are selected from a group consisting of LlslgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the endogenous genomic target locus comprises a coding region. In some embodiments, the endogenous genomic target comprises an intron. In some embodiments, a modification is made to two or more genomic target loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 124 and 33. In some embodiments modified gene loci are selected from SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. For example, in some embodiments two or more genes comprise modifications reflected in the modified gene loci of SEQ ID NOs: 5- 7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64,74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 1 10, 1 19, 100, 101 , 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142,143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32.

[0111] In some embodiments, the genomic target loci ACD2gB and Lis IgA are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 5-7 in combination with any one of SEQ ID NOs: 22-24.

[0112] In some embodiments, the genomic target loci ACD2gD and LlslgB are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138,143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with any one of SEQ ID NOs: 26-27, 29, 34, 40 and 51. In some embodiments, modified genomic target loci comprise a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of the other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified loci of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117.

[0113] In some embodiments, a modification is made to both ACD2gD and CPgC loci. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143,144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, modified genomic target loci comprises modification of one allele of CPgC comprising SEQ ID NO: 56 and other allele of-SO-CPgC comprising SEQ ID NO: 57. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of CPgC comprising SEQ ID NO: 56 and other allele of CPgC comprising SEQ ID NO: 57. In some embodiments, modified genomic target loci comprises a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and the other allele of CPgC comprising any one of SEQ ID NOs 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32.

[0114] In some embodiments, a modification is made to both ACD2gD and PP2 B12gA loci. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141 and other allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141. In some embodiments, modified genomic target loci comprises a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141.

[0115] In some embodiments, a modification is made to both ACD2gD and PP2 B 12gB loci. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 9- 12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, modified genomic target loci comprises a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110,126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156.

[0116] In some embodiments, the genomic target loci CPgC and LlslgB are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, modified genomic target loci comprises a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26- 27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117.

[0117] In some embodiments, the genomic target loci CPgC and PP2 Bl 2g A are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs:16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101 , 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, modified genomic target loci comprises a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141.

[0118] In some embodiments, the genomic target loci PP2 Bl 2g A and LlslgB are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 139, 140, 155 and 141 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, modified genomic target loci comprises a modification of one allele of PP2 Bl 2g A comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and a modification of another allele of PP2 B 12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117.

[0119] In some embodiments, the genomic target loci CPgC and PP2 B12gB are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, modified genomic target loci comprises a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156.

[0120] In some embodiments, the genomic target loci PP2 B12gB and LlslgB are modified. In some embodiments, modified genomic target loci comprises any one of SEQ ID NOs:142 and 156 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51 , 62, 71 , 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, modified genomic target loci comprises a modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156and a modification of another allele of PP2 B12gB comprising any one of SEQ ID NOs; 142 and 156in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26- 27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117.

[0121] In some embodiments, a citrus plant, a citrus plant part or a citrus plant seed is provided that comprises plant cells that in turn comprises a modification to three or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot l(Llsl). In some embodiments, a citrus rootstock, interstock and / or citrus scion comprises plant cells that in turn comprises a modification to three or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12 and Lethal Leaf Spot l(Llsl). In some embodiments, any of the modifications disclosed herein are made to corresponding homologs of these genes in solanaceous crops.

[0122] In some embodiments, a modification is made to three or more of SEQ ID NOS: 1, 2, 3, 36, 37, 38, 45, 46, 47, 48, 49, 58, 67, 79, 60, 69, 81, 59, 68, 80, 89, 102, 113, 92, 93, 105, 115, 90, 91, 103, 104, 121, 122, 123, 124 or 114, or sequences comprising at least 95% identity therewith.

[0123] In some embodiments, a modification is made to three or more genomic target loci, wherein the target loci is selected from a group consisting of LlslgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the endogenous genomic target locus comprises a coding region. In some embodiments, wherein the endogenous genomic target comprises an intron. In some embodiments, modifications to the genomic target loci comprising three or more of SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124 and 120 result inmodified gene loci comprising three or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142,143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32.

[0124] In some embodiments, the genomic target loci ACD2gD, CPgC, PP2 B12gA, and LlslgB are modified. In some embodiments, modified genomic target loci comprise any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and any one of SEQ ID NOs: 139, 140, 155 and 141.

[0125] In some embodiments, modified genomic target loci comprise modification of one allele of ACD2gD comprising SEQ ID NO: 53 and another allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, modified genomic target loci comprises modification of one allele of CPgC comprising SEQ ID NO: 56 and another allele of CPgC comprising SEQ ID NO: 57. In some embodiments, modified genomic target loci comprise modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and another allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, modified genomic target loci comprise modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 141 and another allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 141. In some embodiments, modified genomic target loci comprise modification of one allele of ACD2gD comprising SEQ ID NO: 53 and another allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of CPgC comprising SEQ ID NO: 56 and another allele of CPgC comprising SEQ ID NO: 57 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and another allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising anyone of SEQ ID NOs: 9-12, 31 , 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131 , 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and other allele of CPgC comprising any one of SEQ ID NOs 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and another allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and another allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141.

[0126] In some embodiments, any of the modifications disclosed herein is made to homologs of these genes in solanaceous crops. In a non-limiting example, the modification is made to PTC gene in tomato plant, which is a homolog of Lethal Leaf Spot 1 (Llsl) gene. In another non-limiting example, the modification is made to Cyp gene in tomoto plant, which is a homolog of Cysteine Protease (CP) gene. In some embodiments, the modification(s) disclosed herein confers resistance to Candidatus Liberibacter solanacearum infections. In some embodiments, the modification(s) disclosed herein disrupts the interaction of the modified gene with a bacterial effector protein. In some embodiments, the bacterial load in the modified plant, plant part or plant seed is lower relative to the same variety of plant, plant part or plant seed lacking the said modification. In some embodiments, a genetic modification can be made anywhere in the genome which disrupts expression, and in turn, may disrupt an S-protein-SDE interaction from activating a deleterious mechanism of action. In some embodiments, an S-gene or a regulatory element thereof is modified. In some embodiments, a modification may be made elsewhere in the genome, but ultimately disrupts an S-protein-SDE interaction, for a non-limiting example, inserting genetic material encoding a polypeptide capable of disrupting an S-protein-SDE interaction anywhere in the genome.

[0127] In some embodiments, the genetic modifications to S-proteins can be combined with additional gene modifications to confer additional traits to the commercial plants.Genomic Editing

[0128] The genome of a citrus or solanaccous plant, citrus or solanaccous rootstock, interstock and / or scion may be modified using one or more genome editing techniques. As used herein, “genome editing” and “genome-engineering” are terms used interchangeably and refer to the modification of a genome through mutagenesis. For example, in plant genome engineering, endonucleases may be used to generate double-strand DNA breaks (DSBs) and activate genome repair pathways. These DSB repair pathways may repair the break cleanly, i.e., without altering the starting sequence, or, alternatively, induce a mutation through an error in repair. In some embodiments, genome editing is used to insert, delete, or substitute one or more base pairs at one or any combination of genetic loci. In some embodiments, a genome editing technique is used to create a mutation, for example, a point mutation or single nucleotide polymorphism.

[0129] In some embodiments the DSB repair pathway is non-homologous end-joining (NHEJ) or microhomology mediated end joining (MMEJ). During NHEJ, any nucleotide overhangs on the break ends are either resected or filled to form blunt ends that are ligated. During MMEJ, the break ends are processed to reveal overhangs comprising microhomology sequences that are then ligated together. The insertions or deletions resulting from the terminal end processing in both the NHEJ and MMEJ pathways can be referred to as indels. In some embodiments, the NHEJ or MHEJ that occurs can be relied upon to introduce a genome modification including, but not limited to, a silent mutation, a neutral mutation, a missense mutation, a nonsense mutation, or a frameshift mutation.

[0130] In other embodiments, the DSB repair pathway is homologous recombination (HR). During HR, a DSB is repaired using a template with sequences with homology to the DNA flanking the break, i.e., a homologous chromosome. In plant genome editing, a linear DNA polynucleotide flanked by sequences (e.g., of 50 base pairs or more) homologous to those flanking a targeted genomic locus, may be introduced into the genome when a DSB is repaired by HR. In some embodiments, this approach is used to introduce, substitute, or delete a DNA sequence at a genomic locus. Any DNA sequence of interest may be introduced, deleted, or substituted. An introduced or substituted DNA sequence may encode an RNA molecule with a specific activity or function, a DNA molecule with a specific activity or function (e.g., encoding a polypeptide, representing a detectable marker, etc.), a DNA molecule comprising cis-regulatory elements, or a DNA molecule encoding a polypeptide, a motif thereof, or domain thereof. In some embodiments,the nucleic acid encoding the linear DNA sequence that will act as the HR template is encoded by an expression vector. In some embodiments, the nucleic acid encoding the linear DNA sequence of interest is encoded by a DNA sequence separate from the expression vector. For example, and without limitation, the nucleic acid encoding a DNA sequence of interest may be a linear DNA polynucleotide that is co-transformed with an expression vector.

[0131] In some embodiments, single-strand breaks or “nicks” are introduced into the target DNA sequence. As used herein, the term “single- strand break inducing agent” or “nickase” refers to any agent that can induce a single-strand break (SSB) in a DNA molecule. In some embodiments two SSBs are introduced into the target DNA to generate a DSB. These breaks may also be repaired by HR, NHEJ, or MMEJ. In some embodiments, sequence modifications occur at or near the SSB sites, which can include deletions or insertions that result in modification of the nucleic acid sequence, or integration of exogenous nucleic acids by HR or NHEJ.

[0132] In one aspect, a “modification” comprises the insertion of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 25, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, at least 5000, or at least 10,000 nucleotides. In another aspect, a “modification” comprises the deletion of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 25, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, at least 5000, or at least 10,000 nucleotides. In a further aspect, a “modification” comprises the inversion of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 25, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, at least 5000, or at least 10,000 nucleotides. In still another aspect, a “modification” comprises the substitution of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 25, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 3000, at least 4000, at least 5000, or at least 10,000 nucleotides. In some embodiments, a “modification” comprises the substitution of an “A” for a “C,” “G” or “T” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of an “C” for an “A,” “G” or “T” in a nucleic acid sequence. In some embodiments, a“modification” comprises the substitution of a “G” for an “A,” “C” or “T” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of a “T” for an “A,” “C” or “G” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of a “C” for an “U” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of a “G” for an “A” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of an “A” for a “G” in a nucleic acid sequence. In some embodiments, a “modification” comprises the substitution of a “T” for a “C” in a nucleic acid sequence.

[0133] In some embodiments, genome editing of a citrus plant or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may encompass techniques that employ methods of targeting endonucleases to one or more genetic loci. In some embodiments, synthetic polypeptides, for example, Transcription Activator-Like Effectors (TALEs) and zinc fingers (ZFs), or nucleic acids, for example, Clustered Regularly Interspaced Short Palindromic Repeats / Cas (CRISPR / CAS) single guide RNAs or NgAgo (Argonaute) single strand DNAs, are used to target endonucleases to any genomic locus. The targeted endonucleases may catalyze a DSB at a target locus. Upon detecting these breaks, a cell may initiate any DSB repair pathway. In some embodiments, genome editing is carried out at more than one genomic locus simultaneously (i.e., multiplex genome engineering). In some embodiments, multiplex genome engineering may be used to remove a sequence of any size from the genome. In some embodiments, any combination and number of endonuclease targeting techniques may be used to target one or more genetic loci.RNA- and DNA-Guided Genome Editing Systems

[0134] In some embodiments, genome engineering of a citrus or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may employ RNA- guided endonucleases including, but not limited to CRISPR / Cas systems. CRISPR / Cas systems have been described in U.S. Patent Application Publication Nos. 2017 / 0191082 and 2017 / 0106025, each of which are incorporated herein by reference in their entirety. In some embodiments, a targeted genome modification as described herein comprises the use of at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten RNA-guided nucleases. In some embodiments, a CRISPR / Cas9 system,a CRISPR / Cpf 1 system, a CRISPR / CasX system, or a CRISPR / CasY system are alternatives that may be used to generate modifications to target sequences as described herein.

[0135] The CRISPR systems are based on RNA-guided endonucleases that use complementary base pairing to recognize DNA sequences at target sites. CRISPR / Cas systems are part of the adaptive immune system of bacteria and archaea, protecting them against invading DNA, such as viral DNA, by cleaving the foreign DNA in a sequence-dependent manner. The immunity is acquired by the integration of short fragments of the invading DNA known as spacers between two adjacent repeats at the proximal end of a CRISPR locus. The CRISPR arrays, including the spacers, are transcribed during subsequent encounters with invasive DNA and are processed into small interfering CRISPR RNAs (crRNAs) approximately 40 nt in length, which combine with the trans-activating CRISPR RNA (tracrRNA) to activate and guide the Cas9 nuclease. This cleaves homologous double- stranded DNA sequences known as protospacers in the invading DNA.

