Melon plants with resistance against tolcndv-es
Patent Information
- Authority / Receiving Office
- EP · EP
- Patent Type
- Applications
- Current Assignee / Owner
- Filing Date
- 2024-05-17
- Publication Date
- 2026-04-01
AI Technical Summary
Melon plants lack effective resistance against the Spanish strain of Tomato Leaf Curl New Delhi Virus (ToLCNDV-ES), which has broken previous resistance mechanisms, leading to severe disease symptoms and yield losses.
Introduction of a new Quantitative Trait Locus (QTL) on chromosome 5, named QTL5/7?, which confers resistance to ToLCNDV-ES through a modified endogenous gene encoding a TIR-NBS-LRR resistance protein, and the use of specific SNP markers for identifying and selecting resistant melon plants.
The QTL5/7? provides dominant resistance to ToLCNDV-ES infection, reducing disease symptoms and maintaining yield quality even in infested areas, allowing for the cultivation of melon varieties with high agronomic value.
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Abstract
Description
[0001] Melon plants with resistance against ToLCNDV-ES
[0002] The application concerns melon plants (Cucumis meld) resistant to infection with the Spanish strain of tomato leaf curl New Delhi virus (ToLCNDV-ES). The resistant melon plants have in one aspect a genomic introgression fragment on chromosome 5 which confers resistance to ToLCNDV-ES in a dominant manner. Also disclosed are markers for identifying those fragments, methods for identifying or producing resistant melon plants. Further, the causal gene underlying the QTL is provided, as are methods of selecting or modifying the causal gene. In one aspect the resistant melon plants comprise a modified endogenous gene, which confers resistance.
[0003] Tomato Leaf Curl New Delhi Virus (ToLCNDV) is a bi-partite begomovirus which is transmitted by white fly vectors, Bemisia tabaci Genn. (Hemiptera: Aleyrodidae) and causes severe symptoms of leaf yellowing and curling and plant stunting in susceptible hosts.
[0004] Until 2016 ToLCNDV was limited to India and other Asian countries, where it was mainly prevalent on Solanaceae host plants, especially tomato, but since then it has been reported in Spain and other countries of the Mediterranean basin, where it is mostly prevalent on Cucurbitaceae hosts and seemed to have adapted to Cucurbitaceae hosts (Fortes et al., Viruses 2016, 8, 307; doi: 10.3390 / v8110307). The Spanish isolate (ToLCNDV-ES) was found to be phylogenetically in a different cluster from other ToLCNDV isolates based on DNA-A sequence analysis.
[0005] The Mediterranean ToLCNDV isolates (also referred to as the European ToLCNDV isolates) are referred to as ToLCNDV-ES and it is now known that all ToLCNDV-ES isolates are highly genetically uniform (>99% identity, Juarez et al., 2019, Natural hosts and genetic diversity of the emerging tomato leaf curl New Delhi virus in Spain. Frontiers Microbiology, 10, 140. https: / / doi.org / 10.3389 / fmicb.2019.00140) and are distinct from all other ToLCNDV isolates found outside Europe. Although ToLCNDV-ES is infective to tomato (Ruiz et al., 2017, Biological characterization of Tomato leaf curl New Delhi virus from Spain. Plant Pathology, 66, 376-382), TolCNDV-ES appears poorly adapted to this host; in contrast, it very efficiently infects Cucurbitaceae like squash, melon, cucumber and pumpkin.
[0006] This genetic uniformity of the European isolates is also thought to explain their preference and adaptation to Cucurbitaceae hosts.
[0007] W02018 / 011075 describes a QTL on chromosome 5 of the melon genome which confers resistance against ToLCNDV. Also the variety Coliseo Fl (Nunhems) has been commercialized containing the QTL. The wild donor used to introgress the QTL has small fruits (no more than 6 cm long), with white acidic tasting flesh. The donor had an average ToLCNDV disease score of 7.4 on a scale of scale of 1 = dead plant to 9 = no symptoms, while the elite line into which the QTL was backcrossed had an average disease score of about 5.1. The QTL was mapped to the region delimited by SNP_01 to SNP_06. Seeds were deposited under NCIMB 42585 which were cultivated melon plants of the BC4S4 generation comprising the introgression fragment in homozygous form, with the donor nucleotide being present in homozygous form for SNP_01 to SNP_06. The TolCNDV resistance was later fine-mapped to he in between SNP_03 and SNP_04, with two SNP markers added in-between these two markers, named SNP_07 and SNP_08, see US11591611B2, incorporated herein by reference.
[0008] It was found that the resistance conferred by the above QTL was broken in the field in Spain, by the ToLCNDV-ES isolates.
[0009] It is an object of the invention to provide a QTL on chromosome 5 which confers resistance to the resistance-breaking ToLCNDV-ES strain.
[0010] The present invention discloses melon plant cells and melon plants being resistant to infections by the current TolCNDV-ES strains present in Spain.
[0011] It is commonly known that ToLCNDV-ES does infect various different plant species of the Curcubitaceae species, including melon species. It is also well known that ToLCNDV-ES is transmitted persistently from infected plants to non-infected plants by the plant sucking pest Bemisia tabaci (whitefly). Transfer of ToLCNDV-ES from one crop species to different crop species or even from weed species to crop species has been demonstrated. Whiteflies may pick up ToLCNDV-ES from outside the controlled area even from different species and transfer it to melon plants grown in the controlled area. Whitefly vector control therefore is of limited effectiveness for preventing ToLCNDV-ES infection. TolCNDV-ES resistant melon plants have the advantage that they would withstand infection with TolCNDV-ES without major yield losses, even if plants around the area where the melon plants are grown are infected with ToLCNDV- ES.
[0012] The inventors found a new, wild ToLCNDV-ES resistant donor accession of the species C. melo ssp. melo which remained symptomless (average score 9.0) to the most aggressive ToLCNDV-ES strains in Spain, which strains were able to cause more severe disease symptoms on the previously resistant melon plants comprising the QTL described in W02018 / 011075 and US11591611B2.
[0013] When mapping the resistance from a selected donor line (the original accession was highly variable for the resistance) in an F2 population derived from a cross between the new donor and a susceptible elite melon breeding line, it was surprisingly found that the QTL mapped to the same region on chromosome 5 as described in W02018 / 011075 and US11591611B2. However, the region was clearly different, as the SNP haplotype was different (see Figure 3) and as the average disease score was high, compared to the previous QTL on chromosome 5, when tested with the most recent ToLCNDV-ES strains. The QTL from the new donor was, thus, able to withstand infection with the most recent ToLCNDV-ES strains. The most recent strains are, therefore, also referred to as ‘resistance-breaking strains’, as they are able to overcome the resistance of W02018 / 011075. This does not mean that the resistance of the QTL described in W02018 / 011075 is completely lost due to the new strains, but the resistance has become less effective, as disease symptoms caused by the new ToLCNDV-ES strains have become more severe, especially under high virus pressure.
[0014] To differentiate between the QTL5 of W02018 / 011075 (and US11591611B2), the QTL5 is herein named QTL5r6, for ‘resistance breaking QTL5’, i.e. the QTL5r6 confers resistance against the most aggressive ToLCNDV-ES strains.
[0015] QTL5 / 7? confers resistance in a monogenic, dominant manner.
[0016] The chromosome 5 region to which the QTL5 / 7? was mapped contains the largest cluster of NBS-LRR genes in melon, Gonzalez et al. BMC Genomics 2014, 15: 1131 (title: Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome), but by using various eliminations, the causal gene could be identified herein.
[0017] The underlying causal gene was mapped and was found to encode a TIR-NBS-LRR resistance protein, which was compared to and found to be different from the TIR-NBS-LRR protein of the previous QTL5 (of W02018 / 011075). The two proteins, when compared by pairwise alignment (using Needle), had 95.2% sequence identity to one another. Also, when compared to the corresponding protein in the reference genome (melonomics.net, DHL92 version 4) and to the susceptible variety Vedantrais, the protein of the instant donor has 98.6% sequence identity to the reference genome protein and to the protein in Vedrantais. The proteins were identical in the reference genome and in variety Vedrantais.
[0018] The Quantitative Trait Locus (QTL) on chromosome 5 (QTL5 / 7?) was introgressed from the wild donor accession into an elite cultivated melon line. Seeds of a selection of the wild donor, wherein the QTL5 / 7? introgression is fixed and the donor SNP nucleotides are homozygous, were deposited by Nunhems B.V. under Accession number NCIMB 44139 in accordance with the Budapest Treaty. In these seeds the donor genotype for the Single Nucleotide Polymorphism (SNP) markers (SNP_01 to SNP_07) provided herein is present.
[0019] The wild donor itself is not uniform and is not an accession of agronomic value. By identifying and transferring QTL5 / 7? from the donor into cultivated melon, it is now possible to make cultivated melon varieties and cultivars of high agronomic value (with uniform characteristics and marketable fruits having high brix and good shelf life) with resistance against the resistance-breaking ToLCNDV-ES strains and thus it is possible to cultivate those melon varieties in ToLCNDV-ES infested areas without yield loss.
[0020] “Melon plant cells” or “melon plants” also designated as muskmelon plant cells or muskmelon plants in the art shall be understood in context with the present invention to be plant cells originating from the species Cucumis melo or to be plants belonging to the species Cucumis melo. Cucumis me lo. can be classified into: C. melo cantalupensis, C. melo inodorous and C. melo reticulatus. C. melo cantalupensis are also referred to as Cantaloupes and are primarily round in shape with prominent ribs and almost no netting. Most have orange, sweet flesh and they are usually very fragrant. In contrast to the European cantaloupe, the North American 'Cantaloupe' is not of this type, but belongs to the true muskmelons. C. melo inodorous (or winter melons) can be subdivided into different types, such as Honeydew melon, Piel de Sapo, Sugar melon, Japanese melon, etc. C. melo reticulatus is the true muskmelon, with reticulated skin (netted) and includes Galia melons, Sharlyn melons and the North American cantaloupe.
[0021] Melon and the wild relatives of melon is / are diploid and has / have 12 pairs of homologous chromosomes, numbered 1 to 12.
[0022] “Resistant” or “being resistant to” shall be understood in context of the present invention to mean a plant which is a host species of a particular pathogen and can therefore be infected by a given pathogen, but wherein the plant comprises a genetic element (e.g. an introgression fragment) resulting in reduction of pathogen growth and / or spreading in the plant after infection compared to the susceptible plant lacking the genetic element. In context of the present invention “resistant” or “being resistant to” in particular refers to plant cells or plants being resistant to ToLCNDV-ES, especially to the most aggressive ToLCNDV-ES strains, such as the resistance-breaking strains. Resistance is a relative term which can span a range of (different) reactions in the plant cell or plant, triggered by pathogen infection. The effect of those reactions by the plant cell or plant can be measured by various means. Typically, the effect is measured by defining a symptom level appearing in the plant cell or plant. Typically, average symptoms of several plants of a line (e.g. 10 or more) are compared to average symptoms of several plants of a control line or variety, preferably a susceptible control line or variety. Thus at least 10 or more individual plants of a line or variety are scored at one time point and the average disease score is calculated.
[0023] Concerning the present invention, the following commonly known symptom levels are applied according to phenotypic observations taken after ToLCNDV-ES infection:
[0024] 1 = Dead plant
[0025] 2 = Severe mosaic and curling, chlorosis and growth reduction. No recovery
[0026] 3 = Strong mosaic and curling, chlorosis and growth reduction. No recovery
[0027] 4 = Curling and mosaic, chlorosis, no or mild growth reduction. No recovery
[0028] 5 = Curling and mosaic, chlorosis, no growth reduction. Slight recovery of the upper plant zone
[0029] 6 = Mild curling, mosaic and chlorosis, no growth reduction. Recovery of the upper middle plant 7 = Mild curling, mosaic and chlorosis, no growth reduction. Symptoms appear only in the lower plant zone
[0030] 8 = Faint mosaic
[0031] 9 = No symptoms
[0032] For determining the symptom level (or disease score) preferably young plants are infected with ToLCNDV-ES. Young plants are preferably plants having the age of the first true leaf being expanded, preferably approximately 12-15 days after sowing. Infection is preferably carried out via feeding of the vector (Bemisia) carrying the virus. For this purpose, plants are germinated and grown under optimal or close to optimal conditions. The symptom level is preferably determined at least once, e.g. 30 or 40 days after infection (or later, e.g. 31, 32, 33, 34, 35, 40, 41 days after infection). Optionally symptom level is determined twice or even three times at different time-points following infection to confirm the result, e.g. a first scoring at approximately 15, 20 or 25 days after infection and a second scoring at approximately 30 or 40 days after infection (or later) with ToLCNDV-ES. See also the Examples. In one aspect a plant line is said to be resistant against ToLCNDV-ES infection if it has an average disease score of at least 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4 or 8.5 or 8.6, or 8.7, or 8.8 or 8.9 or higher, e.g. at least 9.0, while the susceptible control line or variety, such as variety Gandalf (or Gandalf Fl, Nunhems B.V.) or Vedantrais, has an average disease score of 2.5 or less, or 2.0 or less, when grown under the same conditions and infected in the same way. In one aspect a plant line comprising QTL5 / 7? in homozygous or heterozygous form is said to be resistant against ToLCNDV-ES infection if it has a higher average disease score to the ToLCNDV- ES resistance breaking strain than plants comprising QTL5 of US11,591,611, such as NCIMB42585 or variety Coliseo Fl (Nunhems).
[0033] It has been observed that introgression of QTL5 / 7? located on chromosome 5 from a wild melon donor plant into cultivated melon plants confers resistance to ToLCNDV-ES infection in cultivated melon plants or cells derived therefrom. It is sufficient that the respective fragment is present only in the heterozygous state for conferring ToLCNDV-ES resistance, demonstrating that the fragment confers resistance to ToLCNDV-ES infection in a dominant manner. Single Nucleotide Polymorphisms (SNPs) on chromosome 5 were identified which are closely linked to QTL5 / 7? conferring ToLCNDV-ES resistance. Also, the causal gene underlying QTL5 / 7? has been identified herein. The SNP nucleotide of the resistant donor (i.e. the nucleotide of the introgression fragment) is present in homozygous form in the deposited seeds, i.e. the donor nucleotide is present in homozygous form for SNP_01 to SNP_07 (linked to QTL5 / 7?). The SNPs can, therefore, be used to test the presence of the introgression fragment comprising the QTL5 / 7? in a plant cell, plant tissue, plant part, and / or in marker assisted selection (MAS) to transfer the QTLs into elite melon lines or varieties. The SNPs can also be used to select plants comprising smaller introgressions fragments than the fragments present in the deposited seeds, whereby the smaller sub-fragments retain the QTL5 / 7?. For example it was found that backcross lines with the resistant donor nucleotide for only SNP_03, SNP_04 and SNP_05 (and not for SNP_01, SNP_02, SNP_06 and SNP_07) all retained the QlL5rb. see Examples. Alternatively, one or more of the SNPs and / or the causal gene sequence underlying QTL5 / A can be used to identify other donors which comprise QTL5 / A and to introgress the QTL into cultivated melon or to transfer the QTL5 / 7? from one cultivated melon plant into another.
[0034] The present invention, therefore, relates in one aspect to cultivated melon plant cells or melon plants comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the donor plant in-between SNP_01 and SNP_07, preferably the sequence of the donor plant in-between SNP_01 and SNP_06, or in-between SNP_01 and SNP_05, or in-between SNP_01 and SNP_04, or in-between SNP_02 and SNP_06, or inbetween SNP_03 and SNP_05, more preferably the sequence of the donor plant in between SNP_01 and SNP_04, or in-between SNP_02 and SNP_04 or SNP_03 and SNP_04. The ToLCNDV-ES resistance conferring QTL5 / A is present on the introgression fragment, as can be determined by a resistance assay as described herein.
[0035] Therefore, the present invention relates in one aspect to melon plant cells or melon plants comprising an introgression fragment on chromosome 5 derived from (obtained from, obtainable from) a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between markers selected from:
[0036] SNP_01 and SNP_07 and comprising the donor SNP nucleotide for SNP_02 (i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand), SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3), SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand), SNP 05 (a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand) and / or SNP_06 (an Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_01 and / or SNP_07 may be present, i.e. a Cytosine at nucleotide 81 of SEQ ID NO: 1 (SNP_01) and / or a Cytosine at nucleotide 81 of SEQ ID NO: 7 (SNP_07);
[0037] SNP_01 and SNP_06 and comprises the donor SNP nucleotide for SNP_02 (i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand), SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3), SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand) and / or SNP 05 (a Thymine at nucleotide 101 ofSEQ ID NO: 5 oran Adenine in the complementary strand) ; optionally the donor nucleotide for SNP_01 and / or SNP_06 may be present, i.e. a Cytosine at nucleotide 81 of SEQ ID NO: 1 (SNP_01) and / or a Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand (SNP_06); SNP_01 and SNP_05 and comprises the donor SNP nucleotide for SNP_02 (i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand), SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3) and / or SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_01 and / or SNP_05 may be present, i.e. a Cytosine at nucleotide 81 of SEQ ID NO: 1 (SNP_01) and / or a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand (SNP_05);
[0038] SNP_02 and SNP_07 and comprising the donor SNP nucleotide for SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3), SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand) and / or SNP 05 (a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand) and / or SNP_06 (an Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_02 and / or SNP_07 may be present, i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand (SNP_02) and / or a Cytosine at nucleotide 81 of SEQ ID NO: 7 (SNP 07);
[0039] SNP_02 and SNP_06 and comprises the donor SNP nucleotide for SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3), SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand) and / or SNP 05 (a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand); optionally the donor nucleotide for SNP_02 and / or SNP_06 may be present, i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand (SNP_02) and / or a Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand (SNP_06);
[0040] SNP_02 and SNP_05 and comprises the donor SNP nucleotide for SNP_03 (i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3) and / or SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_02 and / or SNP_05 may be present, i.e. a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine in the complementary strand (SNP_02) and / or a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand (SNP_05);
[0041] SNP_03 and SNP_07 and comprising the donor SNP nucleotide for SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand) and / or SNP_05 (a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand) and / or SNP 06 (an Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_03 and / or SNP_07 may be present, i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3 (SNP_03) and / or a Cytosine at nucleotide 81 of SEQ ID NO: 7 (SNP_07);
[0042] SNP_03 and SNP_06 and comprises the donor SNP nucleotide for SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand) and / or SNP_05 (a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complement strand); optionally the donor nucleotide for SNP_03 and / or SNP_06 may be present, i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3 (SNP_03) and / or an Adenine at nucleotide 101 of SEQ ID NO: 6 or a Thymine in the complementary strand (SNP_06);
[0043] SNP_03 and SNP_05 and comprises the donor SNP nucleotide for SNP_04 (i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand); optionally the donor nucleotide for SNP_03 and / or SNP_05 may be present, i.e. a Guanine at nucleotide 81 of SEQ ID NO: 3 (SNP_03) and / or a Thymine at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand (SNP_05);
[0044] SNP_03 and SNP_04 and comprises the donor SNP nucleotide (i.e. a Guanine) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 and / or comprises the donor SNP nucleotide for SNP_04, i.e. an Adenine at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand.
[0045] The term ‘in-between’ does not exclude that the first mentioned and / or last-mentioned SNP nucleotide is also the donor nucleotide, so e.g. ‘in-between SNP_01 and SNP_07’ in one aspect refers to SNP_01 and / or SNP_07 comprising the resistant donor nucleotide. The resistant donor nucleotide is shown e.g. in Table 1 herein. However, the first and last-mentioned SNP may also be a different nucleotide, e.g. of the recurrent parent. Furthermore, when SEQ ID NO:s are mentioned, in one aspect also variants of the mentioned sequences are encompassed, i.e. the mentioned SNP nucleotide at the equivalent nucleotide position in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to the SEQ ID NO mentioned. There may, thus, be slight variation in the nucleotides preceding or following the mentioned SNP nucleotide.
[0046] Thus, when referring herein to the introgression fragment comprising the sequence “in-between” two SNPs (Single Nucleotide Polymorphisms), this encompasses in one aspect that one or both of the two SNPs themselves are also from the resistant donor, i.e. have the donor nucleotide at the SNP position. In another aspect, the two SNPs are from the recipient, e.g. the susceptible melon plant, while only a region between the two SNPs is from the resistant donor and confers ToLCNDV-ES resistance, i.e. the resistance conferring donor fragment, which comprises QTL5 / 7?. lies in-between the two SNP markers. So, for example, a plant may comprise the introgression fragment comprising the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_03 and SNP_04, this plant in one aspect comprises a Guanine (G) at nucleotide 81 of SEQ ID NO: 3 and / or an Adenine (A) at nucleotide 101 of SEQ ID NO: 4 (or a Thymine in the complementary strand), i.e. the donor nucleotides. In another aspect only a region (the whole region or a part thereof) between these two SNPs is from the donor, while SNP_03 and SNP_04 are from the recipient.
[0047] Thus, regarding the QTL5 / 7? on chromosome 5, SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07 may all have the resistant donor haplotype (or genotype). Or only SNP_03 and SNP_04 may have the resistant donor haplotype (or genotype). Or only a single SNP, i.e. only SNP_03, or only SNP_04 has the resistant donor nucleotide. The SNPs that do not have the resistant donor nucleotide thus have another nucleotide, e.g. the recipient nucleotide. The recipient nucleotide for a SNP may be any of the other 3 nucleotides, i.e. for SNP_03 the recipient nucleotide may be Adenine, Cytosine or Thymine. Thus, for example when stating that the introgression fragment is in-between SNP_03 and SNP_04 regarding the QTL5 / A on chromosome 5, SNP_03 and SNP_04 may both have the resistant donor haplotype (or genotype). Or only a single SNP, i.e. only SNP_03 or only SNP_04 may have the resistant donor nucleotide; or even neither SNP_03 nor SNP_04 has the resistant donor nucleotide, while the sequence in-between still contains QTL5 / 7?.
[0048] In one aspect the QTL5 / 7? comprises a gene (the causal gene underlying QTL5 / A) which encodes a TIR- NBS-LRR protein (‘resistance protein’ or resistance conferring protein), which protein comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following 4 amino acid changes compare to the susceptible protein of SEQ ID NO: 10 (or a susceptible protein comprising at least 98%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9% or 99%, or 99.5% or 99.8% sequence identity to SEQ ID NO: 10):
[0049] 1. an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2;
[0050] 2. a change of amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0051] 3. A change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2; 4. A change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2.
[0052] In other words, QTL5 / 7? comprises a gene (the causal gene underlying QTL5 / A) which encodes a TIR- NBS-LRR protein (‘resistance protein’ or resistance conferring protein) of SEQ ID NO: 8 or a protein which comprises at least 96%, 97%, 98%, 99% or 100% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following amino acid nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at least 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at least 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at least 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at least 96% sequence identity to SEQ ID NO: 8.
[0053] The two TIR-NBS-LRR proteins from QTL5 / 7? and from the QTL5 (of which resistance has been broken by the new ToLCNDV-ES strains) have 95.2% sequence identity to each other. However, they have the above 4 changes in common, compared to the protein in the reference genome of melon and compared to the protein in the susceptible variety Vendretais (these two ‘susceptible proteins’ are 100% identical). Therefore, one or more or all of these 4 common changes must be responsible for changing the susceptible protein into a resistance protein. Gene editing or mutagenesis of the susceptible protein can be done, to introduce each of the four changes or combinations thereof (or all four changes), in order to verify the effect of each and of their combination on ToLCNDV-ES resistance. Alternatively, wild donors can be screened for genes encoding the protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 8 and preferably comprising one or more or all of the four changes. The effect of the gene edited or mutant gene underlying QTL5 / 7?. or other wild donors comprising such a gene, on ToLCNDV-ES resistance can be analyzed in a disease assay.
[0054] The reason that not all of the SNPs provided herein, which are linked to QTL5 / 7?. need to have the resistant donor genotype is that the introgression fragment comprising the QTL5 / 7? from the donor may be smaller than the chromosome fragment mapped herein to the QTL5 / 7? region, but the fragment still comprises the QTL5 / 7?. Still, a plant can be recognized to contain the introgression fragment (comprising the QTL5 / 7?) by the phenotype, and / or by transferring the fragment to a susceptible plant and thereby transferring the ToLCNDV-ES resistance phenotype, or by sequencing the region between the SNP markers to identify the donor fragment, or other methods known to the skilled person, such as saturating the region with more SNP markers, allelism tests, etc. Also the presence and / or the nucleotide sequence of the causal gene between SNP_03 and SNP_04 can be checked.
[0055] Thus, a combination of methods can be used to show that the QTL5 / 7? is present in a plant cell or plant, even if not for all of the linked SNPs the donor SNP genotype is present. QTL5 / 7? confers an average ToLCNDV-ES resistance of at least 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8 or 9.0 when transferred into a susceptible line or variety and is dominant.
[0056] In a preferred embodiment of the invention the introgression fragment on chromosome 5 from the donor plant comprising the sequence of the donor plant in-between SNP_01 and SNP_07, in-between SNP_01 and SNP_06, in-between SNP_01 and SNP_05, in-between SNP_01 and SNP_04, in-between SNP_02 and SNP_07, in-between SNP_02 and SNP_06, in-between SNP_02 and SNP_05, in-between SNP_02 and SNP_04, in-between SNP_03 and SNP_07, in-between SNP_03 and SNP_06, in-between SNP_03 and SNP_05, preferably in-between SNP_03 and SNP_04 confers resistance to ToLCNDV-ES to the cultivated melon plant cells according to the invention or to the cultivated melon plants according to the invention.
[0057] In one aspect the introgression fragment (and / or the QTL5 / 7? and / or the causal gene underlying QTL5 / A) is obtainable (or obtained from, or derivable, or derived from) seeds deposited under accession number NCIMB 44139, or progeny thereof, which progeny retain the QTL5 / 7? as present in the deposited seeds.
[0058] In one aspect the introgression fragment comprises the donor nucleotide for SNP_03 and SNP_04 and the QTL5rb. In one aspect the introgression fragment comprises the donor nucleotide for SNP_03 and SNP_04 and SNP_05 and the QTL5rb. In one aspect this fragment is obtainable from NCIMB 44139, progeny (descendants) of NCIMB 44139 or ascendants of NCIMB 44139, or from another wild donor as described herein.
[0059] Thus, in one aspect QTL5rb is obtainable from seeds, a representative sample of which has been deposited under accession number NCIMB 44139, or progeny thereof which retain QlL5rb. or from another wild donor (e.g. another wild Cucumis melo donor) which comprises the following SNP marker haplotype: a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5.
[0060] As the resistance was fine mapped to be located in-between SNP_03 and SNP_04, with the causal gene encoding the TIR-NBS-LRR protein of SEQ ID NO: 8 lying in-between SNP 03 and SNP 04, it is an aspect herein that the introgression fragment comprises the donor sequence in-between SNP_03 and SNP_04 and / or comprises the gene encoding the protein of SEQ ID NO: 8, or encoding a protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following 4 amino acid changes compare to the protein of SEQ ID NO: 10: an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2; a change of amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0061] A change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2;
[0062] A change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2.
[0063] In other words, the introgression fragment comprises in one aspect a gene which encodes a TIR-NBS- LRR protein (‘resistance protein’ or ‘resistance conferring protein’) of SEQ ID NO: 8 or a protein which comprises at least 96%, 97%, 98%, 99% or 100% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8.
[0064] Preferably, the melon plant cell according to the invention originates from a cultivated melon plant or the melon plant according to the invention is a cultivated melon plant, and not a wild melon plant. Preferably the donor is a wild melon plant. In another aspect, described elsewhere herein, the endogenous gene encoding the ‘susceptible protein’ is modified to encode a resistant protein of SEQ ID NO: 8 or a protein which comprises at least 96%, 97%, 98%, 99% or 100% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the four changes mentioned e.g. above and on Figures 1 and 2.
[0065] In one aspect the present invention relates to cultivated melon plant cells or melon plants (or plant parts, such as a cell or tissue) comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment confers ToLCNDV-ES resistance (i.e. it comprises QTL5 / 7? and / or the causal gene underlying QTL5 / 7?) and the introgression fragment is detectable by (comprises) the SNP haplotype of the donor plant for one or more (or all) of the following SNPs: SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and / or SNP_07, and optionally any SNP in-between SNP_01 and SNP_07; in one aspect the introgression fragment is detectable by (comprises) the SNP haplotype of the donor plant for one or more (or all) of the following SNPs: SNP_02, SNP_03, SNP_04, SNP_05 and / or SNP_06, and optionally any SNP in-between SNP_02 and SNP_06; in another aspect the introgression fragment is detectable by (comprises) the SNP haplotype of the donor plant for one or more (or all) of the following SNPs: SNP_02, SNP_03, SNP_04 and / or SNP_05, and optionally any SNP in-between SNP_02 and SNP_05; in another aspect the introgression fragment is detectable by (comprises) the SNP haplotype of the donor plant for one or more (or all) of the following SNPs: SNP_03, SNP_04 and / or SNP_05, and optionally any SNP in-between SNP_03 and SNP_05; in yet a different aspect the introgression fragment is detectable by (comprises) the SNP haplotype of the donor plant for one or more (or all) of the following SNPs: SNP_03 and / or SNP_04, and optionally any SNP in-between SNP_03 and SNP_04.
[0066] Thus, in one aspect the plant, plant part or plant cell comprises QTL5 / 7? (and / or the causal gene underlying QTL5 / 7?) and comprises the SNP donor haplotype for at least SNP_03 and / or SNP_04, as these SNPs flank the causal gene conferring ToLCNDV-ES resistance (QTL5 / 7?). In a further aspect the plant, plant part or plant cell comprises the SNP donor haplotype for at least SNP_03 and SNP_04, or for at least SNP_03 and SNP_02, or for at least SNP_04 and SNP_05. Optionally, the plant, plant part or plant cell comprises QTL5 / 7? and comprises the SNP donor haplotype for at least SNP_02, SNP_03 and SNP_04; or for at least SNP_03, SNP_04 and SNP_05.
[0067] An introgression fragment may, therefore, comprise the donor SNP haplotype for all SNP markers linked to QTL5 / 7) (as in the seeds deposited herein), or a smaller fragment, whereby one or more of the SNP markers is not present. As described further below, even all or all but one donor SNP markers may be absent, while QTL5 / A is still present on the introgression fragment.
[0068] The nucleotide sequences SEQ ID NO: 1 to SEQ ID NO: 7 comprising the SNPs provided herein (referred to as SNP_01 to SNP_07) are the nucleotide sequences of the resistant donor, i.e. they contain the donor SNP nucleotide. Therefore, in one aspect the present invention relates to cultivated melon plant cells or melon plants (or plant parts) comprising an introgression fragment on chromosome 5 from a ToLCNDV- ES resistant donor plant, wherein the introgression fragment confers ToLCNDV-ES resistance and the introgression fragment is detectable by (comprises):
[0069] SEQ ID NO: 1 or a Cytosine at nucleotide 81 of SEQ ID NO: 1 or a Cytosine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 1, and / or
[0070] SEQ ID NO: 2 or a Cytosine at nucleotide 242 of SEQ ID NO: 2 (or a Guanine at nucleotide 242 in the complementary strand of SEQ ID NO: 2) or a Cytosine (or Guanine in the complement strand) at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 2, and / or
[0071] SEQ ID NO: 3 or a Guanine at nucleotide 81 of SEQ ID NO: 3 or a Guanine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 3, and / or
[0072] SEQ ID NO: 4 or an Adenine at nucleotide 101 of SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4) or an Adenine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 4, and / or
[0073] SEQ ID NO: 5 or a Thymine at nucleotide 101 of SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5) or a Thymine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 5, and / or
[0074] SEQ ID NO: 6 or an Adenine at nucleotide 101 of SEQ ID NO: 6 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 6) or an Adenine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 6, and / or
[0075] SEQ ID NO: 7 or a Cytosine at nucleotide 101 of SEQ ID NO: 7 or a Cytosine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 7.
[0076] The term ‘at the equivalent nucleotide (or position) of a sequence (or in a sequence) having substantial sequence identity to’ a given sequence refers to the SNP nucleotide in a variant sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to the given sequence, when aligned pairwise (using e.g. the program Needles with default parameters). Similarly, ‘at the equivalent position in a sequence having substantial sequence identity to’ a given sequence refers to the amino acid in a variant sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to the given sequence, when aligned pairwise.
[0077] Provided is in one aspect a (cultivated) Cucumis melo plant, or part thereof, comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / A located in between a Cytosine for SNP O 1 at nucleotide 81 of SEQ ID NO: 1 (or a Cytosine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 1) and a Cytosine for SNP 07 at nucleotide 81 of SEQ ID NO: 7 (or a Cytosine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 7) , said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a Cytosine for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or a Guanine at nucleotide 242 in the complementary strand of SEQ ID NO: 2) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 2 (or the complement strand), a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3, an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4 (or the complement), a Thymine for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 5 (or the complement), an Adenine for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 6) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 6 (or the complement).
[0078] Therefore provided is in a further aspect a (cultivated) Cucumis melo plant, or part thereof, comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / A located in between a Cytosine for SNP 01 at nucleotide 81 of SEQ ID NO: 1 (or a Cytosine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 1) and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7 (or a Cytosine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 7) , said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3, an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4 (or the complement strand), a Thymine for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 5 (or the complement strand).
[0079] Especially provided is in one aspect a (cultivated) Cucumis melo plant, or part thereof, comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / 7?. said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3, an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4 (or the complement strand), a Thymine for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5) or at the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 5 (or the complement strand).
[0080] In the above plant QTL5rb is e.g. located in the region between a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3 (or a Guanine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 3) and a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5 or a Thymine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5 or an Adenine at the equivalent position in a sequence comprising at least 95% sequence identity to the complement strand of SEQ ID NO: 5).