[0136] A prerequisite for cleavage is the presence of a conserved protospacer-adjacent motif (PAM) downstream of the target DNA, which usually has the sequence 5'-NGG-3' but less frequently NAG. Specificity is provided by the so-called “seed sequence” approximately 12 bases upstream of the PAM, which must match between the RNA and target DNA. Cpfl acts in a similar manner to Cas9, but Cpfl does not require a tracrRNA. Specificity of the CRISPR / Cas system is based on an RNA-guide that use complementary base pairing to recognize target DNA sequences. In some embodiments, the site-specific genome modification enzyme is a CRISPR / Cas system. In an aspect, a site-specific genome modification enzyme provided herein can comprise any RNA- guided Cas endonuclease (non-limiting examples of RNA-guided nucleases include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, CsxlS, Csfl, Csf2, Csf3, Csf4, Cpfl, homologs thereof, or modified versions thereof); and, optionally, the guide RNA necessary for targeting the respective nucleases.

[0137] In some embodiments, an RNA-guided endonuclease is the DNA cleavage domain of a restriction enzyme fused to a deactivated Cas9 (dCas9), for example dCas9-Fokl. As used herein, a “dCas9” refers to a endonuclease protein with one or more amino acid mutations that result in a Cas9 protein without endonuclease activity, but retaining RNA-guided site-specificDNA binding. As used herein, a “dCas9-restriction enzyme fusion protein” is a dCas9 with a protein fused to the dCas9 in such a manner that the restriction enzyme is catalytically active on the DNA.

[0138] In some embodiments, genome editing of a citrus or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may employ DNA-guided endonucleases including, but not limited to, N Ago systems. In one aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more guide RNAs or DNAs. In another aspect, a CRISPR / CAS system, dCas9-restriction enzyme fusion protein, NgAgo system provided herein is capable of generating a targeted DSB in a target sequence as described herein. In one aspect, vectors comprising nucleic acids encoding one or more, two or more, three or more, four or more, or five or more guide RNAs or DNAs and the corresponding CRISPR / CAS system, dCas9-restriction enzyme fusion protein, NgAgo system are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium- mediated transformation).Transcription Activator-Like Effector Nucleases

[0139] In some embodiments, genome editing of a citrus or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may employ Transcription Activator-Like Effector Nucleases (TALENs). TALENs have been described in U.S. Patent Application Publication Nos. 2016 / 0369301 and 2015 / 0203871 (both of which are incorporated herein by reference in their entirety) and are well known in the art. TALENs are artificial restriction enzymes generated by fusing the transcription activator-like effector (TALE) DNA binding domain to an endonuclease domain. In one aspect, the nuclease is selected from a group consisting of PvuII, MutH, TevI and Fokl, Alwl, Mlyl, Sbll, Sdal, StsI, CleDORF, Clo051, Pept071. The term TALEN, as used herein, is broad and includes a monomeric TALEN that can cleave double stranded DNA without assistance from another TALEN. The term TALEN is also used to refer to one or both members of a pair of TALENs that work together to cleave DNA at the same site.

[0140] TALEs can be engineered to bind practically any DNA sequence, such as a target sequence as described herein. TALE proteins are DNA-binding domains derived from various plant bacterial pathogens of the genus Xanthomonas. The X pathogens secrete TALEs into the host plant cell during infection. The TALE moves to the nucleus, where it recognizes and bindsto a specific DNA sequence in the promoter region of a specific DNA sequence in the promoter region of a specific gene in the host genome. TALE has a central DNA-binding domain composed of 13-28 repeat monomers of 33-34 amino acids. The amino acids of each monomer are highly conserved, except for hypervariable amino acid residues at positions 12 and 13. The two variable amino acids are called repeat-variable diresidues (RVDs). The amino acid pairs NI, NG, HD, and NN of RVDs preferentially recognize adenine, thymine, cytosine, and guanine / adenine, respectively, and modulation of RVDs can recognize consecutive DNA bases. This simple relationship between amino acid sequence and DNA recognition has allowed for the engineering of specific DNA binding domains by selecting a combination of repeat segments containing the appropriate RVDs.

[0141] In one aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more TALENs. In another aspect, a TALEN provided herein is capable of generating a targeted DSB in a target sequence as described herein. In one aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more TALENs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium- mediated transformation).Zinc Finger Nucleases

[0142] In some embodiments, genome engineering of a citrus or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may employ Zinc Finger Nucleases (ZFNs). ZFNs have been described in U.S. Pat. No. 9,322,006 (incorporated herein by reference in its entirety) and are well known in the art. ZFNs are synthetic proteins consisting of an engineered zinc finger DNA-binding domain fused to the cleavage domain of an endonuclease, for example, Fokl. ZFNs can be designed to cleave almost any long stretch of double-stranded DNA by the modification of the zinc finger DNA-binding domain. ZFNs form dimers from monomers composed of a non-specific DNA cleavage domain of Fokl nuclease fused to a zinc finger array engineered to bind a target DNA sequence. The DNA-binding domain of a ZFN is typically composed of 3-4 zinc-finger arrays. The amino acids at positions -1, +2, +3, and +6 relative to the start of the zinc finger co-helix, which contribute to site-specific binding to the target DNA, can be changed and customized to fit specific target sequences. The other amino acids form the consensus backbone to generate ZFNs with different sequence specificities. Rules forselecting target sequences for ZFNs are known in the art. The FokI nuclease domain requires dimerization to cleave DNA and therefore two ZFNs with their C-tcrminal regions arc needed to bind opposite DNA strands of the cleavage site (separated by 5-7 nt). The ZFN monomer can cut the target site if the two-ZF-binding sites are palindromic. The term ZFN, as used herein, is broad and includes a monomeric ZFN that can cleave double stranded DNA without assistance from another ZFN. The term ZFN is also used to refer to one or both members of a pair of ZFNs that are engineered to work together to cleave DNA at the same site.

[0143] Without being limited by any scientific theory, because the DNA-binding specificities of zinc finger domains can in principle be re-engineered using one of various methods, customized ZFNs can theoretically be constructed to target nearly any gene sequence. Publicly available methods for engineering zinc finger domains include Context-dependent Assembly (CoDA), Oligomerized Pool Engineering (OPEN), and Modular Assembly.

[0144] Several embodiments relate to a method and / or composition provided herein comprising one or more, two or more, three or more, four or more, or five or more ZFNs directed to a target sequence as described herein. In another aspect, a ZFN provided herein is capable of generating a targeted DSB. In one aspect, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more ZFNs are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium-mediated transformation).Meganucleases

[0145] In some embodiments, genome engineering of a citrus or a solanaceous plant, citrus or solanaceous rootstock, interstock and / or scion as described herein may employ a meganuclease. Meganucleases, which are commonly identified in microbes, are unique enzymes with high activity and long recognition sequences (>14 nt) resulting in site-specific digestion of target DNA. Engineered versions of naturally occurring meganucleases typically have extended DNA recognition sequences (for example, 14 to 40 nt). The engineering of meganucleases can be more challenging than that of ZFNs and TALENs because the DNA recognition and cleavage functions of meganucleases are intertwined in a single domain. Specialized methods of mutagenesis and high-throughput screening have been used to create novel meganuclease variants that recognize unique sequences and possess improved nuclease activity.

[0146] In one aspect, a method and / or composition provided herein comprises one or more, two or more, three or more, four or more, or five or more mcganuclcascs directed to a target sequence as described herein. In some embodiments, a meganuclease provided herein is capable of generating a targeted DSB. In some embodiments, vectors comprising polynucleotides encoding one or more, two or more, three or more, four or more, or five or more meganucleases are provided to a cell by transformation methods known in the art (e.g., without being limiting, viral transfection, particle bombardment, PEG-mediated protoplast transfection or Agrobacterium- mediated transformation).Site-Specific Genome Modification

[0147] The genome of a citrus or a solanaceous plant can be modified using sitespecific genome modification techniques. In some embodiments, site-specific genome modification of a citrus or a solanaceous plant as described herein may employ any site-specific genome modification enzyme. As used herein, the term “site- specific genome modification enzyme” refers to any enzyme that can modify a nucleotide sequence in a sequence-specific manner. In some embodiments, a site-specific genome modification enzyme modifies the genome by inducing a single-strand break. In some embodiments, a site-specific genome modification enzyme modifies the genome by inducing a double-strand break. In some embodiments, a sitespecific genome modification enzyme is a recombinase. In some embodiments, a site-specific genome modification enzyme is a transposase. In the present disclosure, site-specific genome modification enzymes include, but are not limited to, nucleases, endonucleases, recombinases, invertases, transposases, methytransferase, demethlylases, aminases, deaminases, helicases, and any combination thereof.

[0148] In some embodiments, the site-specific genome modification enzyme is a recombinase. Non-limiting examples of recombinases include a tyrosine and serine recombinases and coupled with a DNA recognition motif, for example, a Cre recombinase, a Gin recombinase, a Flp recombinase, and a Tnpl recombinase. In another aspect, a serine recombinase coupled with a DNA recognition motif, for example, a PhiC31 integrase, an R4 integrase, and a TP-901 integrase. In an aspect, a recombinase is tethered to a zinc-finger DNA-binding domain, or a TALE DNA-binding domain, or a Cas9 nuclease.

[0149] The Flp-FRT site-directed recombination system comes from the 2p plasmid from the baker’s yeast Saccharomyces cerevisiae. In this system, Flp recombinase (flippase)recombines sequences between flippase recognition target (FRT) sites. FRT sites comprise 34 nucleotides. Flp binds to the “arms” of the FRT sites (one arm is in reverse orientation) and cleaves the FRT site at either end of an intervening nucleic acid sequence. After cleavage, Flp recombines nucleic acid sequences between two FRT sites.

[0150] Cre-lox is a site-directed recombination system derived from the bacteriophage Pl that is similar to the Flp-FRT recombination system. Cre-lox can be used to invert a nucleic acid sequence, delete a nucleic acid sequence, or translocate a nucleic acid sequence. In this system, Cre recombinase recombines a pair of lox nucleic acid sequences. Lox sites comprise 34 nucleotides, with the first and last 13 nucleotides (arms) being palindromic. During recombination, Cre recombinase protein binds to two lox sites on different nucleic acids and cleaves at the lox sites. The cleaved nucleic acids are spliced together (reciprocally translocated) and recombination is complete. In another aspect, a lox site provided herein is a loxP, lox 2272, loxN, lox 511, lox 5171, lox71, lox66, M2, M3, M7, or Mil site.

[0151] In another aspect, the site-specific genome modification enzyme is a dCas9- recombinase fusion protein. As used herein, a “dCas9-recombinase fusion protein” is a dCas9 with a protein fused to the dCas9 in such a manner that the recombinase is catalytically active on the DNA. In some embodiments, dCas9 may be fused with the catalytic domain of any enzyme such that the catalytic domain is catalytically active on DNA. In another aspect, a DNA transposase is attached to a DNA binding domain for example, a TALE-piggyBac and TALE-Mutator.

[0152] Several embodiments relate to promoting DNA recombination by providing a site-specific genome modification enzyme to a plant cell. In some embodiments, recombination is promoted by providing a strand separation inducing reagent. In one aspect, the site-specific genome modification enzyme is selected from an endonuclease, a recombinase, an invertase, a transposase, a helicase or any combination thereof. In some embodiments, recombination occurs between B chromosomes. In some embodiments, recombination occurs between a B chromosome and an A chromosome.

[0153] Several embodiments relate to promoting integration of one or more DNAs of interest by providing a site-specific genome modification enzyme. In some embodiments, integration of one or more DNAs of interest is promoted by providing a strand separation inducing reagent. In one aspect, the site- specific genome modification enzyme is selected from an endonuclease, a recombinase, a transposase, a helicase or any combination thereof. Any DNAsequence can be integrated into a target site of a chromosome sequence by introducing the DNA sequence and the provided site- specific genome modification enzymes. Any method provided herein can utilize any site-specific genome modification enzyme provided herein.

[0154] Several embodiments relate to a method and / or a composition provided herein comprising at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site-specific genome modification enzymes. In yet another aspect, a method and / or a composition provided herein comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten polynucleotides encoding at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten site- specific genome modification enzymes.Antisense and RNAi Constructs

[0155] In the methods and compositions of the present disclosure, endogenous gene activity can be down-regulated by any means known in the art, including through the use of ribozymes or aptamers. Endogenous gene activity can also be down-regulated with an antisense or RNAi molecule.