[0081] In one aspect in the above plant QTL5rb is e.g. located in the region between a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3 (or a Guanine at the equivalent position in a sequence comprising at least 95% identity to SEQ ID NO: 3) and an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4 or an Adenine at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4 or a Thymine at the equivalent position in a sequence comprising at least 95% sequence identity to the complement strand of SEQ ID NO: 4). In one aspect herein throughout the description the SNP nucleotide mentioned herein, for any of the SNPs, can also be referred to (in addition or in the alternative) by the nucleotide position on the chromosome 5 of the reference genome, as indicated e.g. in Table 2.
[0082] The ToLCNDV-ES resistance conferring QTL5 / A is present on the introgression fragment.
[0083] The sequences provided herein for Seq ID NO: 2 (comprising SNP_02), SEQ ID NO: 4 (comprising SNP_04), SEQ ID NO: 5 (comprising SNP_05) and SEQ ID NO: 6 (comprising SNP_06) are (-) strand / reverse strand sequences of the double stranded DNA of chromosome 5 when comparing these sequences to the sequence orientation given for the reference genome of melon.
[0084] Therefore, another way to refer to the sequences and the SNP nucleotide is to refer to the (+) strand / forward strand, which is the complement nucleotide or sequence of the (-) strand. Thus, e.g. SNP_02 is a Cytosine at nucleotide 242 of SEQ ID NO: 2 or a Guanine at nucleotide 242 of the complementary strand of SEQ ID NO: 2. So in one aspect SNP_02 is a Cytosine at nucleotide 242 of SEQ ID NO: 2 (or a Guanine at nucleotide 242 in the complementary strand of SEQ ID NO: 2) or a Cytosine (or Guanine in the complement strand) at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 2. Likewise SNP_04 is an Adenine at nucleotide 101 of SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 4) or a Adenine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 4; SNP_05 is a Thymine at nucleotide 101 of SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complementary strand of SEQ ID NO: 5) or a Thymine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 5; and SNP_06 is an Adenine at nucleotide 101 of SEQ ID NO: 6 (or a Thymine at nucleotide 101 in the complementary strand of SEQ ID NO: 6) or an Adenine at the equivalent nucleotide of a sequence having substantial sequence identity to SEQ ID NO: 6.
[0085] “Donor plant cell” or “donor plant” in connection with the present invention shall mean a melon plant cell or melon plant being resistant to ToLCNDV-ES, especially to the resistance breaking strains. Likewise, the term DNA fragment or introgression fragment from the donor plant or cell shall mean a fragment of chromosome 5 of a melon plant resistant to ToLCNDV-ES, whereby the fragment confers ToLCNDV-ES resistance when transferred into a ToLCNDV-ES susceptible melon plant. In a preferred embodiment of the invention, the donor plant is a wild species or wild accession of melon. In a particular embodiment, DNA fragments or introgression fragments from donor plant cells or plants are the donor fragments obtained from (or obtainable from, or derived from, or derivable from, or as present in) plants grown from seeds deposited under NCIMB 44139 or progeny obtained from plants grown from seeds deposited under NCIMB 44139 or plants obtained by crosses with plants grown from seeds deposited under NCIMB 44139. Likewise, in one aspect a QTL5 / A. or a causal gene underlying QTL5 / A. from donor plant cells or plants are the QTL5 / A. or a causal gene underlying QTL5 / A. obtained from (or obtainable from, or derived from, or derivable from, or as present in) plants grown from seeds deposited under NCIMB 44139 or progeny obtained from plants grown from seeds deposited under NCIMB 44139 or plants obtained by crosses with plants grown from seeds deposited underNCIMB 44139.
[0086] Donor melon plants can be obtained from various other sources. A person skilled in the art knows how to detect other sources of ToLCNDV-ES resistant donor plants comprising QTL5 / 7?. especially donor plants that are resistant for the new resistance-breaking ToLCNDV-ES strains. For detecting such sources of ToLCNDV-ES resistant donor plants, basically e.g. melon plants or accessions (e.g. wild melon plants or accessions) can be infected with ToLCNDV-ES (especially resistance-breaking strains), either by mechanical means, as described in Lopez et al. (2015, Euphytica 204(3), 679-691) or by transmission of the virus by whiteflies. Preferably, infection occurs by whitefly infection in the context with the present invention. Plants showing reduced symptom levels compared to susceptible controls can then be selected and used as a source for genome fragments or sequences conferring ToLCNDV-ES resistance. A preferred method of how to infect melon plants with ToLCNDV-ES and methods for determining the symptom level of infected plants are given herein under “General Methods”.
[0087] In the context of the present invention the donor plants preferably have an average symptom level equal to or above 7.7, even more preferred equal to or above 8.0 or 8.5 and most preferred equal to or above 9.0.
[0088] In one aspect the donor plant comprises the donor SNP haplotype or genotype for one or more or all of SNP_01, SNP_2, SNP_3, SNP_04, SNP_05, SNP_06 and SNP_07, as shown in Table 1 and 2. In one aspect the donor plant comprises the donor SNP haplotype or genotype for one or more of SNP_03, SNP_04 and / or SNP_05, or for SNP_03 and SNP_04, as shown in Table 1 and 2. Preferably the SNP donor genotype is homozygous. The donor is herein e.g. a wild melon having no agronomic value, e.g. producing acidic fruits, etc.
[0089] As mentioned above, potential donor melon plants (e.g. wild accessions from seedbanks) can also be screened for the presence of the SNP haplotype or genotype of one or more of the SNP markers provided herein and indicative of the presence of QTL5r6, and / or they can be screened for the presence of a TIR- NBS-LRR resistance protein, i.e. for the presence of a gene encoding a protein of SEQ ID NO: 8, or encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and preferably comprising one or more or all of the four changes that are present in the resistant proteins but absent in the susceptible proteins, as shown in Figure 2 herein and as described.
[0090] “Recurrent plant cell” or “recurrent plant” or “recipient plant” in connection with the present invention shall be understood to be a melon plant cell or melon plant being sensitive (used herein synonymously with susceptible) or non-resistant to ToLCNDV-ES infection, especially to infection by ToLCNDV-ES resistance breaking strains, or significantly less resistant to ToLCNDV-ES infection than the resistant donor. Whether a plant is sensitive or non-resistant, or significantly less resistant, to ToLCNDV-ES infection (especially resistance breaking strains) can be determined by observation of the symptom levels after ToLCNDV-ES infection (with especially a resistance breaking strain). A recurrent plant for example has an average symptom level below 3.0, or equal to or below 2.5 or equal to or below 2.0. Symptom levels and methods how to infect melon plants with ToLCNDV-ES are described elsewhere herein and are applicable here accordingly. In a preferred embodiment of the invention, the recurrent melon plant cell according to the invention originates from a cultivated melon plant or the recurrent melon plant according to the invention, is a cultivated melon plant. Preferably it is an elite line, breeding line or variety. In one aspect one can also use a parent line comprising QTL5 as recurrent parent and introduce QTL5 / A at the locus on chromosome 5, basically replacing QTL5 with QTL5 / 7?.
[0091] “Modified plant cell” or “modified plant” or “mutated or mutant plant cell” or “mutated or mutant plant” in connection with the present invention shall be understood to be a melon plant cell or melon plant in which the endogenous TIR-NBS-LRR protein on chromosome 5 has been modified or mutated, whereby the plant is less sensitive, or is resistant, to ToLCNDV-ES infection, especially to infection by ToLCNDV- ES resistance breaking strains, e.g. significantly more resistant to ToLCNDV-ES infection than the nonmodified or non-mutated plant. Whether a plant is less sensitive or if it is resistant, or significantly more resistant, to ToLCNDV-ES infection (especially resistance breaking strains) can be determined by observation of the symptom levels after ToLCNDV-ES infection (with especially a resistance breaking strain) of the modified or mutated plant compared to the non-modified or non-mutated plant. Symptom levels and methods how to infect melon plants with ToLCNDV-ES are described elsewhere herein and are applicable here accordingly. In a preferred embodiment of the invention, the modified or mutated melon plant cell or plant according to the invention is a cultivated melon plant in which the endogenous TIR-NBS-LRR gene on chromosome 5 encoding the susceptible TIR-NBS-LRR protein (e.g. the protein of SEQ ID NO: 10, or a susceptible protein comprising at least 98%, 98.5%, 99% sequence identity to SEQ ID NO: 10) has been modified or mutated to encode a resistant TIR-NBS-LRR protein (e.g. the protein of SEQ ID NO: 8 or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 and preferably comprises one or more or all of the four changes described herein and e.g. shown in Figure 2). Preferably it is an elite line, breeding line or variety. The plant cell or plant, thus, comprises in its genome a “modified TIR-NBS-LRR gene” as defined elsewhere herein.
[0092] "Introgression fragment" refers to a chromosome fragment, chromosome part or region which has been introduced into another plant of the same or related species by crossing or traditional breeding techniques. The introgression of the fragment from a donor plant into a recurrent plant introduces into the offspring of a cross between the donor and recurrent plant a phenotype, which was not present in the recurrent plant. Concerning the present invention, the phenotype transferred from the donor plant to the recurrent plant is resistance to ToLCNDV-ES (especially resistance breaking strains), e.g. an average disease score of at least 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9 or 9.0. For introgression of a fragment into a specific breeding line or variety the first crossing step can e.g. be followed by one or more backcrossings with the intended breeding line or variety. As understood herein, introgression can mean a first crossing of a ToLCNDV-ES resistant donor plant with a ToLCNDV-ES susceptible or less resistant (e.g. QTL5 being present) recurrent plant and further back-crossing one or several times ToLCNDV-ES resistant plants obtained from the first crossing with plants of the recipient into which ToLCNDV-ES resistance shall be introgressed. In such a case, the introgressed fragment is the result of breeding methods referred to by the verb "to introgress" (such as backcrossing) into a recipient variety or breeding line. Thus, introgression of ToLCNDV-ES resistance into a recurrent plant is a technical process directed by man. In particular introgression herein refers to a man-made breeding process or method. One or more or all of the molecular markers (SNP markers) provided herein and / or QTL5 / 7? and / or the causal gene underlying QTL5 / 7? can be used in that process, e.g. to assist selection of plants comprising QTL5r / r The resulting plant, i.e. the cultivated line or variety comprising one introgression fragment (on chromosome 5) from a donor, i.e. comprising a recombinant chromosome 5, is also man-made and does not exist in nature.
[0093] The introgression fragment can be large, e.g. even half of a chromosome, but is preferably smaller, such as about 15 Mb or less, such as about 10 Mb or less, about 9 Mb or less, about 8 Mb or less, about 7 Mb or less, about 6 Mb or less, about 5 Mb or less, about 4 Mb or less, about 3 Mb or less, about 2 Mb or less, about 1 Mb (equals 1 ,000,000 base or less), or about 0.8 Mb (equals 800,000 base pairs) or less.
[0094] The introgression fragment can originate from a wild melon plant or wild melon accession or wild relatives of melon or landraces (donor). Wild melon plants or wild melon accessions or wild relatives of melon plants or landraces can be used to introgress fragments of the donor genome into the genome of cultivated melon, Cucumis melo, to generate breeding lines or varieties with good agronomic characteristics. Such a cultivated melon plant thus has a "genome of cultivated C. melo'', but comprises in its genome a fragment of a donor, e.g. an introgression fragment of a related wild Cucumis genome, such as Cucumis melo ssp. agrestis, C. melo ssp. melo, C. melo ssp. acidulous, C. callosus, C. trigonus, C. picrocarpus. or another wild melon or wild relative of melon. It is understood that the term "introgression fragment" never includes a whole chromosome, but only a part of a chromosome. The chromosomes carrying the introgression therefore also comprise a part or parts of the recurrent (recipient) melon plant and in addition parts of the donor melon plant.
[0095] When the chromosome 5 of cultivated melon comprises an introgression fragment, this therefore means that the cultivated melon plant comprises a recombinant chromosome 5, whereby the introgressed fragment comprises the ToLCNDV-ES resistance conferring QTL5 / 7>. As described elsewhere, the introgression fragment from the donor may comprise one or more or all of the donor SNP nucleotides (for SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and / or SNP_07) or one or more or all of the sequences comprising the donor SNP nucleotides (SEQ ID NO: 1, 2, 3, 4, 5, 6 and / or SEQ ID NO: 7).
[0096] In one aspect the introgression fragment comprises (and is detectable by the presence of) the causal gene conferring the QTL5 / 7? resistance, i.e. the introgression fragment comprises a gene encoding the TIR- NBS-LRR resistance protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following 4 amino acid changes compare to the protein of SEQ ID NO: 10: an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2; a change from amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0097] A change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2;
[0098] A change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2.
[0099] In other words, the introgression fragment comprises (and is detectable by the presence of) the causal gene conferring the QTL5 / 7? resistance, i.e. the introgression fragment comprises a gene encoding the TIR- NBS-LRR resistance protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8.
[0100] So, e.g. in one aspect the introgression fragment (in homozygous or heterozygous form) may comprise, and is detectable by, one or more or all of the following SNP genotypes or haplotypes: the CC genotype (homozygous for the donor nucleotide) or CX haplotype (heterozygous for the donor nucleotide, X may be any other nucleotide) for SNP O 1 at nucleotide 81 of SEQ ID NO: 1 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 1), the CC genotype or CX haplotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 2), or the GG genotype or GX haplotype when referring to the complement strand, the GG genotype or GX haplotype for SNP_03 at nucleotide 81 of SEQ ID NO: 3 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3), the AA genotype or AX haplotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4), or the TT genotype or TX haplotype when referring to the complement strand, the TT genotype or TX haplotype for SNP 05 at nucleotide 101 of SEQ ID NO: 5 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 5), or the AA genotype or AX haplotype when referring to the complement strand, the AA genotype or AX haplotype for SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 6), or the TT genotype or TX haplotype when referring to the complement strand, and / or the CC genotype or CX haplotype for SNP_01 at nucleotide 81 ofSEQ ID NO: 7 (orthe equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 7).
[0101] The SNP genotype being homozygous (e.g. CC) refers thus to the donor nucleotide being present on both chromosomes 5 in the melon genome. The SNP haplotype being heterozygous (e.g. CX) refers to one of the two chromosomes 5 comprising the donor SNP, while the other chromosome 5 may comprise the recurrent parent SNP nucleotide, e.g. X may be any nucleotide e.g. any other than the donor nucleotide (e.g. in this example X may be nucleotide T, A or G). In one aspect the introgression fragment does not comprise a gene encoding a protein of SEQ ID NO: 9 (TIR-NBS-LRR protein of QTL5) or SEQ ID NO: 10 (susceptible TIR-NBS-LRR protein). Thus, in one aspect the plant or plant cell does not comprise a gene encoding a protein of SEQ ID NO: 9 (TIR-NBS- LRR protein of QTL5) or SEQ ID NO: 10 (susceptible TIR-NBS-LRR protein). Of course, when QTL5 / 7? is present in heterozygous form in the plant, the other chromosome 5 may comprise e.g. SEQ ID NO: 9 or SEQ ID NO: 10.
[0102] In one aspect the donor plant is of the species Cucumis melo subsp. melo, e.g. a wild plant of the species Cucumis melo subsp. melo.
[0103] In one aspect the donor plant of the invention is not of the species Cucumis melo subsp. agrestis.
[0104] In one aspect the donor plant of the invention is not one of the five Cucumis melo subsp. agrestis accessions (subsp. agrestis var. momordica'. Mom-Khalnd / Kharbuja, Mom-PI124Ind / PI124112, Mom- PI124Ind / PI414723 and subsp. agrestis wild types: Ag-WM9Ind / WM9, Ag-WM7Ind / WM7) resistant to ToLCNDV identified by Lopez et al., 2015, Euphytica 204(3), 679-691.
[0105] The term "breeding" encompasses herein crossing, backcrossing, selfing, selection, double haploid production, embryo rescue, protoplast fusion, marker assisted selection, mutation breeding etc. as known to the breeder (i.e. methods other than genetic modification / transformation / transgenic methods), by which, for example, a recombinant chromosome 5 can be obtained, identified, produced and / or transferred.
[0106] In a preferred embodiment of the present invention, the introgression fragment originates form a wild Cucumis plant or a wild Cucumis accession, most preferably the introgression fragment originates from wild Cucumis melo ssp. melo, e.g. having fruits with acid tasting fruit flesh. This donor was used in the instant invention and has been deposited under accession number NCIMB 44139, but other donors can be identified by the skilled person which comprise e.g. the same SNP genotype or SNP haplotype as this donor for one or more of SNP_01 to SNP_07, or SNP_02 to SNP_05, or SNP_02 to SNP_06, or SNP_03 to SNP_05, or SNP_03 and / or SNP_04, and / or comprising a gene encoding a TIR-NBS-LRR protein of SEQ ID NO: 8, or encoding a protein comprising at least 96%, 97%, 98%, 99% or more sequence identity to the protein of SEQ ID NO: 8 and which protein preferably comprises one or more or all of the amino acid changes compare to the susceptible TIR-NBS-LRR protein of SEQ ID NO: 10 (encoded by the gene present in the susceptible reference genome) described above and as shown in Figure 2 under changes numbered 1, 2, 3 and 4.
[0107] A suitable donor is in one aspect a wild C. melo plant or accession having an average ToLCNDV-ES disease score (preferably using a resistance breaking strain) of at least 7.7, 7.8, 7.9, 8.0 or 8.5 or 8.6, 8.7, 8.8, 8.9 or 9.0, on a scale of 1 = dead plant to 9 = no symptoms. Such a donor further preferably comprises e.g. the same SNP genotype or SNP haplotype as present in NCIMB44139 for one or more or all of SNP_01 to SNP_07, or SNP_02 to SNP_05, or SNP_02 to SNP_06, SNP_03 to SNP_05, or SNP_03 and / or SNP_04, and / or comprising a gene encoding a protein of SEQ ID NO: 8, or encoding a protein comprising at least 96%, 97%, 98%, 99% or more sequence identity to the resistance TIR-NBS-LRR protein of SEQ ID NO: 8 and which protein preferably comprises one or more or all of the amino acid changes compare to the susceptible TIR-NBS-LRR protein of SEQ ID NO: 10 (encoded by the gene present in the susceptible reference genome) described above and as shown in Figure 2 under changes numbered 1, 2, 3 and 4.
[0108] In a particular embodiment, plant cells and plants provided herein are characterized in that the introgression fragment or the QTL5 / 7? or the causal gene underlying QTL5 / 7? that is present in the cells (conferring ToLCNDV-ES resistance) originates from the seeds deposited under NCIMB 44139 or progeny thereof, whereby the progeny retain the gene encoding the resistant TIR-NBS-LRR protein of SEQ ID NO: 8.
[0109] In one aspect the melon plant cell or melon plant, therefore, comprises in its genome on chromosome 5 the genomic sequence of SEQ ID NO: 11, which encodes the protein of SEQ ID NO: 8. The plant cell or plant will transcribe the mRNA (depicted as cDNA) of SEQ ID NO: 12. In one aspect the melon plant or plant cell comprises SEQ ID NO: 11, but with some nucleotide variation in the intron sequences of SEQ ID NO: 11. In one aspect the melon plant or plant cell comprises a genomic sequence, wherein the exon sequences are preferably 100% identical to the exon sequences of SEQ ID NO: 11. The exon sequences can be identified by aligning SEQ ID NO: 11 with the cDNA (mRNA) of SEQ ID NO: 12. In one aspect the melon plant cell or melon plant, therefore, comprises in its genome on chromosome 5 a genomic sequence, which encodes the protein of SEQ ID NO: 8. In one aspect the melon plant cell or melon plant, therefore, comprises in its genome on chromosome 5 a genomic sequence, which will transcribe the mRNA (depicted as cDNA) of SEQ ID NO: 12.
[0110] It was, for example, found that the genomic sequence of the susceptible reference genome DHL92 and the genomic sequence of the susceptible variety Vedrantais are identical, except that the third intron in the sequence of Vedrantais lacks one single nucleotide, i.e. it has a 1 nucleotide gap. Both of these genomic sequences encode the same susceptible protein of SEQ ID NO: 10 (as was found in a pairwise protein alignment using Needle, whereby the percentage of sequence identity between SEQ ID NO: 10 and the susceptible protein sequence of Vedrantais have 100% sequence identity).
[0111] In a further preferred embodiment, the melon plant cell provided originates from a cultivated melon plant or the melon plant provided herein is a cultivated melon plant and the introgression fragment or QTL5 / 7? originates from a wild Cucumis melo accession or from a wild Cucumis melo ssp. melo accession, or from donor plants described herein to be preferred donor plants, or is obtained from / or is obtainable from seeds deposited under NCIMB 44139 or progeny thereof. In a further aspect, melon plants and melon plant cells are provided wherein the endogenous gene encoding the susceptible TIR-NBS-LRR protein on chromosome 5 (which does not confer resistance) has been gene edited or mutated to encode a TIR-NBS-LRR protein which confers resistance to the ToLCNDV-ES resistance breaking strains. Susceptible plants and cells comprise a gene encoding a protein of SEQ ID NO: 10, or aprotein comprising at least 98%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%, 99%, 99.5% or 99.8% sequence identity to the protein of SEQ ID NO: 10. The gene encoding this “susceptible protein” can be edited to encode a “resistance protein”, by modifying one, two, three or all four of the amino acid differences in the “susceptible protein”, which one, two, three or four differences cause the protein to confer resistance, i.e. to become a “resistance protein”.
[0112] As mentioned, the causal gene conferring the QTL5 / 7? resistance comprises a gene encoding the protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following 4 amino acid changes compare to the protein of SEQ ID NO: 10:
[0113] “Change number 1”: an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2;
[0114] “Change number 2”: a change of amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0115] “Change number 3”: a change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2;
[0116] “Change number 4”: a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2. Introducing one or more of these 4 changes into the susceptible protein, for example by gene editing techniques (e.g. Crispr based techniques) or by random mutagenesis techniques (such as chemical mutagenesis or radiation mutagenesis) will convert the susceptible protein into a resistant protein.
[0117] In one aspect the gene encoding the susceptible protein of SEQ ID NO: 10 (or a protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% sequence identity to SEQ ID NO: 10) is modified by introducing one or more of the four changes (change number 1 to change number 4) into the gene and the encoded protein. In SEQ ID NO: 36 the genomic sequence on chromosome 5, which encodes the susceptible protein of SEQ ID NO: 10, is provided. Thus, in one aspect the genomic gene sequence of SEQ ID NO: 36, or a genomic sequence encoding a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% sequence identity to SEQ ID NO: 10, is modified, e.g. by generating one or more of the changes of change number 1, 2, 3 and / or 4 above.
[0118] The codons underlying the four changes are shown in Figure 4. By e.g. modifying one or more of the codons of the genomic sequence of e.g. SEQ ID NO: 36, or a genomic sequence encoding a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% sequence identity to SEQ ID NO: 10 (such as inserting one or more codons, changing a codon to code for a different amino acid, etc.) the ‘susceptible protein’ can be modified into a ‘resistance protein’.
[0119] In one aspect a modified or mutated melon plant or plant cell or plant part is provided, said plant or plant cell or plant part comprises an endogenous TIR-NBS-LRR gene at the locus on chromosome 5, whereby the endogenous gene is modified or mutated so that it encodes a resistant protein, e.g. the protein of SEQ ID NO: 10 (or a protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% sequence identity to SEQ ID NO: 10) is modified so that it comprises one or more of change number 1, 2, 3 and / or 4, or whereby the endogenous gene is modified or mutated so that it encodes a resistant protein comprising at least 96%, 97%, 98% or 99% to the resistant protein of SEQ ID NO: 8 and comprising one or more of change number 1, 2, 3 and / or 4.
[0120] FIGURES
[0121] Figure 1: multiple sequence alignment of the TIR-NBS-LRR protein of SEQ ID NO: 8 (QTL5 / 7?). of SEQ ID NO: 9 (QTL5 of US11,591,611) and of SEQ ID NO: 10 (susceptible variety Vedrantais and DHL92v4 reference genome). Boxes with dashed lines are the leucine-rich-repeats present in the protein.
[0122] Figure 2: pairwise sequence alignment of SEQ ID NO: 8 (resistant protein) and SEQ ID NO: 10
[0123] (susceptible protein), with four changes that differ between resistant proteins and susceptible proteins being indicated with numbers 1 (Change number 1), 2 (change number 2), 3 (change number 3) and 4 (change number 4). These are also shown in Figure 1.
[0124] Figure 3: SNP haplotype of QTL5 / 7? and QTL5 of US11,591,611; the SNP nucleotide shown is the nucleotide present on the plus strand with respect to the reference genome.
[0125] Figure 4: Pairwise sequence alignment of the genomic sequence SEQ ID NO: 36, encoding a susceptible protein of SEQ ID NO: 10, and of the genomic sequence SEQ ID NO: 11, encoding a resistant protein of SEQ ID NO: 8. The differences at nucleotide level, which result in the four differences (numbered 1 to 4, i.e. change number 1 to change number 4) at protein level are indicated in boxes. For example, change number 1 is an insertion of two times the codon TCT, which encodes a Serine, resulting in two Serines being present in the resistant protein. Change number 2 is the change of codon GTG (Valine, V) to ATG (Methionine, M), change number 3 is the change of codon GAG (Glutamic Acid, E) to AAG (Lysine, K) and change number 4 is the change of codon TAT (Tyrosine, Y) to CAT (Histidine, H).
[0126] Figure 5: shown are average disease scores of 15 plants per genotype (N=15) at 40 dpi (days post inoculation or infection), on the scale 1 (dead plant) to 9 (no symptoms), as described in the Examples.
[0127] Figure 6: shown are average ct-values (q-PCR) of 10 plants per genotype (N=10) at 55 dpi
[0128] GENERAL DEFINITIONS
[0129] As used herein, the term “plant” includes the whole plant or any parts or derivatives thereof, preferably having the same genetic makeup as the plant from which it is obtained, such as plant organs (e.g. harvested or non-harvested fruits, leaves, flowers, anthers, etc.), plant cells, plant protoplasts, plant cell tissue cultures from which whole plants can be regenerated, plant calli, plant cell clumps, plant transplants, seedlings, plant cells that are intact in plants, plant clones or micropropagations, or parts of plants, such as plant cuttings, embryos, pollen, anthers, ovules, fruits (e.g. harvested tissues or organs), flowers, leaves, seeds, clonally propagated plants, roots, stems, root tips, grafts (scions and / or root stocks) and the like. Also any developmental stage is included, such as seedlings, cuttings prior or after rooting, etc. When “seeds of a plant” are referred to, these either refer to seeds from which the plant can be grown or to seeds produced on the plant, after self-fertilization or cross-fertilization.
[0130] As used herein, the term “variety” or “cultivar” means a plant grouping within a single botanical taxon of the lowest known rank, which can be defined by the expression of the characteristics resulting from a given genotype or combination of genotypes. A plant characterized by the presence of alleles of a single gene is not a variety or cultivar, as the remainder of the genome is not characterized.
[0131] “Fl, F2, F3, etc.” refers to the consecutive related generations following a cross between two parent plants or parent lines. The plants grown from the seeds produced by crossing two plants or lines is called the Fl generation. Selfing the Fl plants results in the F2 generation, etc.
[0132] “Fl hybrid” plant (or Fl hybrid seed) is the generation obtained from crossing two inbred parent lines. Thus, Fl hybrid seeds are seeds from which Fl hybrid plants grow. Fl hybrids are more vigorous and higher yielding, due to heterosis. Inbred lines are essentially homozygous at most loci in the genome.
[0133] A “plant line” or “breeding line” refers to a plant and its progeny. As used herein, the term "inbred line" refers to a plant line which has been repeatedly selfed and is nearly homozygous. Thus, an “inbred line” or “parent line” refers to a plant which has undergone several generations (e.g. at least 5, 6, 7 or more) of inbreeding, resulting in a plant line with a high uniformity.
[0134] “Uniformity” or “uniform” relates to the genetic and phenotypic characteristics of a plant line or variety. Inbred lines are genetically highly uniform as they are produced by several generations of inbreeding. Likewise, and the Fl hybrids which are produced from such inbred lines are highly uniform in their genotypic and phenotypic characteristics and performance.
[0135] “Chromosome 5 of a melon plant” is to be understood in context of the present invention to be the chromosome number 5 as e.g. found on the melonomics.net website, DHL92 version 4.
[0136] "Orthologous chromosome 5" refers to the chromosome 5 of wild melons or wild relatives of melon, parts of which can be introgressed into cultivated melon chromosome 5.
[0137] A “recombinant chromosome 5” refers to a chromosome 5 having a new genetic makeup arising through crossing over between homologous chromosomes, e.g. a “recombinant chromosome 5”, i.e. a chromosome 5 which is not present in either of the parent plants and arose through a rare crossing-over event between homologous chromosomes of a chromosome 5 pair. Herein, for example, a recombinant melon chromosome 5 comprising a ToLCNDV-ES -resistance conferring QTL5 / A is provided. The recombinant chromosome 5, therefore, is in one aspect a chromosome of cultivated melon, with an introgression fragment from a wild donor, whereby the introgression fragment comprises the ToLCNDV-ES resistance conferring QTL5 / 7).
[0138] “The causal gene underlying QTL5 / 7?" refers herein to the TIR-NBS-LRR gene encoding a resistant protein of SEQ ID NO: 8 or a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and preferably comprising at least one, preferably at least two, three or all four of the following amino acids: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8. The causal gene underlying QTL5 / 7? can, in one aspect, be identified in donor plants and introgressed into cultivated melon or it can be generated de novo by modifying the endogenous TIR-NBS-LRR gene (encoding e.g. a susceptible protein) at the locus, e.g. by targeted gene editing or by random mutagenesis.
[0139] A “modified TIR-NBS-LRR gene” or “modified causal gene underlying QTL5 / A" or “refers to a chromosome 5 whereby the endogenous TIR-NBS-LRR gene has been modified by e.g. targeted gene editing or by random mutagenesis, so that the protein encoded by the modified gene is the protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98%, 99% or more sequence identity to the protein of SEQ ID NO: 8 and which protein preferably comprises one or more or all of the amino acid changes compare to the protein of SEQ ID NO: 10 (encoded by the gene present in the susceptible reference genome) described elsewhere herein and as shown in Figure 2 under changes numbered change 1, change 2, change 3 and change 4.
[0140] “Targeted gene editing” is referred to techniques whereby endogenous target genes can be modified, e.g. one or more nucleotides can be inserted, replaced and / or deleted e.g. in the promoter or coding sequence. For example CRISPR based techniques, such as Crispr-t z / .s'Q gene editing, Crispr-Cp / 7 gene editing, or more recent techniques called ‘base editing’ or ‘primer editing’ can be used to modify endogenous target genes, such as the endogenous TIR-NBS-LRR gene in melon (e.g. encoding the susceptible protein of SEQ ID NO: 10, or a wild type susceptible protein comprising at least 98%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9% sequence identity to SEQ ID NO: 10).
[0141] “Random mutagenesis” refers to methods whereby mutations are introduced in the genome at random locations, whereby thereafter mutations in a target gene can be selected. Random mutagenesis involves e.g. treatment of seeds or plant cells or plant parts with a mutagenic agent, such as radiation (e.g. UV treatment) or a chemical mutagenic agent, such as EMS.
[0142] A “DH plant” or “doubled-haploid plant” is a diploid plant produced by doubling the haploid genome of the diploid plant using e.g. in vitro techniques. A DH plant is, therefore, homozygous at all loci.
[0143] "Cultivated melon plant" refers to plants of Cucumis melo i.e. varieties, breeding lines or cultivars of the species C. melo, cultivated by humans and having good agronomic characteristics, especially producing edible and marketable fruits of good size and quality and uniformity; such plants are not "wild melon plants", i.e. plants which generally have much poorer yields and poorer agronomic characteristics than cultivated plants and e.g. grow naturally in wild populations. "Wild plants" include for example ecotypes, PI (Plant Introduction) lines, landraces or wild accessions or wild relatives of a species.
[0144] A “SNP (= Single Nucleotide Polymorphism)” in context with the present invention is to be understood as a variation in a single nucleotide that occurs at a specific position in the genome. A SNP is the variation of the single nucleotide at the given position in a genome between two plants. If a wild melon plant having a ToLCNDV-ES resistance (donor plant) shows in its corresponding sequence at a specific single position a nucleotide which is different from the corresponding nucleotide at the same position of e.g. a cultivated melon plant, the position defines a SNP between the wild melon and the cultivated melon. If the donor plant has one of the four possible nucleotides (A, C, T or G) at a specific position, a SNP occurs, when e.g. the cultivated plant has either of the remaining three possible nucleotides at the same corresponding sequence position. In a cultivated melon plant comprising an introgression fragment from a donor, it can therefore easily be determined if the single nucleotide of the SNP is from the donor or from the cultivated melon (recipient).
[0145] ‘SNP nucleotide’ refers to the single nucleotide, while ‘SNP genotype’ refers to the pair of nucleotides in a diploid plant cell. So, for SNP_01, the SNP nucleotide of the ToLCNDV-ES resistant donor is a Cytosine (C) for nucleotide 81 of SEQ ID NO: 1, while the SNP genotype of a plant or cell comprising SEQ ID NO: 1 can be ‘CC’ (Cytosine on both chromosomes) or ‘CX’ (Cytosine on one chromosome 5 and X , i.e. a different nucleotide, e.g. Thymine, on the other chromosome 5; or this may also be written as ‘C’), whereby the ToLCNDV-ES resistant donor SNP nucleotide (Cytosine), and thus SEQ ID NO: 1 (or a sequence substantially identical to SEQ ID NO: 1), is homozygous or heterozygous. “SNP haplotype” refers to the nucleotide for the SNP markers on one chromosome 5 in a diploid cell, so a SNP haplotype for SNP_01 - SNP_02 - SNP_03 - SNP_04 is C - G - G - T , see e.g. Figure 3.