[0156] In particular, constructs comprising a coding sequence, including fragments thereof, in antisense orientation, or combinations of sense and antisense orientation, may be used to decrease or effectively eliminate the expression of the gene in a plant such as a citrus tree or variety. Accordingly, this may be used to “knock-out” the function of the coding sequence or homologous sequences thereof.

[0157] Techniques for RNAi are well known in the art and are described in, for example, Lehner et al., (2004) and Downward (2004). The technique is based on the ability of double stranded RNA to direct the degradation of messenger RNA with sequence complementary to one or the other strand (Fire et al., 1998). Therefore, by expression of a particular coding sequence in sense and antisense orientation, either as a fragment or longer portion of the corresponding coding sequence, the expression of that coding sequence can be down-regulated.

[0158] Antisense and in some aspects RNAi, methodology takes advantage of the fact that nucleic acids tend to pair with “complementary” sequences. By complementary, it is meant that polynucleotides are those which are capable of base-pairing according to the standard Watson / Crick complementarity rules. That is, the larger purines will base pair with the smallerpyrimidines to form combinations of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of DNA, or adenine paired with uracil (A:U) in the case of RNA. Inclusion of less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others in hybridizing sequences does not interfere with pairing.

[0159] Targeting double-stranded (ds) DNA with polynucleotides leads to triple-helix formation; targeting RNA will lead to double-helix formation. Antisense oligonucleotides, when introduced into a target cell, specifically bind to their target polynucleotide and interfere with transcription, RNA processing, transport, translation and / or stability. Antisense and RNAi constructs, or DNA encoding such RNA’s, may be employed to inhibit gene transcription or translation or both within a host cell, either in vitro or in vivo, such as within a host plant cell. In certain embodiments of the disclosure, such an oligonucleotide may comprise any unique portion of a nucleic acid sequence provided herein. In certain embodiments of the disclosure, such a sequence comprises at least 18, 30, 50, 75, or 100 or more contiguous nucleic acids of the nucleic acid sequence of a gene, and / or complements thereof, which may be in sense and / or antisense orientation. By including sequences in both sense and antisense orientation, increased suppression of the corresponding coding sequence may be achieved.

[0160] Constructs may be designed that are complementary to all or part of the promoter and other control regions, exons, introns or even exon-intron boundaries of a gene. It is contemplated that the most effective constructs may include regions complementary to intron / exon splice junctions. Thus, it is proposed that an embodiment includes a construct with complementarity to regions within 50-200 bases of an intron-exon splice junction. It has been observed that some exon sequences can be included in the construct without seriously affecting the target selectivity thereof. The amount of exonic material included will vary depending on the particular exon and intron sequences used. One can readily test whether too much exon DNA is included simply by testing the constructs in vitro to determine whether normal cellular function is affected or whether the expression of related genes having complementary sequences is affected.

[0161] As stated above, “complementary” or “antisense” means polynucleotide sequences that are substantially complementary over their entire length and have very few base mismatches. For example, sequences of fifteen bases in length may be termed complementary when they have complementary nucleotides at thirteen or fourteen positions. Naturally, sequences which are completely complementary will be sequences which are entirely complementarythroughout their entire length and have no base mismatches. Other sequences with lower degrees of homology also arc contemplated. For example, an RNAi or antisense construct which has limited regions of high homology, but also contains a non-homologous region (e.g., as in a ribozyme) could be designed. Methods for selection and design of sequences that generate RNAi are well known in the art (e.g. Reynolds, 2004). These molecules, though having less than 50% homology, would bind to target sequences under appropriate conditions.

[0162] It may be advantageous to combine portions of genomic DNA with cDNA or synthetic sequences to generate specific constructs. For example, where an intron is desired in the ultimate construct, a genomic clone will need to be used. The cDNA or a synthesized polynucleotide may provide more convenient restriction sites for the remaining portion of the construct and, therefore, would be used for the rest of the sequence. Constructs useful for generating RNAi may also comprise concatemers of sub-sequences that display gene regulating activity.Plant Transformation Constructs

[0163] Vectors used for plant transformation may include any vector that is generally known in the art. Some non-limiting examples of the vectors that can be used areplasmids, cosmids, YACs (yeast artificial chromosomes), BACs (bacterial artificial chromosomes) or any other suitable cloning system, as well as fragments of DNA therefrom. Thus, when the term “vector” or “expression vector” is used, all of the foregoing types of vectors, as well as nucleic acid sequences isolated therefrom, are included. In some embodiments, a viral vector based on a plant virus such as a Citrus Tristeza Virus may be used in accordance with the disclosure. It is contemplated that utilization of cloning systems with large insert capacities will allow introduction of large genetic sequences comprising more than one selected gene. In accordance with the disclosure, this could be used to introduce genetic material corresponding to an entire biosynthetic pathway into a plant. Introduction of such sequences may be facilitated by use of bacterial or yeast artificial chromosomes (BACs or YACs, respectively), or even plant artificial chromosomes. For example, the use of BACs for Agrobacterium-mediated transformation was disclosed by Hamilton et al. (1996).

[0164] Particularly useful for transformation arc expression cassettes that have been isolated from such vectors. DNA segments used for transforming plant cells will, of course, generally comprise the cDNA, gene or genes which one desires to introduce into and haveexpressed in the host cells. These DNA segments can further include structures such as promoters, enhancers, polylinkers, or even regulatory genes as desired. The DNA segment or gene chosen for cellular introduction will often encode a protein which will be expressed in the resultant genetically modified cells resulting in a screenable or selectable trait and / or will impart an improved phenotype to the resulting genetically modified plant. However, this may not always be the case, and the present disclosure also encompasses genetically modified plants incorporating nonexpressed transgenes.

[0165] In accordance with the disclosure, a nucleic acid vector comprising a coding sequence may be introduced into a plant such as a citrus tree or variety, such that, when the vector is transformed into a citrus variety or plant as described herein, the coding sequence is expressed in the plant. In some embodiments the coding sequence may be expressed in, for example, the phloem or roots of the plant, or any other part of the plant. Expression of the coding sequence in the resulting genetically modified citrus tree or variety results in the tree exhibiting increased tolerance or resistance to HLB when compared to a tree lacking expression of the coding sequence.Methods of Genetic transformation

[0166] Suitable methods for transformation of plant or other cells for use with the current disclosure are believed to include virtually any method by which DNA can be introduced into a cell, such as by direct delivery of DNA such as by PEG-mediated transformation of protoplasts, desiccation / inhibition-mediated DNA uptake, electroporation, nanoparticle mediated gene transformation, ribonucleoprotein complex mediated transformation, Agrobacterium- mediated transformation and acceleration of DNA coated particles, etc. Through the application of techniques such as these, the cells of virtually any plant species may be stably transformed, and these cells developed into genetically modified plants.

[0167] Agro / ?acterzMm-mediated transfer is a widely applicable system for introducing genes into plant cells because the DNA can be introduced into whole plant tissues, thereby bypassing the need for regeneration of an intact plant from a protoplast. The use of Agrobacterium- mediated plant integrating vectors to introduce DNA into plant cells is well known in the art.

[0168] Another method for delivering transforming DNA segments to plant cells in accordance with the disclosure is microprojectile bombardment (U.S. Pat. Nos. 5,550,318; 5,538,880; 5,610,042; and PCT Application WO 94 / 09699; each of which is specificallyincorporated herein by reference in its entirety). In this method, particles may be coated with nucleic acids and delivered into cells by a propelling force.

[0169] Another method for plant transformation is PEG-mediated transformation, which can be used to deliver plasmids or ribonucleoproteins, and can be used to introduce transformation without introduction of foreign material in TO plants.Production of plants after genomic editing

[0170] In addition to direct transformation of a particular plant genotype with a construct prepared according to the current disclosure, genetically modified plants may be made by crossing a plant having a selected genetic modification of the disclosure to a second plant lacking the modification. For example, a selected lignin biosynthesis coding sequence can be introduced into a particular plant variety by crossing, without the need for ever directly transforming a plant of that given variety. Therefore, the current disclosure not only encompasses a plant directly modified or regenerated from cells which have been modified in accordance with the current disclosure, but also the progeny of such plants.

[0171] As used herein the term “progeny” denotes the offspring of any generation of a parent plant prepared in accordance with the instant disclosure, wherein the progeny comprises a selected DNA construct. “Crossing” a plant to provide a plant line having one or more added transgenes relative to a starting plant line, as disclosed herein, is defined as the techniques that result in a coding sequence of the disclosure being introduced into a plant line by crossing a starting line with a donor plant line that comprises a first selected DNA of the disclosure. To achieve this in a plant such as a citrus tree one could, for example, perform the following steps:(a) plant seeds of the first (starting line) and second (donor plant line that comprises a first selected DNA of the disclosure) parent plants;(b) grow the seeds of the first and second parent plants into plants that bear flowers;(c) pollinate a flower from the first parent plant with pollen from the second parent plant; and(d) harvest seeds produced on the parent plant bearing the fertilized flower.

[0172] Backcrossing is herein defined as the process including the steps of:(a) crossing a plant of a first genotype containing a desired gene, DNA sequence or element to a plant of a second genotype lacking the desired gene, DNA sequence or element;(b) selecting one or more progeny plant containing the desired gene, DNA sequence or element;(c) crossing the progeny plant to a plant of the second genotype; and(d) repeating steps (b) and (c) for the purpose of transferring a desired DNA sequence from a plant of a first genotype to a plant of a second genotype.

[0173] Introgression of a DNA element into a plant genotype is defined as the result of the process of backcross conversion. A plant genotype into which a DNA sequence has been introgressed may be referred to as a backcross converted genotype, line, inbred, or hybrid. Similarly a plant genotype lacking the desired DNA sequence may be referred to as an unconverted genotype, line, inbred, or hybrid.

[0174] In some embodiments, asexual reproduction or propagation may be used to obtain a progeny plant in accordance with the disclosure. Techniques to achieve asexual propagation or reproduction in citrus trees or varieties may include, for example, grafting, budding, top-working, layering, runner division, cuttings, rooting, T-budding, and the like. In some embodiments, one citrus variety into which a coding sequence has been introduced may be grafted onto the rootstock of another variety. In other embodiments, a coding sequence may be introduced into the rootstock. In either of these situations, one or both of the plant varieties may exhibit increased tolerance or resistance to HLB.Modified Plants

[0175] Citrus and solanaceous plants, comprising the modifications discussed above are provided. Citrus varieties contemplated by this disclosure include, but are not limited to, cultivated citrus types such as sweet orange, bitter orange, blood orange, sour orange, grapefruit, pomelo, citron, poncirus, clementine, naval orange, lemon, lime, mandarin, tangerine, tangelo, or the like. In some embodiments, the citrus plant is a Valencia sweet orange plant. In some embodiments, the citrus plant is a Hamlin sweet orange plant. In some embodiments, the citrus plant is a Carrizo Citrange plant. Solanaceous plant varieties include tomato, potato, eggplant,bell / chili peppers, or the like. In some embodiments, the citrus and / or solanaceous plants disclosed herein may be used as a scion, intcrstock and / or rootstock.

[0176] In some embodiments, the citrus plant disclosed herein exhibits tolerance and / or resistance to HLB. In some embodiments, the citrus plant disclosed herein exhibits tolerance and resistance to Canker disease. In some embodiments, the citrus plant disclosed herein exhibits tolerance and resistance to both HLB and Canker disease. In some embodiments, the citrus plant is a non-transgenic plant. In some embodiments, the citrus plant, is a transgenic plant. In some embodiments, the citrus plant is a non-transgenic Valencia sweet orange plant. In some embodiments, the citrus plant is a non-transgenic Hamlin sweet orange plant. In some embodiments, the citrus plant is a non-transgenic Carrizo Citrange plant.

[0177] In some embodiments, the citrus plant comprises a modification to at least one endogenous gene or regulatory element thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot 1 (Llsl). In some embodiments, the citrus plant comprises a modification to Accelerated Cell Death 2 (ACD2) gene, comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith. In several embodiments, the citrus plant comprises a modification to Cysteine Protease (CP) gene, comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant comprises a modification to Lethal Leaf Spot 1 (Llsl) gene comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 58, SEQ ID NO: 67, SEQ ID NO: 79, SEQ ID NO: 89, SEQ ID NO: 102, SEQ ID NO: 113, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant comprises a modification to Putative F-box protein (PP2-B12) gene comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0178] In some embodiments, the citrus plant comprises a modification to one or more of the genomic target loci, wherein the target loci is selected from a group consisting of Lis IgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO:8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), ), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the modified ACD2gB locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 5-7. In some embodiments, the modified ACD2gD locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119. In some embodiments, the modified CPgA locus in the citrus plant comprises the modification in SEQ ID NO: 14. In some embodiments, the modified CPgC locus in the citrus plant comprises the modifications in any one of the SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the modified Lis IgA locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 22-24. In some embodiments, the modified LlslgB locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the modified PP2 B12gA locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the modified PP2 B12gB locus in the citrus plant comprises any one of the modifications in SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock. In some embodiments, the endogenous genomic target locus comprises a modification in both the alleles. In some embodiments, the endogenous genomic target locus comprises a modification in one allele. In some embodiments, both alleles of the endogenous genomic target locus comprise the same modification. In some embodiments, both alleles of the endogenous genomic target locus comprise different modifications. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide deletions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions and deletions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide substitutions. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25, 50, 100, 200, 300, 400, 500, 1000, 2000, 5000, or 10,000 nucleotides, or nucleotides in ranges in between are modified. In some embodiments, the modified endogenous genomic target locus comprises nucleotide substitutions, insertions and / or deletions.

[0179] In some embodiments, the citrus plant comprises a modified gene loci comprising one or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40,42, 44, 51 , 53, 54, 56, 57, 62, 71 , 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142,143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0180] In some embodiments, the citrus plant comprises a modification to two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot 1 (Llsl). As discussed above, the polypeptides encoded by the said endogenous genes interact with at least one effector protein secreted by one or more bacterial species from the genus Ca. Liberibacter, and the modification may confer resistance or tolerance to Ca. Liberibacter infection in the plant, plant part or the plant seed relative to the plant, plant part or the plant seed of the same variety lacking the modification. Accordingly, the modification may confer resistant to HLB. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0181] In some embodiments, the citrus plant comprises a modification to both an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47 SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith, and a Lethal Leaf Spot 1 (Llsl) gene, for example comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0182] In some embodiments, the citrus plant comprises a modification to both an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith, and a PP2-B12 gene, for example comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0183] In several embodiments, the citrus plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ IDNO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81 , SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith and a Lethal Leaf Spot 1 (Llsl) gene, for example comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0184] In some embodiments, the citrus plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and a PP2-B12 gene, for example comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0185] In several embodiments, a citrus plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0186] In some embodiments, the citrus plant comprises a modification to two or more of the genomic target loci, wherein the target loci are selected from a group consisting of Lis IgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the citrus plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22- 24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130,131 , 133, 134, 138, 135, 136, 139, 140, 141 , 142,143, 144, 145, 146, 149, 150, 147, 148, 151 , 152, 153, 154, 155, 156 and 32. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock. In some embodiments, the endogenous genomic target locus comprises a coding region. In some embodiments, wherein the endogenous genomic target comprises an intron. In some embodiments, the endogenous genomic target locus comprises a modification in both the alleles. In some embodiments, the endogenous genomic target locus comprises a modification in one allele. In some embodiments, both alleles of the endogenous genomic target locus comprise the same modification. In some embodiments, the alleles of the endogenous genomic target locus comprise different modifications. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide deletions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions and deletions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide substitutions. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25, 50, 100, 200, 300, 400, 500, 1000, 2000, 5000, or 10,000 nucleotides, or nucleotides in ranges in between are modified. In some embodiments, the modified endogenous genomic target locus comprises nucleotide substitutions, deletions and / or insertions.

[0187] In some embodiments, the modification is made to both ACD2gB and Lis IgA loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 5-7 in combination with any one of SEQ ID NOs: 22-24. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0188] In some embodiments, the citrus plant comprises a modification to both ACD2gD and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 43, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146,149, 150 and 1 19 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26- 27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified LlslgB locus comprising SEQ ID No:51. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and other allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0189] In some embodiments, the citrus plant comprises a modification to both ACD2gD and CPgC loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising oneallele that comprises any one of SEQ TD Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and other allele of CPgC comprising any one of SEQ ID NOsl6-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0190] In some embodiments, the citrus plant comprises a modification to both ACD2gD and PP2 B12gA loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, the citrus plant comprises a modified genomic target loci comprising modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141 and other allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one alleleof PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0191] In some embodiments, the citrus plant comprises a modification to both ACD2gD and PP2 B12gB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, the citrus plant comprises a modified genomic target loci comprising modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156and other allele of PP2 B 12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0192] In some embodiments, the citrus plant comprises a modification to both CPgC and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs:16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101 , 1 14, 135, 136, 153, 154 and 32 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0193] In some embodiments, the citrus plant comprises a modification to both CPgC and PP2 B12gA loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0194] In some embodiments, the citrus plant comprises a modification to both CPgC and PP2 B12gB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0195] In some embodiments, the citrus plant comprises a modification to both PP2 B12gA and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomictarget loci comprising any one of SEQ ID NOs: 139, 140, 155 and 14 lin combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and a modification of another allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0196] In some embodiments, the citrus plant comprises a modification to both PP2 B12gB and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 142 and 156 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the citrus plant comprises a modified genomic target loci comprising a modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and a modification of another allele of PP2 B12gB comprising any one of SEQ ID NO: 142 and 156 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0197] In some embodiments, the citrus plant comprises a modification to at least three or more of the genomic target loci, wherein the target loci is selected from a group consisting of LlslgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the citrus plant comprises a modified gene loci comprising three or more of the modifications of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128,129, 132, 137, 126, 127, 130, 131 , 133, 134, 138, 135, 136, 139, 140, 141 , 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0198] In some embodiments, a citrus plant comprises a modification to ACD2gD, CPgC and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0199] In some embodiments, a citrus plant comprises a modification to ACD2gD, CPgC and PP2 B12gA. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and in combination with a modified genomic target loci of any one of SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12,31 , 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 1 10, 126, 127, 130, 131 , 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143,144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0200] In some embodiments, a citrus plant comprises a modification to ACD2gD, CPgC and PP2 B12gB. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and in combination with a modified genomic target loci of any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144,145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified PP2 B12gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156 and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0201] In some embodiments, a citrus plant comprises a modification to ACD2gD, LlslgB and PP2 B12gA. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98,109, 110, 126, 127, 130, 131 , 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117 and in combination with a modified genomic target loci of any one of SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0202] In some embodiments, a citrus plant comprises a modification to ACD2gD, LlslgB and PP2 B12gB. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified genomic target loci of any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137,147, 148, 151 , 152 and 1 17 in combination with a modified PP2 B 1 gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156 and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0203] In some embodiments, a citrus plant comprises a modification to CPgC, PP2 B12gA and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified genomic target loci of any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0204] In some embodiments, a citrus plant comprises a modification to CPgC, PP2 B12gB and LlslgB loci. In some embodiments, the citrus plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114,135, 136, 153, 154 and 32 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified genomic target loci of any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135,136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgBlocus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51 , 62, 71 , 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified PP2 B12gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156 and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0205] In some embodiments, the citrus plant disclosed herein is a non-transgenic plant. In some embodiments, the non-transgenic citrus plant is a Valencia sweet orange plant. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 5-7 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 22-24. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31 and 35 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 26-27, 29 and 34. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31 and 35 and second allele that comprises any one of SEQ ID Nos: 9-12, 31 and 35 in combination with a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29 and 34 and second allele that comprises any one of SEQ ID Nos: 26-27, 29 and 34. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 12 in combination with a second modified genomic target locus comprising SEQ ID NO: 26. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 29 and / or 34 in combination with a second modified genomic target locus comprising SEQ ID NO: 31 and / or 35. In some embodiments, the non- transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising anyone of SEQ TD NOs: 9-12, 31 and 35 in combination with a modified genomic target loci comprising any one of SEQ ID NOs: 16-20 and any one of SEQ ID NOs: 26-27, 29 and 34. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0206] In some embodiments, the citrus plant disclosed herein is a non-transgenic plant. In some embodiments, the non-transgenic citrus plant is a Valencia sweet orange plant. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117and second allele that comprises any one of SEQ ID Nos: 26- 27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 12 in combination with a second modified genomic target locus comprising SEQ ID NO: 26. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 29 and / or 34 in combination with a second modified genomic target locus comprising SEQ ID NO: 31 and / or 35. In some embodiments, the non-transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci comprising any one of SEQ ID NOs: 16-20 and any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0207] In some embodiments, the citrus plant disclosed herein is a transgenic plant. In some embodiments, the transgenic citrus plant is a Valencia sweet orange plant. In some embodiments, the transgenic Valencia sweet orange plant comprises a modified gene loci comprising one or more of SEQ ID NOs: 143, 144, 148, 149, 150, 151 and 152. In some embodiments, the transgenic Valencia sweet orange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 143, 144, 148, 149, 150, 151 and 152. In some embodiments, the transgenic Valencia sweet orange plant comprises a modified gene loci comprising three or more of SEQ ID NOs: 143, 144, 148, 149, 150, 151 and 152. In some embodiments, the transgenic Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 144, 149 and 150 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 148, 151 and 152. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0208] In some embodiments, the citrus is a Valencia sweet orange plant. In some embodiments, the Valencia sweet orange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 5-7 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 22-24. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31 and 35 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 26-27, 29 and 34. In some embodiments, the Valencia sweet orange plant comprises a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31 and 35 and second allele that comprises any one of SEQ ID Nos: 9-12, 31 and 35 in combination with a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 26- 27, 29 and 34 and second allele that comprises any one of SEQ ID Nos: 26-27, 29 and 34. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 12 in combination with a second modified genomic target locus comprising SEQ ID NO: 26. In some embodiments, the Valencia sweet orange plant comprises amodified genomic target locus comprising SEQ ID NO: 29 and / or 34 in combination with a second modified genomic target locus comprising SEQ ID NO: 31 and / or 35. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31 and 35 in combination with a modified genomic target loci comprising any one of SEQ ID NOs: 16-20 and any one of SEQ ID NOs: 26-27, 29 and 34. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0209] In some embodiments, the citrus plant is a Valencia sweet orange plant. In some embodiments, the Valencia sweet orange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 5-7 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 22-24. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a second modified genomic target loci comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Valencia sweet orange plant comprises a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target locus comprising SEQ ID NO: 12 in combination with a second modified genomic target locus comprising SEQ ID NO: 26. In some embodiments, the Valencia sweet orange plantcomprises a modified genomic target locus comprising SEQ ID NO: 29 and / or 34 in combination with a second modified genomic target locus comprising SEQ ID NO: 31 and / or 35. In some embodiments, the Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci comprising any one of SEQ ID NOs: 16-20 and any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0210] In some embodiments, the citrus plant is a Hamlin sweet orange citrus plant. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98,109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109,110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125,128, 129, 132, 137, 147, 148, 151 , 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 135, 136, 153, 154 and 114 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 135, 136, 153, 154 and 114 and in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the citrus plant disclosed herein may be a scion, interstock and / or rootstock.

[0211] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising one or more of SEQ ID NOs: 51, 53, 54, 56 and 57. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51.

[0212] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NO: SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117.

[0213] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NO: SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117.1n some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising SEQ ID NO: 51 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 53 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 54 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 56 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 57 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin citrus plant comprises a modified genomic locus comprising SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 56 and SEQ ID NO: 57.

[0214] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising SEQ ID NO: 95 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 107 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 117 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 97 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 98 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 109 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 110 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 119 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 100 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 101 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 112 or a sequence comprising at least 95% identity therewith and SEQ ID NO:32 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified genomic locus comprising SEQ ID NO: 95, SEQ ID NO: 107, SEQ ID NO: 117, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 112 and SEQ ID NO: 32.

[0215] In some embodiments, the citrus plant is a non-transgenic Hamlin sweet orange citrus plant. In some embodiments, the non-transgenic Hamlin sweet orange citrus plant comprises a modified gene loci comprising one or more of SEQ ID NOs:125-131. In some embodiments, the non-transgenic Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 126, 127, 130 and 131 and second allele that comprises any one of SEQ ID Nos: 126, 127, 130 and 131. In some embodiments, the non- transgenic Hamlin sweet orange citrus plant comprises a modified LlslgB locus comprising one allele that comprises a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 125, 128 and 129 and second allele that comprises any one of SEQ ID Nos: 125, 128 and 129. In some embodiments, the non-transgenic Hamlin sweet orange citrus plant comprises a modified gene loci comprising two or more of SEQ ID NOs:125-131. In some embodiments, the non-transgenic Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 126, 127, 130 and 131 and second allele that comprises any one of SEQ ID Nos: 126, 127, 130 and 131 in combination with a modified LlslgB locus comprising one allele that comprises a modified LlslgB locus comprising one allele thatcomprises any one of SEQ ID Nos: 125, 128 and 129 and second allele that comprises any one of SEQ ID Nos: 125, 128 and 129.