[0146] The verb "to comprise" and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article "a" or "an" thus usually means "at least one", e.g. “a plant” refers also to several cells plants, etc. Similarly, “a fruit” or “a plant” also refers to a plurality of fruits and plants.
[0147] The term “allele(s)” means any of one or more alternative forms of a gene at a particular locus, e.g. the TIR-NBS-LRR locus (where the TIR-NBS-LRR gene is located on chromosome 5; the genomic transcribed region of the TIR-NBS-LRR gene being in the region starting at nucleotide 26.034.368 and ending at nucleotide 26.027.838 of chromosome 5 on melonomics.net V4); the alleles of the gene may be alleles encoding a susceptible TIR-NBS-LRR protein (e.g. the protein of SEQ ID NO: 10), which does not confer ToLCNDV-ES resistance (also referred to as a ‘susceptible protein’) or alleles encoding a resistant TIR-NBS-LRR protein (e.g. the protein of SEQ ID NO: 8 or a protein comprising at least 96% sequence identity to SEQ ID NO: 8), which does confer ToLCNDV-ES resistance (also referred to as ‘resistance protein’). In a diploid cell of an organism, alleles of a given gene are located at a specific location, or locus (loci plural) on a chromosome. One allele is present on each chromosome of the pair of homologous chromosomes. A diploid plant species may comprise a large number of different alleles at a particular locus. These may be identical alleles of the gene (homozygous) or two different alleles (heterozygous).
[0148] “TIR-NBS-LRR gene” is a single gene identified in melon on chromosome 5 (comprising the transcribed region starting at nucleotide 26.034.368 and ending at nucleotide 26.027.838 of chromosome 5 on the reference genome found e.g. on melonomics.net V4), which encodes a ‘resistance protein’ (e.g. the protein of SEQ ID NO: 8 or a protein comprising at least 96% sequence identity to SEQ ID NO: 8) or a ‘susceptible protein’ (e.g. the protein of SEQ ID NO: 10). A single copy in the plant genome (i.e. heterozygous) of an allele of the gene encoding a ‘resistance protein’ is sufficient to confer the resistance phenotype to the plant.
[0149] The term “gene” means a (genomic) DNA sequence comprising a region (transcribed region), which is transcribed into a pre-mRNA, which is processed (by intron splicing) into a messenger RNA molecule (mRNA) in a cell, and an operably linked regulatory region (e.g. a promoter). An example is the TIR-NBS- LRR gene described herein. Different alleles of a gene are, thus, different alternatives form of the gene, which may be in the form of e.g. differences in one or more nucleotides of the genomic DNA sequence (e.g. in the promoter sequence, the exon sequences, intron sequences, etc.), mRNA and / or amino acid sequence of the encoded protein.
[0150] “Induced mutant alleles” are mutant alleles in which the mutation(s) is / are / have been induced by human intervention, e.g. by mutagenesis via physical or chemical mutagenesis methods or via e.g. tissue culture (as described in e.g. Zhang et al. Pios 9(5) e96879), including also targeted gene editing techniques (such as Crispr based techniques, TALENS, Base editing, etc.) and also insertional mutagenesis techniques, such as targeted transposon insertion techniques, etc. (For a review see Gao et al. https: / / doi.Org / 10.1016 / j.cell.2021.01.005).
[0151] “Vegetative propagation” or “clonal propagation” refers to propagation of plants from vegetative tissue, e.g. by in vitro propagation or grafting methods (using scions and rootstocks). In vitro propagation involves in vitro cell or tissue culture and regeneration of a whole plant from the in vitro culture. Grafting involves propagation of an original plant by grafting onto a rootstock. Clones (i.e. genetically identical vegetative propagations) of the original plant can thus be generated by either in vitro culture or grafting. “Cell culture” or “tissue culture” refers to the in vitro culture of cells or tissues of a plant. “Regeneration” refers to the development of a plant from cell culture or tissue culture or vegetative propagation. “Nonpropagating cell” refers to a cell which cannot be regenerated into a whole plant.
[0152] “Melon plant cells” or “melon plants” or “cultivated melon plants or cells” also designated as muskmelon plant cells or muskmelon plants in the art shall be understood in context with the present invention to be plant cells originating from the species Cucumis melo or to be plants belonging to the species Cucumis melo. Cucumis melo, can be classified into: C. melo var. cantalupensis. C. melo var. inodorous and C. melo var. reticulatus. C. melo var. cantalupensis are also referred to as Cantaloupes and are primarily round in shape with prominent ribs and almost no netting. Most have orange, sweet flesh and they are usually very fragrant. In contrast to the European cantaloupe, the North American 'Cantaloupe' is not of this type, but belongs to the true muskmelons. C. melo var. inodorous (or winter melons) can be subdivided into different types, such as Honeydew melon, Piel de Sapo, Sugar melon, Japanese melon, etc. C. melo var. reticulatus is the true muskmelon, with reticulated skin (netted) and includes Galia melons, Sharlyn melons and the North American cantaloupe.
[0153] Cultivated melon and the wild relatives of melon is / are diploid and has / have 12 pairs of homologous chromosomes, numbered 1 to 12.
[0154] "Cultivated melon plant" refers to plants of Cucumis melo i.e. varieties, breeding lines or cultivars of the species C. melo, cultivated by humans and having good agronomic characteristics, especially producing edible and marketable fruits of good size and quality and uniformity; preferably such plants are not "wild melon plants", i.e. plants which generally have much poorer yields and poorer agronomic characteristics than cultivated plants and e.g. grow naturally in wild populations. "Wild melon plants" include for example ecotypes, PI (Plant Introduction) lines, landraces or wild accessions or wild relatives of a species.
[0155] “SNP marker” refers to a Single Nucleotide Polymorphism between e.g. a resistant TIR-NBS-LRR allele and a susceptible TIR-NBS-LRR allele, or to one or more SNP marker linked to a resistant TIR-NBS- LRR allele as e.g. shown in figure 3. Using a SNP marker assay which can distinguish between the resistant and susceptible allele of the TIR-NBS-LRR gene (e.g. in an allele specific assay) one can screen pants, plant parts or the DNA therefrom for the presence of the resistant allele, e.g. encoding a protein of SEQ ID NO: 8. For any of the SNP markers a SNP markers assays can be designed based on the sequences provided herein. Such a SNP marker assay can be used to detect the resistant allele, e.g. in Marker Assisted Selection and / or SNP genotyping assays. Thus, using a SNP marker assay one can screen pants, plant parts or the DNA therefrom for the presence of the resistant allele.
[0156] “INDEL marker” refers to an insertion / deletion polymorphism between e.g. a resistant TIR-NBS-LRR allele and a susceptible allele. Using an INDEL marker assay which can distinguish between the resistant and susceptible allele of the gene (e.g. an allele specific assay) one can screen pants, plant parts or the DNA therefrom for the presence of the resistant allele. For example Change number 1 is caused by an INDEL, see Figure 4.
[0157] “Genotyping” methods are methods whereby the genotype or allelic composition of a plant or plant part or seed can be determined. Bi-allelic genotyping assays, such as KASP-assays, can distinguish between two alleles at a locus. For example SNP markers or INDEL markers can be analyzed in a genotyping assay.
[0158] A “chromosome region comprising the resistant TIR-NBS-LRR allele” refers to the genomic region of e.g. chromosome 5 of cultivated melon which region carries the resistant allele. The presence of the allele can be determined phenotypically and / or by the presence of one or more molecular markers, e.g. SNP markers, INDEL markers or other markers, linked to the resistant allele or preferably markers distinguishing different TIR-NBS-LRR alleles or by the genomic sequence of the allele sequence itself. A marker is “linked to the resistant TIR-NBS-LRR allele”, if it is physically coupled to the allele. An “allele specific marker” is a marker which is specific for a particular allele (e.g. a specific resistance allele) and is thus discriminating between e.g. the resistance allele and other alleles. An allele-specific marker is preferably a marker in the allele itself, i.e. in the promoter region or the transcribed region of the gene, e.g. based on a polymorphism between the resistance allele sequence and the susceptible allele sequence. For example, the Change number 1, 2, 3 and / or 4 described herein can be used to design SNP markers or INDEL markers or other markers for genotyping and for detecting which allele is present in the genome.
[0159] A pair of “flanking markers” refers to two markers, preferably two SNP markers or two sequences comprising the SNP markers, which are linked to the resistance allele, e.g. QTL5 / A. whereby the resistance allele is located in-between the two markers or in-between the two sequences comprising the markers.
[0160] “Brix” or “degree Brix” or “° brix” refers to the mean total soluble solids content as measured on several mature fruits using a refractometer. Preferably the mean of at least three fruits, each measured between the centre and the rind of the cut-open fruit, is calculated.
[0161] “Physical distance” between loci (e.g. between molecular markers and / or between phenotypic markers) on the same chromosome is the actually distance expressed in bases or base pairs (bp), kilo bases or kilo base pairs (kb) or megabases or mega base pairs (Mb).
[0162] “Genetic distance” between loci (e.g. between molecular markers and / or between phenotypic markers) on the same chromosome is measured by frequency of crossing-over, or recombination frequency (RF) and is indicated in centimorgans (cM). One cM corresponds to a recombination frequency of about 1%. If no recombinants can be found, the RF is zero and the loci are either extremely close together physically or they are identical. The further apart two loci are, the higher the RF.
[0163] “Uniformity” or “uniform” relates to the genetic and phenotypic characteristics of a plant line or variety. Inbred lines are genetically highly uniform as they are produced by several generations of inbreeding. Likewise, and the Fl hybrids which are produced from such inbred lines are highly uniform in their genotypic and phenotypic characteristics and performance.
[0164] A genetic element, an introgression fragment, or a gene or allele conferring a trait (such as ToLCNDV- ES resistance) is said to be “obtainable from” or can be “obtained from” or “derivable from” or can be “derived from” or “as present in” or “as found in” a plant or seed or tissue or cell if it can be transferred from the plant or seed in which it is present into another plant or seed in which it is not present (such as a ToLCNDV-ES susceptible line or variety) using traditional breeding techniques without resulting in a phenotypic change of the recipient plant apart from the addition of the trait conferred by the genetic element, locus, introgression fragment, gene or allele. The terms are used interchangeably and the genetic element, locus, introgression fragment, gene or allele can thus be transferred into any other genetic background lacking the trait. Cultivated melons containing the genetic element, locus, introgression fragment, gene or allele (e.g. a resistant TIR-NBS-LRR allele) can be generated de novo, e.g. by mutagenesis (e.g. chemical mutagenesis, CRISPR-Cas induced, etc.) and then e.g. be crossed into other cultivated melons.
[0165] “Average” or “mean” refers herein to the arithmetic mean and both terms are used interchangeably. The term “average” or “mean” thus refers to the arithmetic mean of several measurements. The skilled person understands that the phenotype of a plant line or variety depends to some extent on growing conditions and that, therefore, arithmetic means of at least 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50 or more plants (or plant parts) are measured, preferably in randomized experimental designs with several replicates and suitable control plants grown under the same conditions in the same experiment. “Statistically significant” or “statistically significantly” different or “significantly” different refers to a characteristic of a plant line or variety that, when compared to a suitable control show a statistically significant difference in that characteristic (e.g. the p-value is less than 0.05, p < 0.05, using ANOVA) from the (mean of the) control.
[0166] The term “traditional breeding techniques” encompasses herein crossing, backcrossing, selfing, selection, double haploid production, chromosome doubling, embryo rescue, protoplast fusion, marker assisted selection, mutation breeding etc., all as known to the breeder (i.e. methods other than transformation / transgenic methods), by which, for example, a chromosome 5 comprising a resistant TIR-NBS-LRR allele can be obtained, identified and / or transferred.
[0167] “Backcrossing” refers to a breeding method by which a (single) trait, such as the ToLCNDV-ES resistance trait, can be transferred from one (often an inferior) genetic background (also referred to as “donor”) into another (often a superior) genetic background (also referred to as “recurrent parent”. An offspring of a cross (e.g. an Fl plant obtained by crossing e.g. the donor with the recurrent parent melon, or an F2 plant or F3 plant, etc., obtained from selfing the Fl), is “backcrossed” to the parent with e.g. the superior genetic background. After repeated backcrossing, the trait of the one (often inferior) genetic background will have been incorporated into the other (often superior) genetic background.
[0168] “Marker assisted selection” or “MAS” is a process of using the presence of molecular markers (such as SNP markers or INDEL markers), which are genetically and physically linked to a particular locus or to a particular chromosome region or allele specific markers, to select plants for the presence of the specific locus or region or allele. For example, a molecular marker genetically and physically linked to the resistant TIR-NBS-LRR allele or an allele specific marker, can be used to detect and / or select e.g. melon plants, or plant parts, comprising the resistant allele. The closer the linkage of the molecular marker to the locus, the less likely it is that the marker is dissociated from the locus through meiotic recombination. Likewise, the closer two markers are linked to each other the less likely it is that the two markers will be separated from one another (and the more likely they will co-segregate as a unit). Allele specific markers are preferred markers, as they select for the allele directly. For example Change number 1, 2, 3 and / or 4 can be used to develop markers which differentiate between the presence of different alleles.
[0169] A molecular marker (or a sequence comprising a molecular marker) within 5 Mb, 3 Mb, 2.5 Mb, 2 Mb, 1 Mb, 0.5 Mb, 0.4Mb, 0.3Mb, 0.2Mb, 0.1 Mb, 74kb, 50kb, 20kb, lOkb, 5kb, 2kb, Ikb or less of another marker (or a sequence comprising the molecular marker), or of a locus, refers to a marker which is physically located within the 5 Mb, 3 Mb, 2.5 Mb, 2 Mb, 1 Mb, 0.5 Mb, 0.4Mb, 0.3Mb, 0.2Mb, 0.1 Mb, 74kb, 50kb, 20kb, lOkb, 5kb, 2kb, Ikb or less, of the genomic DNA region flanking the marker (i.e. either side of the marker).
[0170] “LOD-score” (logarithm (base 10) of odds) refers to a statistical test often used for linkage analysis in animal and plant populations. The LOD score compares the likelihood of obtaining the test data if the two loci (molecular marker loci and / or a phenotypic trait locus) are indeed linked, to the likelihood of observing the same data purely by chance. Positive LOD scores favour the presence of linkage and a LOD score greater than 3.0 is considered evidence for linkage. A LOD score of +3 indicates 1000 to 1 odds that the linkage being observed did not occur by chance.
[0171] “Transgene” or “chimeric gene” refers to a genetic locus comprising a DNA sequence, such as a recombinant gene encoding e.g. the protein of SEQ ID NO: 8, which has been introduced into the genome of a plant by transformation, such as Agrobacterium mediated transformation. A plant comprising a transgene stably integrated into its genome is referred to as “transgenic plant”.
[0172] An “isolated nucleic acid sequence” or “isolated DNA” refers to a nucleic acid sequence which is no longer in the natural environment from which it was isolated, e.g. the nucleic acid sequence in a bacterial host cell or in the plant nuclear or plastid genome. When referring to a “sequence” herein, it is understood that the molecule having such a sequence is referred to, e.g. the nucleic acid molecule.
[0173] A "host cell" or a "recombinant host cell" or “transformed cell” are terms referring to a new individual cell (or organism) arising as a result of at least one nucleic acid molecule, having been introduced into said cell. The host cell is preferably a plant cell or a bacterial cell. The host cell may contain the nucleic acid as an extra-chromosomally (episomal) replicating molecule, or comprises the nucleic acid integrated in the nuclear or plastid genome of the host cell, or as introduced chromosome, e.g. minichromosome.
[0174] “Sequence identity” and “sequence similarity” can be determined by alignment of two peptide or two nucleotide sequences using global or local alignment algorithms. Sequences may then be referred to as "substantially identical” or “essentially similar” when they are optimally aligned by for example the programs GAP or BESTFIT or the Emboss program “Needle” (using default parameters, see below) share at least a certain minimal percentage of sequence identity (as defined further below). These programs use the Needleman and Wunsch global alignment algorithm to align two sequences over their entire length, maximizing the number of matches and minimising the number of gaps. Generally, the default parameters are used, with a gap creation penalty = 10 and gap extension penalty = 0.5 (both for nucleotide and protein alignments). For nucleotides the default scoring matrix used is DNAFULL and for proteins the default scoring matrix is Blosum62 (Henikoff & Henikoff, 1992, PNAS 89, 10915-10919). Sequence alignments and scores for percentage sequence identity may for example be determined using computer programs, such as EMBOSS as available on the world wide web under ebi.ac.uk / Tools / psa / emboss_needle / ). Alternatively sequence similarity or identity may be determined by searching against databases such as FASTA, BLAST, etc., but hits should be retrieved and aligned pairwise to compare sequence identity. Two proteins or two protein domains, or two nucleic acid sequences have “substantial sequence identity” if the percentage sequence identity is at least 95%, 98%, 99% or more (as determined by Emboss “needle” using default parameters, i.e. gap creation penalty = 10, gap extension penalty = 0.5, using scoring matrix DNAFULL for nucleic acids and Blosum62 for proteins).