[0216] In some embodiments, the citrus plant is a Hamlin sweet orange citrus plant. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98,109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109,110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 126, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 126, 153, 154 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 135, 136, 153, 154 andl l4 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 135, 136, 153, 154 andl 14 114 and in combination with a modified Lis IgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos:26-27, 29, 34, 40, 51 , 62, 71 , 72, 83, 95, 107, 125, 128, 129, 132, 137, 147,148,151 , 152 and 117. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0217] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising one or more of SEQ ID NOs: 51, 53, 54, 56 and 57. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 56 and 57 and second allele that comprises any one of SEQ ID Nos: 56 and 57 in combination with a modified LlslgB locus comprising one allele that comprises SEQ ID No: 51 and second allele that comprises SEQ ID No: 51. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0218] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32. In some embodiments, the Hamlin sweet orange citrus plant comprises amodified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NO: SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0219] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID NOs: 97, 98, 109, 110 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 and second allele that comprises any one of SEQ ID NOs: 100, 101, 112 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NO: SEQ ID NOs: 95, 107 and 117 and second allele that comprises any one of SEQ ID NOs: 95, 107 and 117.1n some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising SEQ ID NO: 51 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 53 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 54 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 56 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 57 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin citrus plant comprises a modified genomic locus comprising SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 56 and SEQ ID NO: 57. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0220] In some embodiments, the Hamlin sweet orange citrus plant comprises a modified gene loci comprising SEQ ID NO: 95 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 107 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 117 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 97 or a sequencecomprising at least 95% identity therewith, SEQ TD NO: 98 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 109 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 110 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 119 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 100 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 101 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 112 or a sequence comprising at least 95% identity therewith and SEQ ID NO:32 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin sweet orange citrus plant comprises a modified genomic locus comprising SEQ ID NO: 95, SEQ ID NO: 107, SEQ ID NO: 117, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 112 and SEQ ID NO: 32. In some embodiments, the citrus plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0221] In some embodiments, the non-transgenic citrus plant is a Carrizo citrange plant. In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112 and 32. In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110 and 119and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 916-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114 and 32. In some embodiments, non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107 and 117. In some embodiments, non-transgenic Carrizo citrange plant comprises a modified CPgC locus comprising one allele that comprises any one ofSEQ ID Nos: 916-20, 44, 56, 57, 66, 77, 78, 88, 100, 101 , 114 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107 and 117.

[0222] In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising SEQ ID No: 42 in combination with a modified CPgC locus comprising SEQ ID No:44. In some embodiments, non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising SEQ ID No: 42 in combination with a modified LlslgB locus comprising SEQ ID No: 40. In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified CPgC locus comprising SEQ ID No: 44 in combination with a modified LlslgB locus comprising SEQ ID No: 40. In some embodiments, the non-transgenic Carrizo citrus plant comprises a modified ACD2gD locus comprising SEQ ID No: 42 in combination with a modified CPgC locus comprising SEQ ID No:44 in combination with a modified LlslgB locus comprising SEQ ID No: 40.

[0223] In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified gene loci comprising SEQ ID NO: 40 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 42 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 44 or a sequence comprising at least 95% identity therewith. In some embodiments, the non- transgenic Carrizo citrange plant comprises a modified genomic locus comprising SEQ ID NO: 40, SEQ ID NO: 42 and SEQ ID NO: 44.

[0224] In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 and second allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88 and second allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88. In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 and second allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83 and second allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83. In someembodiments, the non-transgenic Carrizo citrange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88 and second allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83 and second allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83.

[0225] In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 and second allele that comprises any one of SEQ ID NOs: 64, 74, 75, 85 and 86 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88 and second allele that comprises any one of SEQ ID NOs: 66, 77, 78 and 88 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83 and second allele that comprises any one of SEQ ID NOs: 62, 71, 72 and 83.

[0226] In some embodiments, the non-transgenic Carrizo citrange plant comprises a modified gene loci comprising SEQ ID NO: 64 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 74 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 75 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 85 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 86 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 66 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 77 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 78 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 88 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 62 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 71 or a sequence comprising at least 95% identity therewith or SEQ ID NO: 72 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 83 or a sequence comprising at least 95% identity therewith. In some embodiments, the non-transgenic Carrizo citrus plant comprises a modified genomic locus comprising SEQ ID NO: 64, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 66, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88, SEQ ID NO: 62, SEQ ID NO: 71, SEQ ID NO: 72 and SEQ ID NO: 83.

[0227] In some embodiments, the citrus plant is transgenic. In some embodiments, the transgenic citrus plant is a Carrizo citrange plant. In some embodiments, the transgenic Carrizo citrange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 132-141.In some embodiments, the transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 133, 134 and 138 and second allele that comprises any one of SEQ ID Nos: 133, 134 and 138 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 135 and 136 and second allele that comprises any one of SEQ ID Nos: 135 and 136. In some embodiments, transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 133, 134 and 138 and second allele that comprises any one of SEQ ID Nos: 133, 134 and 138 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 132 and 137 and second allele that comprises any one of SEQ ID Nos: 132 and 137. In some embodiments, the transgenic Carrizo citrange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 135 and 136 and second allele that comprises any one of SEQ ID Nos: 135 and 136 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 132 and 137 and second allele that comprises any one of SEQ ID Nos: 132 and 137. In some embodiments, the transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 133, 134 and 138 and second allele that comprises any one of SEQ ID Nos: 133, 134 and 138 in combination with a modified PP2-B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140 and 141. In some embodiments, the transgenic Carrizo citrange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 133, 134 and 138 and second allele that comprises any one of SEQ ID Nos: 133, 134 and 138 in combination with a modified PP2-B12gB locus comprising one allele that comprises SEQ ID No: 142 and second allele that comprises SEQ ID No: 142. In some embodiments, the transgenic Carrizo citrange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 135 and 136 and second allele that comprises any one of SEQ ID Nos: 135 and 136 in combination with a modified PP2-B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140 and 141. In some embodiments, the transgenic Carrizo citrange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 135 and 136 and second allele that comprises any one of SEQ ID Nos: 135 and 136 in combination with a modified PP2-B12gB locus comprising one allele that comprises SEQ ID No: 142 and secondallele that comprises SEQ ID No: 142. In some embodiments, the transgenic Carrizo citrange plant comprises a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 132 and 137 and second allele that comprises any one of SEQ ID Nos: 132 and 137 in combination with a modified PP2-B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140 and 141. In some embodiments, the transgenic Carrizo citrange plant comprises a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 132 and 137 and second allele that comprises any one of SEQ ID Nos: 132 and 137 in combination with a modified PP2-B12gB locus comprising one allele that comprises SEQ ID No: 142 and second allele that comprises SEQ ID No: 142.

[0228] In several embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith and a Lethal Leaf Spot 1 (Llsl) gene, for example comprising SEQ ID NO: 3, SEQ ID NO:36, SEQ ID NO:45, SEQ ID NO: 121 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0229] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and a PP2-B12 gene, for example comprising SEQ ID NO: 124 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0230] In several embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both a Cysteine Protease (CP) gene, for example comprising SEQ ID NO: 2, SEQ ID NO:38, SEQ ID NO:48, SEQ IDNO:49, SEQ ID NO: 60, SEQ ID NO: 69, SEQ ID NO: 81 , SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 115, SEQ ID NO: 123 or a sequence comprising at least 95% identity therewith, and an Accelerated Cell Death 2 (ACD2) gene, for example comprising SEQ ID NO: 1, SEQ ID NO:37, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO: 59, SEQ ID NO: 68, SEQ ID NO: 80, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 114, SEQ ID NO: 122 or a sequence comprising at least 95% identity therewith. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0231] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to two or more of the genomic target loci, wherein the target loci are selected from a group consisting of Lis IgA (SEQ ID NO: 21), LlslgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified gene loci comprising two or more of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock. In some embodiments, the endogenous genomic target locus comprises a coding region. In some embodiments, wherein the endogenous genomic target comprises an intron. In some embodiments, the endogenous genomic target locus comprises a modification in both the alleles. In some embodiments, the endogenous genomic target locus comprises a modification in one allele. In some embodiments, both alleles of the endogenous genomic target locus comprise the same modification. In some embodiments, the alleles of the endogenous genomic target locus comprise different modifications. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide deletions. In some embodiments, the modified endogenous genomic target locus comprises nucleotide insertions and deletions. In some embodiments, the modifiedendogenous genomic target locus comprises nucleotide substitutions. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25, 50, 100, 200, 300, 400, 500, 1000, 2000, 5000, or 10,000 nucleotides, or nucleotides in ranges in between are modified. In some embodiments, the modified endogenous genomic target locus comprises nucleotide substitutions, deletions and / or insertions.

[0232] In some embodiments, the modification is made to both ACD2gB and Lis IgA loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 5-7 in combination with any one of SEQ ID NOs; 22-24. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0233] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both ACD2gD and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 26- 27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151,152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 43, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151,152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151,152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified LlslgB locus comprising SEQ ID No:51. In some embodiments, modified genomic target loci comprisesmodification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31 , 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26- 27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151,152 and 117 and other allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40,51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151,152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0234] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both ACD2gD and CPgC loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133,134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 16- 20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114,135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 53 and 54 and second allele that comprises any one of SEQ ID Nos: 53 and 54 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one ofSEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101 , 1 14, 135, 136, 153, 154 and 32. In some embodiments, modified genomic target loci comprises modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and other allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127,130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136 and 32 and other allele of CPgC comprising any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0235] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both ACD2gD and PP2 B12gA loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130,131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141 and other allele of PP2 B12gA comprising SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127,130, 131 , 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0236] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both ACD2gD and PP2 B12gB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 40, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130,131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising modification of one allele of ACD2gD comprising SEQ ID NO: 53 and other allele of ACD2gD comprising SEQ ID NO: 54 in combination with modification of one allele of PP2 B 12gB comprising any one of SEQ ID NOs: 142 and 156and other allele of PP2 B 12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and a modification of another allele of ACD2gD comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 74, 75, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0237] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both CPgC and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0238] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both CPgC and PP2 B 12gA loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and the other allele of PP2 B12gA comprising any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments,the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, intcrstock and / or rootstock.

[0239] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both CPgC and PP2 B12gB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modification of another allele of CPgC comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with modification of one allele of PP2 B 12gB comprising any one of SEQ ID NOs: 142 and 156and the other allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein may be a scion, interstock and / or rootstock.

[0240] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both PP2 Bl 2g A and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 139, 140, 155 and 141 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141 and a modification of another allele of PP2 B12gA comprising any one of SEQ ID NOs: 139, 140, 155 and 141in combination with modification of one allele of LlslgB comprising any one of SEQ ID NOs: 26- 27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117 and the other allele of LlslgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148,151, 152 and 117. In some embodiments, the Hamlinsweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein may be a scion, intcrstock and / or rootstock.

[0241] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to both PP2 B 12gB and Lis IgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 142 and 156 in combination with any one of SEQ ID NOs:26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising a modification of one allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 and a modification of another allele of PP2 B12gB comprising any one of SEQ ID NOs: 142 and 156 in combination with modification of one allele of Lis IgB comprising any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and the other allele of Lis IgB comprising any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein may be a scion, interstock and / or rootstock.

[0242]

[0165] In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to at least three or more of the genomic target loci, wherein the target loci is selected from a group consisting of Lis IgA (SEQ ID NO: 21), Lis IgB (SEQ ID NO: 25), ACD2gB (SEQ ID NO: 4), ACD2gD (SEQ ID NO: 8), ACD2gE (SEQ ID NO: 33), CPgA (SEQ ID NO: 13), PP2 B12gA (SEQ ID NO: 124), PP2 B12gB (SEQ ID NO: 124) and CPgC (SEQ ID NO: 15). In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified gene loci comprising three or more of the modifications of SEQ ID NOs: 5-7, 9-12, 14, 16-20, 22-24, 26-27, 29, 31, 34, 35, 40, 42, 44, 51, 53, 54, 56, 57, 62, 71, 72, 83, 64, 74, 75, 85, 86, 66, 77, 78, 88, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112, 125, 128, 129, 132, 137, 126, 127, 130, 131, 133, 134, 138, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 147, 148, 151, 152, 153, 154, 155, 156 and 32. In some embodiments, the Hamlin sweet orangecitrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, intcrstock and / or rootstock.

[0243]

[0166] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to ACD2gD, CPgC and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127,130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130,131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0244] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to ACD2gD, CPgC and PP2 B12gA. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133,134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and in combination with a modified genomic target loci of any one of SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75,85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85,86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0245] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to ACD2gD, CPgC and PP2 B12gB. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and in combination with a modified genomic target loci comprising any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75,85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85,86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 incombination with a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified PP2 B12gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156 and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0246] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to ACD2gD, LlslgB and PP2 B12gA. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified genomic target loci of any one of SEQ ID NO: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64,74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74,75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0247] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to ACD2gD, LlslgB and PP2 B12gB. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 15 and 117 and in combination with a modified genomic target loci of any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified ACD2gD locus comprising one allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75,85, 86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 and second allele that comprises any one of SEQ ID Nos: 9-12, 31, 35, 42, 53, 54, 64, 74, 75, 85,86, 97, 98, 109, 110, 126, 127, 130, 131, 133, 134, 138, 143, 144, 145, 146, 149, 150 and 119 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified PP2 B12gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0248] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to CPgC, PP2 B12gA and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 in combination with a modified genomic target loci of any one of SEQ ID NOs: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweetorange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified PP2 B12gA locus comprising one allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141 and second allele that comprises any one of SEQ ID Nos: 139, 140, 155 and 141. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, interstock and / or rootstock.

[0249] In some embodiments, a Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modification to CPgC, PP2 B12gB and LlslgB loci. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified genomic target loci comprising any one of SEQ ID NOs: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136 and 32 in combination with a modified genomic target loci of any one of SEQ ID NOs: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137 and 117 in combination with a modified genomic target loci of any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweet orange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant comprises a modified CPgC locus comprising one allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 and second allele that comprises any one of SEQ ID Nos: 16-20, 44, 56, 57, 66, 77, 78, 88, 100, 101, 114, 135, 136, 153, 154 and 32 in combination with a modified LlslgB locus comprising one allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and second allele that comprises any one of SEQ ID Nos: 26-27, 29, 34, 40, 51, 62, 71, 72, 83, 95, 107, 125, 128, 129, 132, 137, 147, 148, 151, 152 and 117 and in combination with a modified PP2 B12gB locus comprising one allele that comprises any one of SEQ ID NOs: 142 and 156and second allele that comprises any one of SEQ ID NOs: 142 and 156. In some embodiments, the Hamlin sweetorange citrus plant, Carrizo citrange plant and / or Valencia sweet orange plant disclosed herein also refers to a scion, intcrstock and / or rootstock.

[0250]

[0179] In some embodiments, the citrus plant is a Hamlin sweet orange plant that comprises one or more modifications of the genes that are disclosed herein. In some embodiments, the citrus plant is a Hamlin sweet orange plant that comprises one or more modifications at the genomic target loci that are disclosed herein.

[0251]

[0180] In some embodiments, the citrus plant is a Carizzo citrange plant that comprises one or more modifications of the genes that are disclosed herein. In some embodiments, the citrus plant is a Carizzo citrange plant that comprises one or more modifications at the genomic target loci that are disclosed herein.

[0252] In some embodiments, the solanaceous plant is a non-transgenic plant that exhibits tolerance and resistance to Zebra Chip disease. In some embodiments, the non-transgenic solanaceous plant is a tomato plant. In some embodiments, the non-transgenic solanaceous plant is a potato plant. In some embodiments, the non-transgenic plant is a tomato plant that comprises one or more modifications of the genes that are disclosed herein. In some embodiments, the non- transgenic plant is a tomato plant that comprises one or more modifications at the genomic target loci that are disclosed herein. In some embodiments, the non-transgenic plant is a potato plant that comprises one or more modifications of the genes that are disclosed herein. In some embodiments, the non-transgenic plant is a potato plant that comprises one or more modifications at the genomic target loci that are disclosed herein.

[0253] In some embodiments, a method of generating a modified citrus plant is provided. In some embodiments, the method comprises generating a modified citrus plant that has resistance or tolerance to infection by a bacterial species. In some embodiments, the bacterial species is from the genus Ca. Liberibacter. In some embodiments, the method comprises modifying two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12 and Lethal Leaf Spot 1 (Llsl)gene of a citrus plant cell such that expression of the said genes is knocked-down or reduced and / or interaction of the polypeptide encoded by said genes with at least one effector protein secreted by one or more bacterial species is reduced. In some embodiments, the method further comprises regenerating the modified plant from said plant cell or a progenitor cell thereof, wherein the modified citrus plant is resistant to the bacterial infection relative to a citrus plantlacking the modification. In some embodiments, the bacterial species is from the genus Ca. Libcribactcr.

[0254] In some embodiments, the modified citrus plant that is resistant to the bacterial infection has a reduced bacterial titer relative to a citrus plant lacking modification. In some embodiments, the modified citrus plant that is resistant to the Ca. Liberibacter infection has a reduced bacterial titer relative to a citrus plant lacking modification. In some embodiments, the bacterial titer is reduced by at least 50% in the modified plant relative to a citrus plant lacking the modification. In some embodiments, the bacterial titer is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% in the modified plant relative to a citrus plant lacking the modification.

[0255] In some embodiments, a method of generating a disease resistant citrus plant or tree is provided. In some embodiments, the method comprises grafting a wild-type or unmodified scion onto a modified rootstock as described herein to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a wild-type or unmodified scion onto a modified interstock onto a wild-type or unmodified rootstock as described herein to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a modified scion onto a wild-type or unmodified rootstock as described herein to create a disease resistant citrus plant or tree.

[0256] In some embodiments, combinations of edited or modified rootstock, interstock and / or scion as described herein are utilized to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a modified scion onto a modified rootstock as described herein to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a modified scion onto a modified interstock as described herein to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a modified interstock onto a modified stock and then grafting with a modified scion onto the modified interstock as described herein to create a disease resistant citrus plant or tree. In some embodiments, the method comprises grafting a rootstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl) with a modified scion comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease(CP), PP2-B 12, and Lethal Leaf Spot 1 (Llsl ). Tn some embodiments, the method comprises grafting an intcrstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl) with a modified scion comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl). In some embodiments, the method comprises grafting a rootstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl) with a modified interstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl). In some embodiments, the method comprises grafting a rootstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl) with a modified interstock comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl) and with a modified scion comprising a modification to one or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), PP2-B12, and Lethal Leaf Spot 1 (Llsl). In some embodiments, a rootstock, interstock and / or scion may be from the same or a different plant type or variety. In some embodiments, a rootstock, interstock and / or scion is of a citrus variety. In some embodiments, the citrus variety comprises Poncirus, orange, tangerine / mandarin, lemon or lime, grapefruit, or a hybrid derived from those varieties.

[0257] In some embodiments, the disease resistant citrus plant or tree has resistance or tolerance to infection by a bacterial species. In some embodiments, the bacterial species is from the genus Ca. Liberibacter.ASPECTS

[0258] Embodiments of the present disclosure provided herein are described by way of the following exemplary numbered aspects:1. A plant, a plant part or a plant seed comprising plant cells comprising a modification to two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F- box protein (PP2-B12), and Lethal Leaf Spot 1 (Llsl).2. The plant, plant part or the plant seed of aspect 1, wherein the modification confers resistance or tolerance to infection by one or more bacterial species from the genus Ca. Liberibacter in the plant, plant part or the plant seed relative to the plant, plant pail or the plant seed of the same variety lacking the modification.3. The plant, plant part or the plant seed of aspect 2, wherein the modified plant, plant part or the plant seed has a reduced bacterial titer relative to the plant, plant part or the plant seed lacking the modification.4. The plant, plant part or the plant seed of aspect 3, wherein the bacterial titer is reduced by at least 50% in the modified plant, plant part or the plant seed relative to the plant, plant part or the plant seed of the same variety lacking the modification.5. The plant, the plant part or the plant seed of aspect 2, wherein the one or more bacterial species comprise Candidates Liberibacter asiaticus (CLas), Candidates Liberibacter solanacearum (CLso), or a combination thereof.6. The plant, plant part or the plant seed of aspect 1, wherein the plant, plant part or the plant seed comprises a modification to both ACD2 and Llsl genes.7. The plant, plant part or the plant seed of aspect 1, wherein the plant, plant part or the plant seed comprises a modification to both ACD2 and PP2-B12 genes.8. The plant, plant part or the plant seed of aspect 1, wherein the plant, plant part or the plant seed comprises a modification to both CP and Llsl genes.9. The plant, plant part or the plant seed of aspect 1 , wherein the plant, plant part or the plant seed comprises a modification to both CP and PP2-B12 genes.10. The plant, plant part or the plant seed of aspect 1, wherein the plant, plant part or the plant seed comprises a modification to ACD2, Llsl, and CP genes.11. The plant, plant part or the plant seed of aspect 1 , wherein the plant, plant part or the plant seed comprises a modification to ACD2, Llsl, PP2-B12 and CP genes.12. A plant, a plant part or a plant seed comprising plant cells comprising a modification at two or more wild-type genomic loci, wherein the two or more wild-type genomic loci are independently selected from the genetic loci of SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124,120 or any sequence comprising at least 95% identity therewith.13. The plant, the plant part or the plant seed of aspect 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.14. The plant, the plant part or the plant seed of aspect 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith.15. The plant, the plant part or the plant seed of aspect 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomiclocus comprising any one of SEQ TD NOs: 8, 30, 41 , 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith.16. The plant, the plant part or the plant seed of aspect 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.17. The plant, the plant part or the plant seed of aspect 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111,120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.18. A plant, the plant part or the plant seed comprising plant cells comprising a modification to one or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.19. The plant, the plant part or the plant seed of any of the preceding aspects, wherein the plant, the plant part or the plant seed is of a citrus variety.20. The plant, the plant part or the plant seed of aspect 19, wherein the citrus is a Carrizo, Hamlin, Sour Orange, US-812, Swingle, Flying Dragon, Grapefruit or a Valencia variety.21. The plant, the plant part or the plant seed of aspect 19, wherein the citrus is a rootstock variety.22. The plant, the plant part or the plant seed of aspect 21 , wherein the rootstock variety is a Poncirus, orange, tangcrinc / mandarin, lemon or lime, pomelo, citron, grapefruit, or a hybrid derived from those varieties.23. The plant, the plant part or the plant seed of aspect 19, wherein the citrus is a scion variety.24. The plant, the plant part or the plant seed of aspect 23, wherein the scion variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, grapefruit, pomelo, citron, or a hybrid derived from those varieties.25. The plant, the plant part or the plant seed of aspect 19, wherein the citrus is an interstock variety.26. The plant, the plant part or the plant seed of aspect 25, wherein the interstock variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, grapefruit, pomelo, citron, or a hybrid derived from those varieties.27. The plant, the plant part or the plant seed of any of the preceding aspects, wherein said modification comprises a deletion, a substitution, or an insertion.28. The plant, the plant part or the plant seed of any of the preceding aspects, wherein said modification comprises an indel, and wherein the indel results in a frameshift mutation, a missense mutation, a nonsense mutation, a neutral mutation, or a silent mutation.29. A non-transgenic plant, plant part or a plant seed comprising a modification to two or more endogenous genes or regulatory elements thereof selected from the group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2- B12) and Lethal Leaf Spot 1, (Llsl).30. A non-transgenic plant, plant part or a plant seed comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.31 . The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith.32. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123,120 or a sequence comprising at least 95% identity therewith.33. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith.34. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith and a modification to a genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61 , 70, 82, 94, 106, 121 , 1 16 or a sequence comprising at least 95% identity therewith.35. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith.36. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomiclocus comprising any one of SEQ TD NOs: 8, 30, 41 , 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith.37. The non-transgenic plant, plant part or a plant seed of aspect 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith.38. A Valencia plant, plant pail or a plant seed, comprising plant cells comprising a modification to one or more of wild-type genomic loci comprising any one of SEQ ID NOs: 8, 30, 25, 28, 15 or a sequence comprising at least 95% identity therewith.39. The Valencia plant, plant part or a plant seed of aspect 38, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30 or a sequence comprising at least 95% identity therewith and a modification to a wildtype genomic locus comprising any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith.40. The Valencia plant, plant part or a plant seed of aspect 38, comprising plant cells comprising a modification to a wild-type genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith.41. The Valencia plant, plant part or a plant seed of any one of aspects 38-40, wherein the plant, plant part or the plant seed is non-transgenic.42. The Valencia plant, plant part or a plant seed of any one of aspects 38-40, wherein the plant, plant part or the plant seed is transgenic.43. A method of generating a modified citrus plant having resistance or tolerance to infection by a bacterial species from the genus Ca. Liberibacter, the method comprising the steps of:(a) modifying two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot 1 (Llsl)gene of a citrus plant cell such that expression of the said genes is knocked-down or reduced and / or interaction of the polypeptide encoded by said genes with at least one effector protein secreted by one or more bacterial species from the genus Ca. Liberibacter is reduced; and(b) regenerating the modified plant from said plant cell or a progenitor cell thereof, wherein the modified citrus plant is resistant to Ca. Liberibacter infection relative to a citrus plant lacking the modification.44. The method of aspect 43, wherein the modified citrus plant that is resistant to Ca. Liberibacter infection has a reduced bacterial titer relative to a citrus plant lacking the modification.45. The method of aspect 44, wherein the bacterial titer is reduced by at least 50% in the modified plant relative to a citrus plant lacking the modification.46. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.47. The Carrizo plant, plant part or a plant seed of aspect 46, comprising plant cells comprising a modification to two or more of wild- type genomic loci comprising SEQ ID NO: 39 or a sequence comprising at least 95% identity therewith, SEQ ID NO:41 or a sequence comprising at least 95% identity therewith, SEQ ID NO:43 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 63 or a sequence comprising at least 95% identitytherewith, SEQ ID NO: 73 or a sequence comprising at least 95% identity therewith and SEQ ID NO:84 or a sequence comprising at least 95% identity therewith.48. The Carrizo plant, plant part or a plant seed of aspect 46, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith.49. The Carrizo plant, plant part or a plant seed of aspect 46, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 43, 65, 76, 87 or a sequence comprising at least 95% identity therewith.50. The Carrizo plant, plant part or a plant seed of any one of aspects 46-49, wherein the plant, plant part or the plant seed is non-transgenic.51. The Carrizo plant, plant part or a plant seed of any one of aspects 46-49, wherein the plant, plant part or the plant seed is transgenic.52. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.53. The Hamlin plant, plant part or a plant seed of aspect 52, comprising plant cells comprising a modification to one or more of wild-type genomic loci comprising the SEQ ID NO: 50 or a sequence comprising at least 95% identity therewith, SEQ ID NO:52 or a sequence comprising at least 95% identity therewith, SEQ ID NO:55 or a sequence comprising at least95% identity therewith, SEQ ID NO: 94 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 106 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 116 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 96 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 108 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 118 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 99 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 111 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 120 or a sequence comprising at least 95% identity therewith.54. The Hamlin plant, plant part or a plant seed of aspect 52, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith.55. The Hamlin plant, plant pail or a plant seed of aspect 52, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 55, 99, 111, 120 or a sequence comprising at least 95% identity therewith.56. The Hamlin plant, plant part or a plant seed of any one of aspects 52-55, wherein the plant, plant part or the plant seed is non-transgenic.57. The Hamlin plant, plant pail or a plant seed of any one of aspects 52-55, wherein the plant, plant part or the plant seed is transgenic.58. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising any one of SEQ ID NOs: 40, 62, 71, 72, 83 or a sequence comprising at least 95% identity therewith, any one of SEQ ID NOs: 42, 64, 74, 75, 85, 86 ora sequence comprising at least 95% identity therewith and any one of SEQ TD NOs: 44, 66, 77, 78, 88 or a sequence comprising at least 95% identity therewith.59. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising SEQ ID NO: 51 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 53 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 54 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 56 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 57 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 95 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 107 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 117 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 97 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 98 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 109 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 110 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 119 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 100 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 101 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 112 or a sequence comprising at least 95% identity therewith or SEQ ID NO: 32 or a sequence comprising at least 95% identity therewith.60. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 40, 62, 71, 72, 83, 42, 64, 74, 75, 85, 86, 44, 66, 77, 78 and 88.61. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 51, 53, 54, 56, 57, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112 and 32.62. A Valencia plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.63. The Valencia plant, plant part or a plant seed of aspect 62, wherein the plant, plant part or the plant seed is non-transgcnic.64. The Valencia plant, plant part or a plant seed of aspect 62, wherein the plant, plant part or the plant seed is transgenic.EXAMPLESExample 1 - Modification of Zebra Chip Susceptibility genes in tomato plants