[0175] When reference is made to a nucleic acid sequence (e.g. DNA or genomic DNA) having “substantial sequence identity to” a reference sequence or having a sequence identity of at least 90%, e.g. at least 95%, 96%, 97%, 98%, 99%, 99.2%, 99.5%, 99.9% nucleic acid sequence identity to a reference sequence, in one embodiment said nucleotide sequence is considered substantially identical to the given nucleotide sequence and can be identified using stringent hybridisation conditions.
[0176] “Stringent hybridisation conditions” can be used to identify nucleotide sequences, which are substantially identical to a given nucleotide sequence. Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequences at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridises to a perfectly matched probe. Typically stringent conditions will be chosen in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least 60°C. Lowering the salt concentration and / or increasing the temperature increases stringency. Stringent conditions for RNA-DNA hybridisations (Northern blots using a probe of e.g. lOOnt) are for example those which include at least one wash in 0.2X SSC at 63°C for 20min, or equivalent conditions. Stringent conditions for DNA-DNA hybridisation (Southern blots using a probe of e.g. lOOnt) are for example those which include at least one wash (usually 2) in 0.2X SSC at a temperature of at least 50°C, usually about 55°C, for 20 min, or equivalent conditions.
[0177] “Ml generation” or “Ml plants” in context with the present invention shall refer to the first generation that is produced directly from the mutagenic treatment. A plant grown from seeds treated with a mutagen e.g. is a representative of an Ml generation. “M2 generation” or “M2 plant” shall refer herein to the generation obtained from self-pollination of the Ml generation. A plant grown from seeds obtained from a self-pollinated Ml plant represents a M2 plant. M3, M4, etc. refers to further generations obtained after self-pollination.
[0178] An “mRNA coding sequence” shall have the common meaning herein. An mRNA coding sequence corresponds to the respective DNA coding (cDNA) sequence of a gene / allele apart from that thymine (T) is replaced by uracil (U).
[0179] A “mutation” in a nucleic acid molecule (DNA or RNA) is a change of one or more nucleotides compared to the corresponding wild type sequence, e.g. by replacement, deletion or insertion of one or more nucleotides. Examples of such a mutation are point mutation, nonsense mutation, missense mutation, splice-site mutation, frame shift mutation or a mutation in a regulatory sequence.
[0180] A “nucleic acid molecule” shall have the common understanding in the art. It is composed of nucleotides comprising either of the sugars deoxyribose (DNA) or ribose (RNA).
[0181] A “point mutation” is the replacement of a single nucleotide, or the insertion or deletion of a single nucleotide.
[0182] A “nonsense mutation” is a (point) mutation in a nucleic acid sequence encoding a protein, whereby a codon in a nucleic acid molecule is changed into a stop codon. This results in a pre-mature stop codon being present in the mRNA and results in translation of a truncated protein. A truncated protein may have decreased function or loss of function.
[0183] A “missense or non-synonymous mutation” is a (point) mutation in a nucleic acid sequence encoding a protein, whereby a codon is changed to code for a different amino acid. The resulting protein may have decreased function or loss of function.
[0184] A “splice-site mutation” is a mutation in a nucleic acid sequence encoding a protein, whereby RNA splicing of the pre-mRNA is changed, resulting in an mRNA having a different nucleotide sequence and a protein having a different amino acid sequence than the wild type. The resulting protein may have decreased function or loss of function.
[0185] A “frame shift mutation” is a mutation in a nucleic acid sequence encoding a protein by which the reading frame of the mRNA is changed, resulting in a different amino acid sequence. The resulting protein may have decreased function or loss of function.
[0186] A “deletion” in context of the invention shall mean that anywhere in a given nucleic acid sequence at least one nucleotide is missing compared to the nucleic sequence of the corresponding wild type sequence or anywhere in a given amino acid sequence at least one amino acid is missing compared to the amino acid sequence of the corresponding (wild type) sequence.
[0187] A “truncation” shall be understood to mean that at least one nucleotide at either the 3 ’-end or the 5 ’-end of the nucleotide sequence is missing compared to the nucleic sequence of the corresponding wild type sequence or that at least one amino acid, but preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acids, at either the N-terminus or the C-terminus of the protein is missing compared to the amino acid sequence of the corresponding wild type protein. The 5 ’-end is determined by the ATG codon used as start codon in translation of a corresponding wild type nucleic acid sequence.
[0188] “Replacement” shall mean that at least one nucleotide in a nucleic acid sequence or one amino acid in a protein sequence is different compared to the corresponding wild type nucleic acid sequence or the corresponding wild type amino acid sequence, respectively, due to e.g. an exchange of a nucleotide in the coding sequence of the respective protein.
[0189] “Insertion” shall mean that the nucleic acid sequence or the amino acid sequence of a protein comprises at least one additional nucleotide or amino acid compared to the corresponding wild type nucleic acid sequence or the corresponding wild type amino acid sequence, respectively.
[0190] “Pre-mature stop codon” in context with the present invention means that a stop codon is present in a coding sequence (cds) which is closer to the start codon at the 5 ’-end compared to the stop codon of a corresponding wild type coding sequence.
[0191] A “mutation in a regulatory sequence”, e.g. in a promoter or enhancer of a gene, is a change of one or more nucleotides compared to the wild type sequence, e.g. by replacement, deletion or insertion of one or more nucleotides, leading for example to decreased or no mRNA transcript of the gene being made.
[0192] A “mutation in a protein” is a change of one or more amino acid residues compared to the wild type sequence, e.g. by replacement, deletion, truncation or insertion of one or more amino acid residues.
[0193] “Mutant protein” is herein a protein comprising one or more mutations in the nucleic acid sequence encoding the protein.
[0194] “Knock-out” or “entire knock-out” shall be understood that expression of the respective gene is not detectable anymore.
[0195] “Oligonucleotides” or “oligos” or “oligonucleotide primers or probes” are short, single-stranded polymers of nucleic acid, e.g. at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more nucleotides in length. Oligos may be unmodified or modified with a variety of chemistries depending on their intended use, for example, the addition of 5' or 3' phosphate groups to enable ligation or block extension, respectively, labelling with radionuclides or fluorophores and / or quenchers for use as probes, the incorporation of thiol, amino, or other reactive moieties to enable the covalent coupling of functional molecules such as enzymes, and extension with other linkers and spacers of diverse functionality. DNA oligos are the most commonly used, but RNA oligos are also available. The length of an oligo is usually designated by adding the suffix -mer. For example, an oligonucleotide with 19 nucleotides (bases) is called a 19-mer. For most uses, oligonucleotides are designed to base-pair with a strand of DNA or RNA. The most common use for oligonucleotides is as primers for PCR (polymerase chain reaction). Primers are designed with at least part of their sequence complementary to the sequence targeted for amplification. Optimal primer length for a complementary sequence is e.g. 18 to 22 nucleotides. Optimal primer sequences for PCR are usually determined by primer design software.
[0196] “DNA microarrays” are arrays which have many microscopic spots of DNA, usually oligonucleotides, bound on a solid support. Assay targets can be DNA, cDNA, or cRNA. Depending on the system, the hybridization of targets to specific spots is detected by fluorescence, chemiluminescence, or colloidal silver or gold. Microarrays are used for multiple applications such as simultaneous measurement of the expression of large numbers of genes, enabling genome-wide gene expression analysis, as well as genotyping studies using e.g. single-nucleotide polymorphism (SNP) or InDei analysis.
[0197] “Complementary strands” refer to two strands of complementary sequence, and may be referred to as sense (or plus) and anti-sense (or minus) strands for double stranded DNA. For any of the sequences provided herein only one strand of the sequence is given, but the complementary strand of the given strand is also encompassed herein. The complementary nucleotides of DNA are A complementary to T, and G complementary to C. The complementary nucleotides of RNA are A complementary to U, and G complementary to C.
[0198] “SNP_01 ” refers to nucleotide 81 of SEQ ID NO: 1 , or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 1 (when aligned pairwise). SNP_01 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_01” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_01, which is shown in Table 2. SEQ ID NO: 1 is the forward strand with respect to the reference genome. SNP_01 was mapped to flank the QTL5 / 7? comprising region at one side, with SNP_07 being on the other side.
[0199] “SNP_02” refers to nucleotide 242 of SEQ ID NO: 2, or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 2 (when aligned pairwise). SNP_02 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_02” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_02, which is shown in Table 2. SEQ ID NO: 2 is the reverse strand with respect to the reference genome. Therefore, the nucleotide for SNP_02 on the complement strand may be referred to herein.
[0200] “SNP_03” refers to nucleotide 81 of SEQ ID NO: 3, orthe equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 3 (when aligned pairwise). SNP_03 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_03” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_03, which is shown in Table 2. SEQ ID NO: 3 is the forward strand with respect to the reference genome.
[0201] “SNP_04” refers to nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 4 (when aligned pairwise). SNP_04 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_04” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_04, which is shown in Table 2. SEQ ID NO: 4 is the reverse strand with respect to the reference genome. Therefore, the nucleotide for SNP_04 on the complement strand may be referred to herein.
[0202] “SNP_05” refers to nucleotide 101 of SEQ ID NO: 5, or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 5 (when aligned pairwise). SNP_05 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_05” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_05, which is shown in Table 2. SEQ ID NO: 5 is the reverse strand with respect to the reference genome. Therefore, the nucleotide for SNP_05 on the complement strand may be referred to herein.
[0203] “SNP_06” refers to nucleotide 101 of SEQ ID NO: 6, or the equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 6 (when aligned pairwise). SNP_06 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_06” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_06, which is shown in Table 2. SEQ ID NO: 6 is the reverse strand with respect to the reference genome. Therefore, the nucleotide for SNP_06 on the complement strand may be referred to herein.
[0204] “SNP_07” refers to nucleotide 81 of SEQ ID NO: 1, orthe equivalent nucleotide in a sequence comprising at least 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 7 (when aligned pairwise). SNP_07 corresponds to a specific nucleotide position on chromosome 5 of the melon genome (referring to the melon reference genome DHL92 V4 in the melonomics.net database) as is listed in Table 2. The “donor nucleotide of SNP_07” refers to the nucleotide of the ToLCNDV-ES resistant donor for SNP_07, which is shown in Table 2. SEQ ID NO: 7 is the forward strand with respect to the reference genome. SNP_07 was mapped to flank the QTL5 / A comprising region at one side, with SNP_01 being on the other side.
[0205] DETAILED DESCRIPTION
[0206] Provided herein is, in one aspect, a cultivated melon plant or plant cell of the species Cucumis melo comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises a Quantitative trait locus referred to as QTL5 / A which confers ToLCNDV-ES resistance, especially against resistance breaking strains, and wherein the introgression fragment comprises a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 3 and / or a Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 4.
[0207] Further provided herein is, in one aspect, a cultivated melon plant or plant cell of the species Cucumis melo comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises a Quantitative trait locus referred to as QTL5 / A which confers ToLCNDV-ES resistance, especially against resistance breaking strains, and wherein the introgression fragment comprises at least one, two three, four or five markers selected from the group:
[0208] A Cytosine (C) for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or a Guanine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 2 (or to the complement strand); a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; an Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 4 (or to the complement strand); a Thymine (T) for SNP 05 at nucleotide 101 of SEQ ID NO: 5 (or an Adenine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 5 (or to the complement strand); an Adenine (A) for SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or a Thymine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 6 (or to the complement strand).
[0209] Provided herein is, in yet one aspect, a cultivated melon plant or plant cell of the species Cucumis melo comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises a Quantitative trait locus referred to as QTL5 / A which confers ToLCNDV-ES resistance, especially against resistance breaking strains, and wherein the introgression fragment comprises a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 3 and / or a Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or a Thymine in the complement strand) or at the equivalent nucleotide of a sequence comprising at least 95% sequence identity to SEQ ID NO: 4 (or to the complement strand) and / or wherein the introgression fragment comprises a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0210] In still a different aspect a cultivated melon plant or plant cell of the species Cucumis melo is provided comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises a Quantitative trait locus referred to as QTL5 / A which confers ToLCNDV-ES resistance, especially against resistance breaking strains, and wherein the introgression fragment comprises a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0211] In one aspect, the QTL5 / A (or the introgression fragment comprising it or the causal gene underlying QTL5r / >) is obtainable from (or is obtained from, is derived or derivable from, is as present in) seeds, a representative sample of which has been deposited under accession number NCIMB 44139. The cultivated melon plant and plant cell described above, comprises the introgression fragment which comprises the sequence of the ToLCNDV-ES resistant donor melon plant starting at nucleotide 26034368 and ending at nucleotide 26027838 of chromosome 5 (this region corresponds to the region where SEQ ID NO: 11, or variants thereof, can be found, referring to melonomics.net, V4.0), and optionally wherein the introgression fragment is obtainable from seeds, a representative sample of which has been deposited under accession number NCIMB 44139.
[0212] The cultivated melon plant and plant cell described above, in one aspect comprises SEQ ID NO: 11, or a variant thereof, said variant comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, and / or said variant encodes a protein which preferably comprises at least one, preferably at least two, three or all four of the following amino acids: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8.
[0213] In another aspect the cultivated melon plant and plant cell described above is provided, wherein the introgression fragment comprises the donor SNP nucleotide for one or more SNP markers selected from SNP_02, SNP_03, SNP_04, SNP_05 and SNP_06, especially one or more SNP markers selected from SNP_02, SNP_03, SNP_04 and SNP_05, especially at least SNP_03 and / or SNP_04 or at least SNP_03 and SNP_04 and SNP_05. The SNP haplotype is, therefore, e.g. as for example shown in Figure 3: G-G- T-A-T (for SNP_02 to SNP_06) or e.g. G-G-T-A (for SNP_02 to SNP_05) or G-T (SNP_03 and SNP_04) or G and / or T (SNP_03 and / or SNP_04).
[0214] In another aspect the cultivated melon plant and plant cell described above is provided, wherein the introgression fragment comprises the donor SNP nucleotide for one or more SNP markers selected from SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07, for example: C-G-G-T-A-T-C for SNP_01 to SNP_07, see e.g. Figure 3.
[0215] In one aspect the cultivated melon plant or plant cell comprises the introgression fragment in homozygous form and comprising e.g. the genotype GG-GG-TT-AA-TT (for SNP 02 to SNP 06) or e.g. GG-GG-TT- AA (for SNP_02 to SNP_05) or GG-TT (SNP_03 and SNP_04) or GG and / or TT (SNP_03 and / or SNP_04). In yet a further aspect a cultivated melon plant or plant cell is provided, wherein the introgression fragment further comprises a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3 and / or an Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4, or a Thymine (T) at nucleotide 101 of the complement strand to SEQ ID NO: 4 or at nucleotide 101 of the complement strand of the sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4.
[0216] Also provided is a seed from which a cultivated melon plant as described herein can be grown.
[0217] The cultivated melon seed comprises a plant cell as described herein, comprising QTL5 / A or the causal gene underlying QTL5 / 7).
[0218] Further also a cultivated melon fruit comprising a plant cell as described herein, comprising QTL5 / A or the causal gene underlying QTL5 / A. is provided. Also a fruit produced on said melon plant and comprising at least one chromosome 5 which comprises QTL5 / 7? or the causal gene underlying QTL5 / A.
[0219] Also a cultivated melon plant propagation material comprising a plant cell as described herein, comprising QTL5 / 7) or the causal gene underlying QTL5 / A. is provided.
[0220] A method for producing a ToLCNDV-ES resistant melon plant comprising QTL5 / 7?. or the causal gene underlying QTL5 / 7?. is also provided comprising the following steps a) selecting a ToLCNDV-ES resistant donor plant, especially a plant resistant to the resistant breaking strain of ToLCNDV-ES; b) crossing the donor plant selected in step a) with a plant sensitive to ToLCNDV-ES, especially a plant sensitive to the resistant breaking strain of ToLCNDV-ES; c) obtaining Fl seeds from the plants crossed in step b) or obtaining seeds of further selfing generations such as F2, F3 or further selfing generations, or obtaining seeds of a backcross generation obtained by crossing a ToLCNDV-ES resistant plant back to the ToLCNDV-ES sensitive plant, and optionally d) verifying if the plants grown from the seeds obtained in step c) are resistant to ToLCNDV-ES (especially to the resistant breaking strain) and / or comprise:
[0221] - the donor SNP haplotype for one or more of SNP_01 to SNP_07, or of SNP_02 to SNP_06, or of SNP_03 to SNP_05, or of SNP_03 to SNP_04; and / or - a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3 and / or an Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4, or a Thymine (T) at nucleotide 101 of the complement strand to SEQ ID NO: 4 or at nucleotide 101 of the complement strand of the sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4; and / or
[0222] - a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or
[0223] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, preferably encoding a protein as described herein above.
[0224] The verifying steps in step d) can optionally additionally or alternatively be carried out in step a), i.e. when selecting the donor plant. Thus, the donor plant can e.g. be selected based on the SNP markers and / or based on the gene sequence or nucleotide sequence of step d).
[0225] In one aspect the introgression fragment comprising QTL5 / 7? (or the causal gene underlying QTL5 / A) is obtainable from (or obtained from, derivable from, derived from, etc.) seeds deposited under NCIMB 44139 or progeny thereof, which retain the QTL5 / 7? (or the causal gene underlying QTL5 / A).
[0226] Also provided is a method for producing melon seeds comprising the following steps: a) growing a melon plant comprising at least one chromosome 5 having an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises QTL5 / 7? (or the causal gene underlying QTL5 / A) which confers ToLCNDV-ES resistance and comprises:
[0227] - the donor SNP haplotype for one or more of SNP_01 to SNP_07, or of SNP_02 to SNP_06, or of SNP_03 to SNP_05, or of SNP_03 to SNP_04; and / or
[0228] - a Guanine (G) for SNP_03 at nucleotide 81 of SEQ ID NO: 3 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3 and / or an Adenine (A) for SNP_04 at nucleotide 101 of SEQ ID NO: 4 or at the equivalent nucleotide of a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4, or a Thymine (T) at nucleotide 101 of the complement strand to SEQ ID NO: 4 or at nucleotide 101 of the complement strand of the sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 4; and / or
[0229] - a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or
[0230] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, preferably encoding a protein as described herein above, b) harvesting the fruits of the melon plants grown in step a), and optionally c) collecting the seeds from the fruits obtained in step b).
[0231] In one aspect the introgression fragment comprising QTL5 / 7? (or the causal gene underlying QTL5 / A) is obtainable from (or obtained from, derivable from, or derived from or as present in) seeds deposited under NCIMB 44139 or progeny thereof, which retain the QTL5 / 7).
[0232] In yet another aspect a method for producing hybrid melon seeds is provided comprising the following steps a) crossing a first inbred melon plant comprising at least one chromosome 5 having an introgression fragment on chromosome 5 comprising QTL5 / 7? as described herein, with a second inbred melon plant with or without a chromosome 5 having an introgression fragment on chromosome 5 comprising QTL5 / 7? as described herein, and b) selecting seeds obtained from the cross of step a).
[0233] In another aspect a method for producing a melon fruit is provided comprising the following steps: a) growing a plant melon plant comprising at least one chromosome 5 having an introgression fragment on chromosome 5 comprising QTL5 / 7? as described herein, and b) harvesting the fruits produced by the plants grown in step a).
[0234] Resistance to ToLCNDV-ES conferred by the introgression fragment or by the QTL5 / 7? is expressed in a dominant manner and thus can be observed when only one chromosome 5 comprises the introgression fragment or the QTL5 / 7? (or the causal gene underlying QTL5r6) is present in the plant.
[0235] Other specific embodiments of the present invention therefore relate to melon plant cells or melon plants, wherein the introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant comprising the sequence of the donor plant in-between SNP_01 and SNP_07, in-between SNP_07 and SNP_06, in-between SNP_02 and SNP_05, in-between SNP_03 and SNP_06, in-between SNP_03 and SNP_05, in-between SNP_02 and SNP_04, in-between SNP_03 and SNP_04, in-between SNP_03 and SNP_05 or preferably in-between SNP_03 and SNP_04 is present in heterozygous state. Accordingly, it is sufficient that at least one chromosome 5 in the plant cells or plants comprise the just described introgression fragment. It is however understood that chromosome 5 in respect to the just described introgression fragment can also be present in the homozygous state without diminishing the degree of resistance, because of the dominance of the ToLCNDV-ES resistance conferred by the just described introgression fragment. Thus, the invention comprises plant cells according to the invention or plants according to the invention which comprise the just described introgression fragment in a heterozygous or homozygous state.
[0236] Table 1 illustrates the SNP genotype and haplotype of plants or cells comprising the ToLCNDV-ES resistant donor SNPs in homozygous form (on both chromosomes 5) or heterozygous form (on one chromosome 5). In the table the SNP genotype or haplotype refers to the forward strand in relation to the reference genome.
[0237] Table 1
[0238] *or the nucleotide (nt) at the equivalent position in a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to the given sequence (or the complement sequence).
[0239] In one embodiment a cultivated melon plant (of the species C. melo) is provided which comprises a recombinant chromosome 5, whereby the recombinant chromosome 5 comprises an introgression fragment that confers ToLCNDV-ES resistance onto the melon plant when present in homozygous or heterozygous form and wherein the introgression fragment is from a wild donor of the species C. melo. In one aspect the introgression fragment comprises the SNP donor haplotype for one or more or all of SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and / or SNP_07, optionally of one or more or all of SNP_02, SNP_03, SNP_04, SNP_05 and / or SNP_06. In one embodiment the introgression fragment comprises the donor SNP haplotype for at least SNP_03 and / or SNP_04 or for at least SNP_03, SNP_04 and SNP_05. The SNP haplotype of the donor may be present in homozygous form (if the introgression fragment is in homozygous form) or in heterozygous form (if the introgression fragment is in heterozygous form). So, for example, the plant or plant cell or plant part may comprise the GG or GX genotype for SNP_03 at nucleotide 81 of SEQ ID NO: 3, or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3. Thus, the plant, plant cell, or plant part may comprise SEQ ID NO: 3, or a sequence comprising at least 95%, 97%, 98% or 99% sequence identity to SEQ ID NO: 3, in homozygous form or in heterozygous form.
[0240] In one embodiment cultivated melon plants or cells of these plants are provided which comprise an introgression fragment from a wild donor on chromosome 5, which introgression fragment confers the ToLCNDV-ES resistance (especially to resistance breaking strains), whereby the introgression fragment lies in-between SNP_02 and SNP_06 (or in-between SEQ ID NO:2 and SEQ ID NO:6, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 2 or to SEQ ID NO 6); or whereby the introgression fragment lies in-between SNP_02 and SNP_05 (or in-between SEQ ID NO:2 and SEQ ID NO:5, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 2 or to SEQ ID NO 5), or whereby the introgression fragment lies inbetween SNP_03 and SNP_04 (or in-between SEQ ID NO:3 and SEQ ID NON, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 3 or to SEQ ID NO: 4), or whereby the introgression fragment lies in-between SNP_03 and SNP_05 (or in-between SEQ ID NON and SEQ ID NON, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 3 or to SEQ ID NO 5).
[0241] In one aspect the cultivated melon plants or cells of these plants comprise an introgression fragment from a wild donor on chromosome 5, which introgression fragment confers the ToLCNDV-ES resistance (especially to resistance breaking strains), whereby the introgression fragment lies in-between SNP_02 and SNP_06 (or in-between SEQ ID NON and SEQ ID NO:6, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 2 or to SEQ ID NO 6), or the fragment lies in-between SNP_02 and SNP_05 (or in-between SEQ ID NON and SEQ ID NON, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 2 or to SEQ ID NO 5), or whereby the introgression fragment lies in-between SNP_03 and SNP_04 (or in-between SEQ ID NON and SEQ ID NON, or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 3 or to SEQ ID NO 4), or whereby the introgression fragment lies inbetween SNP_03 and SNP_05 or a sequence comprising at least 95%, or at least 97% or 98% or 99% sequence identity to SEQ ID NO: 3 or to SEQ ID NO 5, and / or whereby the introgression fragment comprises a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or
[0242] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, preferably encoding a protein as described herein above.
[0243] In another aspect the cultivated melon plants or cells of these plants comprise an introgression fragment from a wild donor on chromosome 5, which introgression fragment confers the ToLCNDV-ES resistance (especially to resistance breaking strains), whereby the introgression fragment comprises a gene encoding the protein of SEQ ID NO: 8, or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or
[0244] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, preferably encoding a protein as described herein above.
[0245] In yet another aspect the cultivated melon plants or cells of these plants comprise an endogenous gene on chromosome 5, which gene encodes a TIR-NBS-LRR protein which confers the ToLCNDV-ES resistance (especially to resistance breaking strains), whereby the gene encodes the protein of SEQ ID NO: 8, or a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or
[0246] - wherein the gene comprises the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, and preferably encoding a protein as described herein above.
[0247] In one aspect a cultivated melon plant, plant cell or plant part is provided comprising the above and elsewhere herein described modified endogenous TIR-NBS-LRR gene on chromosome 5. The advantage of modifying the endogenous gene in a cultivated melon line, instead of introgressing a gene from a donor into cultivated melon, is that the genetic background of the melon plant is cultivated background and no linkage drag is introduced into the cultivated background and also no lengthy backcrossing is required. This saves many generations of backcrossing to an elite parent line and removal of undesired linkage drag.
[0248] In one aspect the endogenous gene has been modified by targeted mutagenesis and / or mutated by random mutagenesis, so that the gene does not encode a susceptible TIR-NBS-LRR protein (such as the susceptible protein of SEQ ID NO: 10, or a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% to SEQ ID NO: 10).
[0249] Thus, in one aspect a cultivated melon plant, plant cell and plant part is provided in which the endogenous gene has been modified by targeted mutagenesis and / or mutated by random mutagenesis so that the gene confers QTL5 / 7? resistance, whereby the gene encodes the resistance conferring protein of SEQ ID NO: 8, or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8, and which protein preferably comprises one or more or all of the following 4 amino acid changes compare to the susceptible protein of SEQ ID NO: 10:
[0250] “Change number 1”: an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2;
[0251] “Change number 2”: a change of amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0252] “Change number 3”: A change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2;
[0253] “Change number 4”: A change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2.
[0254] One or more of Change number 1 to Change number 4 are in one aspect introduced by targeted mutagenesis or targeted gene editing (such as Crispr-based gene editing) and / or mutated by random mutagenesis, such as radiation treatment or chemical mutagenesis. Figure 4, for example, shows the nucleotide changes in the genomic sequence, which can be generated by random or targeted mutagenesis in order to insert codons for one or more amino acids (e.g. change number 1) or to replace a codon by a different codon (e.g. change number 2 to 4).
[0255] The modified or mutated cultivated melon plants, plant parts, cells, fruits, tissues, propagating materials or seeds thus do not comprise and introgression fragment of QTL5 / 7?. but comprise a modified endogenous gene at the locus on chromosome 5, which encodes a ‘resistance protein’ and confers resistance to ToLCNDV-ES strains, especially resistance breaking strains.
[0256] Plants and plant parts comprising plant cells according to the invention (e.g. comprising an introgression fragment or comprising a modified or mutated endogenous gene) are another embodiment of the invention. Also seeds from which such plants can be grown are provided herein.
[0257] Fruits, seeds, plants, plant cells, plant tissues, vegetative propagations as described for e.g. introgressions of QTL5 / 7? or the causal gene underlying QTL5 / 7?. are therefore also encompassed herein for the endogenous TIR-NBS-LRR gene (encoding a susceptible protein) that is modified by targeted mutagenesis or random mutagenesis to encode a resistant TIR-NBS-LRR protein. This encompasses growing methods of such plants, selection methods of such plants or plant parts, methods for producing hybrids or inbred lines comprising one or two copies of a modified or mutated endogenous TIR-NBS- LRR gene, etc.
[0258] The melon plant provided herein (e.g. comprising an introgression fragment or comprising a modified or mutated endogenous gene) may be an inbred line, an open pollinated variety (OP) or an Fl hybrid. In one aspect the Fl hybrid comprises the introgression fragment or the modified endogenous gene in heterozygous form, e.g. produced by crossing two inbred parent lines, one of which possesses the introgression fragment or the modified endogenous gene (preferably in homozygous form, although not necessarily) and collecting the Fl hybrid seeds from said cross. The Fl hybrid may also comprise the introgression fragment or the modified endogenous gene in homozygous form, i.e. produced by crossing two inbred parent lines, each comprising the introgression fragment or the modified endogenous gene in homozygous or heterozygous form.
[0259] The melon plant provided herein may be of any type. Preferably it has good agronomic and good fruit quality characteristics, such as large average fruit size (at least 500g, 600g, 700g, 800g, 900g, 1000g or more), high average brix of the fruits (e.g. an average refractometer % total soluble solids of at least 10%, 12%, 14%, 16%, 18% or more), many fruits being produced per plant, firm fruit flesh, etc.
[0260] Also other resistances may be introduced into the melon plants described herein, such as resistance to one or more of the following diseases: Bacterial Wilt, Root Rot, Crown Blight, Melon Rust, Powdery Mildew, Verticillum Wilt, Sulphur Bum, Scab, Watermelon Mosaic, Downy Mildew, Fusarium oxysporum fsp. melonis (Fom) race 0, Fusarium oxysporum fsp. melonis (Fom) race 1 , Fusarium oxysporum fsp. melonis (Fom) race 2, Fusarium oxysporum fsp. melonis (Fom) race 1.2, Fusarium Wilt R2, Root Knot (Nematode), Anthracnose, Cucumber Mosiac, and Squash Mosaic, and / or resistance to one or more of the following pests: Aphid resistance, Pickle Worm, Darkling Ground Beetle, Banded Cucumber Beetle, Mite, Western Spotted Cucumber Beetle, Melon Leafhopper, Melon Worm, Western Striped Cucumber Beetle or Melon Leafminer. Other resistance genes, against pathogenic viruses, fungi, bacteria or pests may also be introduced.
[0261] A specific aspect of the invention concerns plants or plant cells comprising an introgression fragment, which introgression fragment is obtainable from seeds deposited under NCIMB 44139 or from progeny thereof. The seeds deposited are seeds of the wild donor used in the Examples comprising the QTL5 / 7? in homozygous form, with the donor nucleotide being present in homozygous form for SNP_01 to SNP_07. The causal gene of the ToLCNDV-ES resistance is located in-between SNP_03 and SNP_04, which means that the size of the donor introgression can be small, by selecting recombinants having a small introgression fragment, e.g. only the causal gene, encoding the protein of SEQ ID NO: 8. Whether a plant comprises the ToLCNDV-ES resistance from the deposited seeds can be determined by various methods, such as sequencing.
[0262] Melon plants and plant parts (such as leaves, stems, roots, fruits, pollen, flowers, etc.) comprising melon plant cells according to the invention are also an embodiment of the invention. Likewise seeds from which such plants can be grown are encompassed herein, as well as parts of such seeds (e.g. cells or tissues of the seeds such as the seed coat, embryo, etc.).
[0263] A further aspect of the present invention concerns melon seeds or plants comprising an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_06, in-between SNP_02 and SNP_05, in-between SNP_02 and SNP_04 or in-between SNP_03 and SNP_04. In a preferred embodiment of the invention the seeds comprise an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_02 and SNP_06, more preferably in-between SNP_02 and SNP_05 or in-between SNP_03 and SNP_05, even more preferably in-between SNP_02 and SNP_04 and most preferably inbetween SNP_03 and SNP_04.
[0264] Thus, melon plants or seeds or plant parts are encompassed which comprises an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant which comprises QTL5 / 7? (or at least the causal gene underlying QTL5 / 7?) and comprises the donor SNP nucleotide for one or more of SNP_01 to SNP_07, optionally for one or more of SNP_02 to SNP_06, e.g. for one or more of SNP_02 to SNP_05 or of SNP_03 to SNP_05, or for one or more of SNP_02 to SNP_04, or for SNP_03 and / or SNP_04.
[0265] As the causal gene of QTL5 / 7? is mapped to be in-between SNP_03 and SNP_04 on chromosome 5, it is herein one aspect that - e.g. when reference is made herein to an introgression fragment or the QTL5 / A being in-between SNP_03 and SNP_04 - this encompasses the fragment or region of the plant cell, seed, fruit, propagation material, tissue or plant comprises a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or the fragment comprises the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11 and preferably encoding a protein as described above.
[0266] Instead of, or in addition to, detection of the one or more donor SNP nucleotides of SNP_01 to SNP_07, preferably of SNP_02 to SNP_06, the embodiment therefore also encompasses detection and / or selection and / or verification of the plant cell, seed, fruit, propagation material, tissue or plant based on the presence of the causal gene underlying QTL5 / 7?.
[0267] Another embodiment of the invention concerns melon seeds obtainable or obtained from plants according to the invention, or seeds comprising plant cells according to the invention.
[0268] A further aspect of the present invention concerns melon plant fruits, plants, cells, seeds, plant tissues comprising cells comprising e.g. an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_06, inbetween SNP_02 and SNP_05, in-between SNP_03 and SNP_05, in-between SNP_02 and SNP_04 or inbetween SNP_03 and SNP_04.
[0269] In another embodiment the seeds, plants, cells, fruits, plant tissues comprise an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_01 and SNP_07, more preferably in-between SNP_02 and SNP_06, even more preferably in-between SNP_02 and SNP_05 or in-between SNP_03 and SNP_05, furthermore preferably in-between SNP_02 and SNP_04 and most preferably in-between SNP_03 and SNP_04.