[0259] To determine whether the HLB susceptibility genes would translate to zebra chip susceptibility genes, blastp was performed to examine the similarities between the proteins translated from the citrus genes and potato and tomato genes. The two priority target susceptibility genes for citrus have close homologs in both potatoes and tomatoes. Table 1 lists the gene targets as well as the blastp e-values for the corresponding proteins.TABLE 1 - TARGET GENE LISTS

[0260] To determine if the susceptibility and resistance genes identified in citrus for HLB will function similarly in tomatoes, and likely potatoes, for zebra chip disease. Six CRISPR- edited lines of tomato plants were created with approximately 100 total plants, targeting priority genes predicted to confer resistance to zebra chip disease. The CRISPR-edited tomatoes and wildtype control tomatoes against CLso were tested by exposing them to CLso-infected psyllids. The tomatoes where the Llsl homolog PTC and the cysteine protease homolog Cyp were editedshowed strong resistance to CLso as compared to the non-edited plants. The plants exhibited either no symptoms or only mild to medium symptoms during the first 11 weeks of the experiment, while on average mortality occurred in the control plants at week 8 as shown in Figures 1A, IB and 1C.Example 2 - Protoplast transfection and regeneration

[0261] Gene editing of plant cells were performed by transfecting plant protoplasts with gRNA containing plasmids (e.g., pSMulti-ACD2gD / Lls 1 gB plasmid that contains GFP reporter gene). The plasmid was transfected into Valencia, Carizzo and Hamlin protoplasts using the PEG-mediated transfection method and the GFP signal was examined in pSMulti- ACD2gD / LlslgBAran iec protoplast under the microscope. The results showed that the plasmid uptake was very high in both Valencia and Hamlin protoplasts (data not shown), which confirmed that the protoplast transfection method was not only successful, but also highly effective as shown in Figure 2.

[0262] Through the protoplast transfection, up to 88% and 95% gene editing efficiencies of the protoplast were obtained using pSMulti-Cl-86 / C3-g5 plasmid and 48% using C2-213 plasmid as shown in Table 2. The first few sets of protoplast regenerants yielded Valencia plants with edits to both the C 1-86 and C3-5 genes with no foreign DNA inserted into the genome.TABLE 2

[0263] Following the protoplast transfection, protoplasts were regenerated into plantlets and were able to produce a non-transgenic Valencia plant with individual edits to ACD2gD, LlslgB, and CPgC, as well as plants with a double edit to both the ACD2gD and the LlslgB genes as shown in Figures 3A-3C and 4A-D.Example 3- Double and Triple gene editing of HLB Susceptibility genes in Citrus Plants confer stronger resistance to HLB

[0264] To determine if double and triple-edited citrus plants show a stronger resistance to HLB as compared with single gene edited plants, gene editing of the Valencia, Carrizo and Hamlin plant cells were performed by transfecting plant protoplasts with gRNA containing plasmids. The plasmids were transfected into Valencia, Carrizo and Hamlin protoplasts using the PEG-mediated transfection method. Following the protoplast transfection, protoplasts were regenerated into plantlets and were able to produce a non-transgenic Valencia, Hamlin and Carrizo plants with individual edits to ACD2gD, LlslgB, and CPgC, as well as plants with a double edit to both the ACD2gD and the LlslgB genes, and triple edits to ACD2gD, LlslgB, and CPgC genes as shown in Figures 5A-E, 6A-C, 7A-B, 8A-D and 9A-D. Grafting of wild-type Hamlin plant on wild-type Carrizo and wild-type Hamlin plant on wild-type Carrizo were also performed to generate plants as illustrated in FIGS. 11A and 1 IB.

[0265] After HLB graft and psyllid inoculation, edited trees were analyzed through qPCR to confirm that the psyllids did infect the trees with CLas and through visible HLB symptom evaluation. As shown in Figure 10A, while single edits to Llsl, ACD2, and CP genes in the citrus plants exhibited some resistance against HLB, the double-edited citrus plants to both ACD2gD and LlslgB exhibited the strongest resistance to HLB as shown by a reduced copy number of CLas per 100 ng plant gDNA or RNA in leaf midvein or hairy root tissue of edited citrus plants two years, post inoculation with CLas.

[0266] Additionally, the citrus trees were assessed for characteristic HLB symptoms such as blotchy mottling, corky veins, and dieback. As shown in Figure 10B, while single edits to Lis 1 , ACD2, and CP genes in the citrus plants exhibited some resistance to HLB as compared to WT, the double-edited citrus trees to both ACD2gD and LlslgB exhibited increased resistance.Example 4- Gene editing of HLB Susceptibility genes in Citrus rootstock trees confer stronger resistance to HLB

[0267] To determine if edited citrus rootstock trees show a stronger resistance to HLB as compared with control rootstock trees, gene editing of the Valencia, Carrizo and Hamlin rootstock plant cells were performed by transfecting plant protoplasts with gRNA containing plasmids. The plasmids were transfected into Valencia, Carrizo and Hamlin protoplasts using the PEG-mediated transfection method. Following the protoplast transfection, protoplasts were regenerated into plantlets and were able to produce a non-transgenic Valencia, Hamlin and Carrizorootstock trees with individual edits to ACD2, Llsl , PP2-B12 and CP, as well as plants with a double edit to ACD2 and Llsl and triple edit to both the ACD2, CP and the Llsl genes, and triple edits to ACD2, Llsl, and CP genes. CRISPR-edited Carrizo rootstock with single edits to ACD2, PP2-B 12 and CP, double edits to ACD2 and Lis 1 in a Carrizo interstock of HLB diseased Rangpur lime scion and Carrizo rootstock and triple edits at ACD2, Lis 1 and CP genes as shown in Figures 12A-G.

[0268] Grafting of edited plants with edited or wild-type rootstock of other varieties was performed. Figures 13A and 13B illustrate -grafting of CRISPR-edited Hamlin plant targeting Llsl on wild-type US-942 rootstock (FIG. 13A)) and wild-type Hamlin on CRISPR-edited rootstock targeting Llsl gene (FIG. 13B).

[0269] To analyze if gene editing of HLB Susceptibility genes in Citrus rootstock trees confer stronger resistance to HLB, HLB-infected Valencia scion was grafted onto control wildtype Carrizo rootstock as illustrated in FIG. 14A. Additionally, HLB-infected Rangpur Lime scion was grafted onto control wild-type Carrizo rootstock and Carrizo stock edited at PP2-B12 as illustrated in FIG.14B and 14C. As illustrated in FIG. 14C, lime scion grafted onto PP2-B 12 edited rootstock showed a stronger resistance to HLB as compared with wild-type Carrizo rootstock grafted lime scion.

[0270] After HLB grafting and psyllid inoculation, edited rootstock trees were analyzed through qPCR to confirm that the psyllids did infect the trees with CLas and through visible HLB symptom evaluation. As shown in Figure 15 A, while single edits to Llsl, ACD2, and CP genes in the citrus rootstock trees exhibited some resistance against HLB, the double-edited citrus plants to both ACD2gD and LlslgB exhibited the strongest resistance to HLB as shown by a reduced copy number of CLas per 100 ng plant gDNA or RNA in leaf midvein or hairy root tissue of edited citrus rootstock trees three years, post inoculation with CLas.

[0271] Additionally, the citrus rootstock trees were assessed for characteristic HLB symptoms such as blotchy mottling, corky veins, and dieback. As shown in Figure 15B, while single edits to Llsl, ACD2, and CP genes in the citrus rootstock trees exhibited some resistance to HLB as compared to WT, the double-edited citrus rootstock trees to both ACD2gD and LlslgB exhibited increased resistance.

[0272] As used herein, the section headings are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. All literature and similar-Il l-materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages arc expressly incorporated by reference in their entirety for any purpose, including the disclosures specifically referenced herein. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control. It will be appreciated that there is an implied “about” prior to the temperatures, concentrations, times, etc. discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings herein.

[0273] Although this invention has been disclosed in the context of certain embodiments and examples, those skilled in the art will understand that the present invention extends beyond the specifically disclosed embodiments to other alternative embodiments and / or uses of the invention and obvious modifications and equivalents thereof. In addition, while several variations of the invention have been shown and described in detail, other modifications, which are within the scope of this invention, will be readily apparent to those of skill in the ail based upon this disclosure. It is also contemplated that various combinations or sub-combinations of the specific features and aspects of the embodiments may be made and still fall within the scope of the invention. It should be understood that various features and aspects of the disclosed embodiments can be combined with, or substituted for, one another in order to form varying modes or embodiments of the disclosed invention. Thus, it is intended that the scope of the present invention herein disclosed should not be limited by the particular disclosed embodiments described above.

[0274] It should be understood, however, that this detailed description, while indicating preferred embodiments of the invention, is given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art.

[0275] The terminology used in the description presented herein is not intended to be interpreted in any limited or restrictive manner. Rather, the terminology is simply being utilized in conjunction with a detailed description of embodiments of the systems, methods and related components. Furthermore, embodiments may comprise several novel features, no single one of which is solely responsible for its desirable attributes or is believed to be essential to practicing the inventions herein described.

Claims

WHAT IS CLAIMED IS:

1. A plant, a plant part or a plant seed comprising plant cells comprising a modification to two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F- box protein (PP2-B12), and Lethal Leaf Spot 1 (Llsl).

2. The plant, plant part or the plant seed of claim 1, wherein the modification confers resistance or tolerance to infection by one or more bacterial species from the genus Ca. Liberibacter in the plant, plant part or the plant seed relative to the plant, plant pail or the plant seed of the same variety lacking the modification.

3. The plant, plant part or the plant seed of claim 2, wherein the modified plant, plant part or the plant seed has a reduced bacterial titer relative to the plant, plant part or the plant seed lacking the modification.

4. The plant, plant part or the plant seed of claim 3, wherein the bacterial titer is reduced by at least 50% in the modified plant, plant part or the plant seed relative to the plant, plant part or the plant seed of the same variety lacking the modification.

5. The plant, the plant part or the plant seed of claim 2, wherein the one or more bacterial species comprise Candidates Liberibacter asiaticus (CLas), Candidates Liberibacter solanacearum (CLso), or a combination thereof.

6. The plant, plant part or the plant seed of claim 1, wherein the plant, plant part or the plant seed comprises a modification to both ACD2 and Llsl genes.

7. The plant, plant part or the plant seed of claim 1, wherein the plant, plant part or the plant seed comprises a modification to both ACD2 and PP2-B12 genes.

8. The plant, plant part or the plant seed of claim 1, wherein the plant, plant part or the plant seed comprises a modification to both CP and Llsl genes.

9. The plant, plant part or the plant seed of claim 1 , wherein the plant, plant part or the plant seed comprises a modification to both CP and PP2-B12 genes.

10. The plant, plant part or the plant seed of claim 1, wherein the plant, plant part or the plant seed comprises a modification to ACD2, Llsl, and CP genes.

11. The plant, plant part or the plant seed of claim 1 , wherein the plant, plant part or the plant seed comprises a modification to ACD2, Llsl, PP2-B12 and CP genes.

12. A plant, a plant part or a plant seed comprising plant cells comprising a modification at two or more wild-type genomic loci, wherein the two or more wild-type genomic loci are independently selected from the genetic loci of SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124,120 or any sequence comprising at least 95% identity therewith.

13. The plant, the plant part or the plant seed of claim 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising any one of SEQ ID Nos: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.

14. The plant, the plant part or the plant seed of claim 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith.

15. The plant, the plant part or the plant seed of claim 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomiclocus comprising any one of SEQ ID NOs: 8, 30, 41 , 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith.

16. The plant, the plant part or the plant seed of claim 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.

17. The plant, the plant part or the plant seed of claim 12, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 116 or a sequence comprising at least 95% identity therewith.

18. A plant, the plant part or the plant seed comprising plant cells comprising a modification to one or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

19. The plant, the plant part or the plant seed of any of the preceding claims, wherein the plant, the plant part or the plant seed is of a citrus variety.

20. The plant, the plant part or the plant seed of claim 19, wherein the citrus is a Carrizo, Hamlin, Sour Orange, US-812, Swingle, Flying Dragon, Grapefruit or a Valencia variety.

21. The plant, the plant part or the plant seed of claim 19, wherein the citrus is a rootstock variety.

22. The plant, the plant part or the plant seed of claim 21 , wherein the rootstock variety is a Poncirus, orange, tangcrinc / mandarin, lemon or lime, pomelo, citron, grapefruit, or a hybrid derived from those varieties.

23. The plant, the plant part or the plant seed of claim 19, wherein the citrus is a scion variety.

24. The plant, the plant part or the plant seed of claim 23, wherein the scion variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, grapefruit, pomelo, citron, or a hybrid derived from those varieties.

25. The plant, the plant part or the plant seed of claim 19, wherein the citrus is an interstock variety.

26. The plant, the plant part or the plant seed of claim 25, wherein the interstock variety is a Poncirus, orange, tangerine / mandarin, lemon or lime, grapefruit, pomelo, citron, or a hybrid derived from those varieties.

27. The plant, the plant part or the plant seed of any of the preceding claims, wherein said modification comprises a deletion, a substitution, or an insertion.

28. The plant, the plant part or the plant seed of any of the preceding claims, wherein said modification comprises an indel, and wherein the indel results in a frameshift mutation, a missense mutation, a nonsense mutation, a neutral mutation, or a silent mutation.

29. A non-transgenic plant, plant part or a plant seed comprising a modification to two or more endogenous genes or regulatory elements thereof selected from the group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2- B12) and Lethal Leaf Spot 1, (Llsl).

30. A non-transgenic plant, plant part or a plant seed comprising plant cells comprising a modification to two or more wild-type genomic loci comprising SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.31 . The non-transgenic plant, plant part or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith.

32. The non-transgenic plant, plant pail or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123,120 or a sequence comprising at least 95% identity therewith.

33. The non-transgenic plant, plant pail or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith.

34. The non-transgenic plant, plant pail or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30, 41, 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith and a modification to a genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61 , 70, 82, 94, 106, 121 , 1 16 or a sequence comprising at least 95% identity therewith.

35. The non-transgenic plant, plant part or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 4 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild-type genomic locus comprising SEQ ID NO: 21 or a sequence comprising at least 95% identity therewith.

36. The non-transgenic plant, plant part or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a genetic modification to a wild- type genomiclocus comprising any one of SEQ ID NOs: 8, 30, 41 , 52, 63, 73, 84, 96, 108, 122, 118 or a sequence comprising at least 95% identity therewith.

37. The non-transgenic plant, plant part or a plant seed of claim 30, wherein the plant, the plant part or the plant seed comprises a genetic modification to a wild-type genomic locus comprising any one of SEQ ID NO: 15, 43, 55, 65, 76, 87, 99, 111, 123, 120 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 25, 28, 39, 50, 61, 70, 82, 94, 106, 121, 116 or a sequence comprising at least 95% identity therewith.

38. A Valencia plant, plant pail or a plant seed, comprising plant cells comprising a modification to one or more of wild-type genomic loci comprising any one of SEQ ID NOs: 8, 30, 25, 28, 15 or a sequence comprising at least 95% identity therewith.

39. The Valencia plant, plant part or a plant seed of claim 38, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30 or a sequence comprising at least 95% identity therewith and a modification to a wildtype genomic locus comprising any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith.

40. The Valencia plant, plant part or a plant seed of claim 38, comprising plant cells comprising a modification to a wild-type genomic locus comprising SEQ ID NO: 15 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 8, 30 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOS: 25, 28 or a sequence comprising at least 95% identity therewith.

41. The Valencia plant, plant part or a plant seed of any one of claims 38-40, wherein the plant, plant part or the plant seed is non-transgenic.

42. The Valencia plant, plant part or a plant seed of any one of claims 38-40, wherein the plant, plant part or the plant seed is transgenic.

43. A method of generating a modified citrus plant having resistance or tolerance to infection by a bacterial species from the genus Ca. Liberibacter, the method comprising the steps of:(a) modifying two or more endogenous genes or regulatory elements thereof, selected from a group consisting of Accelerated Cell Death 2 (ACD2), Cysteine Protease (CP), Putative F-box protein (PP2-B12) and Lethal Leaf Spot 1 (Llsl)gene of a citrus plant cell such that expression of the said genes is knocked-down or reduced and / or interaction of the polypeptide encoded by said genes with at least one effector protein secreted by one or more bacterial species from the genus Ca. Liberibacter is reduced; and(b) regenerating the modified plant from said plant cell or a progenitor cell thereof, wherein the modified citrus plant is resistant to Ca. Liberibacter infection relative to a citrus plant lacking the modification.

44. The method of claim 43, wherein the modified citrus plant that is resistant to Ca. Liberibacter infection has a reduced bacterial titer relative to a citrus plant lacking the modification.

45. The method of claim 44, wherein the bacterial titer is reduced by at least 50% in the modified plant relative to a citrus plant lacking the modification.

46. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

47. The Carrizo plant, plant part or a plant seed of claim 46, comprising plant cells comprising a modification to two or more of wild- type genomic loci comprising SEQ ID NO: 39 or a sequence comprising at least 95% identity therewith, SEQ ID NO:41 or a sequence comprising at least 95% identity therewith, SEQ ID NO:43 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 63 or a sequence comprising at least 95% identitytherewith, SEQ ID NO: 73 or a sequence comprising at least 95% identity therewith and SEQ ID NO:84 or a sequence comprising at least 95% identity therewith.

48. The Carrizo plant, plant part or a plant seed of claim 46, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith.

49. The Carrizo plant, plant part or a plant seed of claim 46, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 39, 61, 70, 82 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 41, 63, 73, 84 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 43, 65, 76, 87 or a sequence comprising at least 95% identity therewith.

50. The Carrizo plant, plant part or a plant seed of any one of claims 46-49, wherein the plant, plant part or the plant seed is non-transgenic.

51. The Carrizo plant, plant part or a plant seed of any one of claims 46-49, wherein the plant, plant part or the plant seed is transgenic.

52. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

53. The Hamlin plant, plant part or a plant seed of claim 52, comprising plant cells comprising a modification to one or more of wild-type genomic loci comprising the SEQ ID NO: 50 or a sequence comprising at least 95% identity therewith, SEQ ID NO:52 or a sequence comprising at least 95% identity therewith, SEQ ID NO:55 or a sequence comprising at least95% identity therewith, SEQ ID NO: 94 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 106 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 116 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 96 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 108 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 118 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 99 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 111 or a sequence comprising at least 95% identity therewith and SEQ ID NO: 120 or a sequence comprising at least 95% identity therewith.

54. The Hamlin plant, plant part or a plant seed of claim 52, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith.

55. The Hamlin plant, plant part or a plant seed of claim 52, comprising plant cells comprising a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 50, 94, 106, 116 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 52, 96, 108, 118 or a sequence comprising at least 95% identity therewith and a modification to a wild-type genomic locus comprising any one of SEQ ID NOs: 55, 99, 111, 120 or a sequence comprising at least 95% identity therewith.

56. The Hamlin plant, plant part or a plant seed of any one of claims 52-55, wherein the plant, plant part or the plant seed is non-transgenic.

57. The Hamlin plant, plant part or a plant seed of any one of claims 52-55, wherein the plant, plant part or the plant seed is transgenic.

58. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising any one of SEQ ID NOs: 40, 62, 71, 72, 83 or a sequence comprising at least 95% identity therewith, any one of SEQ ID NOs: 42, 64, 74, 75, 85, 86 ora sequence comprising at least 95% identity therewith and any one of SEQ TD NOs: 44, 66, 77, 78, 88 or a sequence comprising at least 95% identity therewith.

59. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising SEQ ID NO: 51 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 53 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 54 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 56 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 57 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 95 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 107 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 117 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 97 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 98 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 109 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 110 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 119 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 100 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 101 or a sequence comprising at least 95% identity therewith, SEQ ID NO: 112 or a sequence comprising at least 95% identity therewith or SEQ ID NO: 32 or a sequence comprising at least 95% identity therewith.

60. A Carrizo plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 40, 62, 71, 72, 83, 42, 64, 74, 75, 85, 86, 44, 66, 77, 78 and 88.

61. A Hamlin plant, plant part or a plant seed, comprising plant cells comprising a modified genomic locus comprising one or more of SEQ ID NOs: 51, 53, 54, 56, 57, 95, 107, 117, 97, 98, 109, 110, 119, 100, 101, 112 and 32.

62. A Valencia plant, plant part or a plant seed, comprising plant cells comprising a modification to two or more wild-type genomic loci selected from SEQ ID NOs: 4, 8, 13, 15, 21, 25, 28, 30, 33, 39, 41, 43, 50, 52, 55, 61, 70, 82, 63, 73, 84, 65, 76, 87, 94, 106, 116, 96, 108, 118, 99, 111, 121, 122, 123, 124, 120 or a sequence comprising at least 95% identity therewith.

63. The Valencia plant, plant part or a plant seed of claim 62, wherein the plant, plant part or the plant seed is non-transgcnic.

64. The Valencia plant, plant part or a plant seed of claim 62, wherein the plant, plant part or the plant seed is transgenic.