[0270] In a further embodiment the plants, cells, seeds, fruits, plant tissues comprise an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant which comprises QTL5 / 7? (or at least the causal gene underlying QTL5 / 7?) and comprises the donor SNP nucleotide for one or more of SNP_01 to SNP_07, optionally for one or more of SNP_02 to SNP_06, e.g. for one or more of SNP_02 to SNP_05 or for one or more of SNP_03 to SNP_05, or for one or more of SNP_02 to SNP_04, or for SNP_03 and / or SNP_04.
[0271] Another embodiment of the invention concerns melon fruits obtainable or obtained from plants according to the invention, or fruits comprising plant cells according to the invention. Preferably melon fruits provided herein in one aspect are characterized in that they comprise an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant comprising the sequence of the donor plant in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_06, inbetween SNP_02 and SNP_05, in-between SNP_02 and SNP_04, in-between SNP_03 and SNP_06, inbetween SNP_03 and SNP_05 or preferably in-between SNP_03 and SNP_04 in heterozygous or homozygous state.
[0272] The preferred and further embodiments described herein for melon plant cells or melon plants according to the invention are applicable to also represent preferred and further embodiments of the melon fruits of melon plants according to the invention, accordingly.
[0273] A further aspect provided herein concerns melon plant propagation material comprising an introgression fragment on chromosome 5 from a ToLCNDV-ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV-ES resistant donor melon plant in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_05, in-between SNP_02 and SNP_04, SNP_03 and SNP_06, in-between SNP_03 and SNP_05 or in-between SNP_03 and SNP_04. Thus, melon plant propagation material is encompassed which comprises an introgression fragment on chromosome 5 from a ToLCNDV- ES resistant donor plant, wherein the introgression fragment comprises the sequence of the ToLCNDV- ES resistant donor melon plant which comprises QTL5 / 7? (or at least the causal gene underlying QTL5 / A) and comprises the donor SNP nucleotide for one or more of SNP_01 to SNP_07, optionally for one or more of SNP_02 to SNP_06, e.g. for one or more of SNP_02 to SNP_05 or for one or more of SNP_03 to SNP_05, or for one or more of SNP_02 to SNP_04, or for SNP_03 and / or SNP_04.
[0274] Another embodiment of the invention concerns melon plant propagation material obtainable or obtained from plants according to the invention, or melon plant propagation material comprising plant cells according to the invention.
[0275] The preferred and further embodiments described herein for plant cells or plants according to the invention are applicable to also represent preferred and further embodiments of the propagation material of melon plants according to the invention, accordingly.
[0276] The term “propagation material” comprises those components of the plant which are suitable for generating progeny via the vegetative (agamic) or generative (gamic, sexual) route. Suitable for vegetative propagation are, for example, cuttings, in vitro tissue, cell, protoplast, embryo or callus cultures, micropropagation methods, rhizomes or tubers. Other propagation material includes, for example, fruits, seeds, seedling, being homozygous or heterozygous for a chromosome 5 introgression fragment or for a modified endogenous gene (e.g. modified by gene editing or random mutagenesis) conferring ToLCNDV- ES resistance etc. The propagation material in one aspect takes the form of cuttings which are propagated by grafting to another rootstock or in vitro tissue culture material, in particular embryo cultures. In particular preferred is propagation material in the form of in vitro tissue culture material, particularly in vitro embryo cultures.
[0277] In one aspect non-propagating plant cells comprising the recombinant chromosome 5 or the modified endogenous gene as described herein are provided.
[0278] A further embodiment of the invention concerns a method for producing a ToLCNDV-ES resistant melon plant (especially resistant against resistance-breaking strains) comprising the following steps a) Selecting a ToLCNDV-ES resistant donor plant b) Crossing the donor plant selected in step a) with a recurrent plant sensitive to ToLCNDV-ES c) Obtaining seeds from the plants crossed in step b) and optionally d) Verifying if the plants grown from the seeds obtained in step c) are resistant to ToLCNDV-ES and / or comprise one or more of the SNPs from the donor plant selected from the group of SNP_01 , SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07, especially selected from SNP_02 to SNP_06; and / or comprise a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids: nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, preferably encoding the above protein.
[0279] A ToLCNDV-ES resistant donor plant in step a) in the method for producing a ToLCNDV-ES resistant melon plant according to the invention can be selected by infection of melon plants with ToLCNDV-ES, especially with a resistance breaking strain, and determining the level of symptoms of ToLCNDV-ES infected melon plants as described elsewhere herein. The same is applicable for verification in steps c) of the method for producing a ToLCNDV-ES resistant melon plant according to the invention, if a plant is ToLCNDV-ES sensitive or resistant, respectively.
[0280] In a preferred embodiment of the method for producing a ToLCNDV-ES resistant melon plant, the ToLCNDV-ES resistant donor plant in step a) comprises a fragment on chromosome 5 conferring ToLCNDV-ES resistance, the fragment comprising the sequence of the donor plant in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_06, in-between SNP_02 and SNP_05, in-between SNP_02 and SNP_04, in-between SNP_03 and SNP_06, in-between SNP_03 and SNP_05 or in-between SNP_03 and SNP_04. Most preferably the fragment on chromosome 5 conferring ToLCNDV-ES resistance comprises the sequence in-between SNP_03 and SNP_04. In a specifically preferred embodiment of the invention, the method for producing a ToLCNDV-ES resistant melon plant according to the invention the ToLCNDV-ES resistant donor plant in step a) comprises the fragment of chromosome 5 conferring ToLCNDV-ES resistance comprising the sequence in-between SNP_01 and SNP_07, in-between SNP_02 and SNP_06, in-between SNP_02 and SNP_05, in-between SNP_02 and SNP_04, in-between SNP_03 and SNP_06, in-between SNP_03 and SNP_05 or in-between SNP_03 and SNP_04, as found in (obtainable from) the seeds deposited under NCIMB 44139.
[0281] In a preferred embodiment of the invention the method for producing a ToLCNDV-ES resistant melon plant according to the invention is used for producing a plant comprising QTL5 / 7? in homozygous or heterozygous form. The preferred and further embodiments as described herein for the plants according to the invention are applicable accordingly to the method for producing a ToLCNDV-ES resistant melon plant comprising QTL5 / 7?.
[0282] Plants obtainable or obtained by a method for producing a ToLCNDV-ES resistant melon plant according to the invention are also an embodiment of the invention.
[0283] A further embodiment of the invention concerns methods for producing melon seeds comprising the following steps of: a) growing a melon plant comprising at least one chromosome 5 having an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, the introgression fragment comprising the sequence of the donor plant in-between SNP_03 and SNP_04 (and / or comprises the donor SNP for one or more of SNP_01 to SNP_07, especially for SNP_03 and / or SNP_04), and / or comprising QTL5 / 7?. and / or comprising the causal gene underlying QTL5 / 7? (which may be a modified endogenous gene of the TIR-NBS-LRR protein encoding gene disclosed herein or a gene identified in a wild donor), b) harvesting the fruits of the melon plants grown in step a) c) collecting the seeds from the fruits obtained in step b).
[0284] Seeds obtainable by the method for producing melon seeds according to the invention are also an embodiment of the invention. The seeds contain at least one copy of the introgression fragment comprising QTL5 / 7? or at least one copy of QTL5 / 7? or the causal gene underlying QTL5 / 7? or the endogenous modified gene encoding the TIR-NBS-LRR protein disclosed herein. Another embodiment of the invention concerns methods for producing hybrid melon seeds comprising the following steps a) providing a first inbred melon plant comprising at least one chromosome 5 having an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, the introgression fragment comprising the sequence of the donor plant in-between SNP_03 and SNP_04 (and / or comprises the donor SNP for one or more of SNP_01 to SNP_07, especially for SNP_03 and / or SNP_04), and / or comprising QTL5 / 7?. and / or comprising the causal gene underlying QTL5 / 7? (which may be a modified endogenous gene of the TIR-NBS-LRR protein encoding gene disclosed herein or a gene identified in a wild donor), b) providing a second inbred melon plant with or without a chromosome 5 having an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, the introgression fragment comprising the sequence of the donor plant in-between SNP_03 and SNP_04 (and / or comprises the donor SNP for one or more of SNP_01 to SNP_07, especially for SNP_03 and / or SNP_04), and / or comprising QTL5 / 7?. and / or comprising the causal gene underlying QTL5 / 7? (which may be a modified endogenous gene of the TIR-NBS-LRR protein encoding gene disclosed herein or a gene identified in a wild donor), c) crossing the plant provided in step a) with the plant provided in step b) d) selecting seeds obtained from the cross of step c).
[0285] The plant of step b) may, thus, in one aspect be a second inbred melon plant that is susceptible to ToLCNDV-ES, especially to resistance breaking strains, or it may be an inbred melon plant comprising QTL5 (e.g. as in variety Coliseo), whereby the hybrid melon comprises both QTL5 and QTL5r / >. Such a stack of both QTLs is particularly advantageous for conferring broad and durable resistance. Thus, in one aspect a cultivated melon plant is provided comprising both QTL5 / 7? (or the causal gene underlying QTL5rb, or the modified or mutated endogenous gene thereof) and QTL5, one on each chromosome 5 of the genome. In one aspect the cultivated melon plant is an Fl hybrid.
[0286] “Inbred plant” or “inbred line” shall mean in connection with the present invention plants which have undergone several generations of selfing and are highly uniform in respect to their genetic setup and phenotypic appearance.
[0287] As mentioned elsewhere herein, when reference is made to a plant, plant part, cell or tissue or fruit or seed comprising a sequence in-between two SNPs, this encompasses in one aspect that the resistant donor nucleotide is present for one or more of the SNP nucleotides disclosed herein, especially of one or both of the SNPs mentioned and / or of the SNPs lying in-between the SNPs mentioned, and optionally also of one or more of the remaining SNPs of the donor disclosed herein. In a preferred embodiment of the invention the inbred lines of steps a) and b) of the method for producing hybrid melon seeds according to the invention has the specific characteristics described as preferred and further embodiments of the plants according to the invention. The preferred and further embodiments as described herein for the plants according to the invention are applicable accordingly to the method for producing a hybrid melon seed according to the invention.
[0288] Hybrid seeds obtainable or obtained by the method for producing hybrid melon seeds according to the invention are also an embodiment of the invention.
[0289] A further embodiment of the present invention are methods for producing a melon fruit comprising the following steps a) growing a plant comprising at least one chromosome 5 having an introgression fragment from chromosome 5 of a ToLCNDV-ES resistant donor plant, the introgression fragment comprising the sequence of the donor plant in-between SNP_03 and SNP_04 and / or comprising QTL5 / A. and / or comprising the causal gene underlying QTL5 / 7? (which may be a modified endogenous gene of the TIR-NBS-LRR protein encoding gene disclosed herein or a gene identified in a wild donor), b) harvesting the fruits produced by the plants grown in step a).
[0290] The term “fruit” in its botanical meaning is commonly understood to be a seed-bearing structure developed from the ovary of angiosperm flowers.
[0291] Melon fruits obtainable or obtained by a method for producing a melon fruit according to the invention are also an embodiment of the invention.
[0292] Melon donor plants being resistant to ToLCNDV-ES (especially resistance breaking strains) can be identified with the aid of the SNP markers, in particular one or more or all of SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07 disclosed herein and / or QTL5 / 7?. and / or by the presence of the causal gene of QTL5r / >, as described herein.
[0293] In one aspect the present invention, therefore, for the first time enables a person skilled in the art to identify donor plants from which an introgression fragment conferring ToLCNDV-ES resistance to melon plants can be transferred into recurrent melon plants or into plants comprising QTL5, which does not confer resistance to resistance-breaking strains. QTL5 can, thus, be replaced by QTL5 / A in melon plants, such as in variety Coliseo Fl (Nunhems).
[0294] Melon donor plants can also be generated de novo by e.g. modifying the endogenous gene using e.g. gene editing methods or mutagenesis methods, so that the endogenous gene encodes a resistant TIR-NBS-LRR protein at the locus on chromosome 5. A further embodiment of the invention therefore pertains the use of one or more or all of SNP_01 , SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07 and / or the causal gene underlying QTL5 / A (e.g., any of the sequences provided herein, e.g. SEQ ID NO: 1 to 7, SEQ ID NO: 8, 11 or 12, or parts thereof), for identification of a ToLCNDV-ES resistant melon plant or parts thereof (such as cells, fruits, leaves), especially resistant against resistance-breaking strains. Preferably the use pertains the identification of ToLCNDV-ES resistant donor melon plants and / or recurrent melon plants, but also to the identification of breeding lines, cultivars or varieties comprising QTL5 / 7?. e.g. derived from the seeds deposited herein or from another wild donor or comprising an endogenous modified gene encoding a resistant TIR-NBS- LRR protein.
[0295] Another embodiment is the use of one or more or all of SNP_0I, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 or SNP_07 and / or QTL5 / 7? and / or the causal gene underlying QTL5 / 7? (e.g., any of the sequences provided herein, e.g. SEQ ID NO: 1 to 7, SEQ ID NO: 8, 11 or 12, or parts thereof) for introgression of ToLCNDV-ES resistance (especially resistance against resistance breaking strains) into a TolCNDV-ES susceptible melon plant and / or into a plant lacking QTL5 / 7? (e.g. comprising QTL5 at the locus), especially a cultivated melon line or variety.
[0296] Also, an embodiment of the invention is the use of one or more or all of SNP_0I, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 or SNP_07 and / or QTL5 / 7? and / or the causal gene underlying QTL5 / 7? (e.g., any of the sequences provided herein, e.g. SEQ ID NO: 1 to 7, SEQ ID NO: 8, 11 or 12, or parts thereof) in breeding ToLCNDV-ES resistant melon plants (especially resistance against resistance breaking strains).
[0297] Also provided is a method of screening plants or plant material or DNA derived therefrom for the presence of a fragment on chromosome 5 conferring TolCNDV-ES resistance. The method comprises the steps of: screening the genomic DNA for the SNP haplotype or genotype of one or more or all of SNP_01 , SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07 and / or QTL5 / 7? and / or the causal gene underlying QTL5 / 7\ and optionally selecting plants or plant material which comprise the resistant donor genotype of one or more or all of SNP_01, SNP_02, SNP_03, SNP_04, SNP_05, SNP_06 and SNP_07 and / or comprising QTL5 / 7? and / or comprising the causal gene underlying QTL5 / A.
[0298] In such screening and / or selection methods any of the SNP markers and / or sequences provided herein, or parts thereof, e.g. SEQ ID NO: 1 to 7, SEQ ID NO: 8, 11 or 12, or parts thereof, may be used.
[0299] Also provided is a method for producing a cultivated C. me lo plant comprising an introgression fragment on chromosome 5, wherein said introgression fragment comprises a ToLCNDV-ES QTL, comprising: a) crossing a first cultivated melon plant being susceptible to ToLCNDV-ES (especially to ToLCNDV-ES resistance breaking strains) with a second wild melon plant being resistant to ToLCNDV-ES (especially to ToLCNDV-ES resistance breaking strains), wherein said second melon plant comprises the CC or CX genotype for SNP_01 at nucleotide 81 of SEQ ID NO: 1, and / or the CC or CX genotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or GG or GX genotype when referring to the complement strand), and / or the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, and / or the AA or AX genotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand), and / or the TT or TX genotype for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or AA or AX genotype when referring to the complement strand) and / or the AA or AX genotype for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or TT or TX genotype when referring to the complement strand), and / or the CC or CX genotype for SNP_07 in SEQ ID NO: 7; and / or wherein the second wild melon plant comprises a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0300] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0301] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0302] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0303] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or wherein the second wild melon plant comprises the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11; b) collecting Fl seeds from said cross and backcrossing an Fl plant to the first melon plant to produce a backcross (BC1) population, or selfing said Fl plants one or more times to produce an F2 or F3 population, and optionally selfing the backcross population to produce a BC1S1 population, wherein said F2, F3, BC1 or BC1S1 plant comprises the CC or CX genotype for SNP_01 at nucleotide 81 of SEQ ID NO: 1, and / or the CC or CX genotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or GG or GX genotype when referring to the complement strand), and / or the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, and / or the AA or AX genotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand), and / or the TT or TX genotype for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or AA or AX genotype when referring to the complement strand) and / or the AA or AX genotype for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or TT or TX genotype when referring to the complement strand), and / or the CC or CX genotype for SNP_07 in SEQ ID NO: 7; and / or wherein said F2, F3, BC1 or BC1S1 plant comprises a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0304] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0305] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0306] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0307] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or wherein said F2, F3, BC1 or BC1S1 plant comprises the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11.
[0308] Also provided is a method for identifying or detecting a cultivated C. melo plant comprising an introgression fragment on chromosome 5, wherein said introgression fragment comprises a ToLCNDV- ES resistance allele, comprising: a) screening a Cucumis melo plant using a molecular marker assay which detects at least one of SNP marker selected from the group consisting of: SNP_01 in SEQ ID NO: 1, SNP_02 in SEQ ID NO: 2, SNP_03 in SEQ ID NO: 3, SNP_04 in SEQ ID NO: 4, SNP_05 in SEQ ID NO: 5, SNP_06 in SEQ ID NO: 6 and / or SNP_07 in SEQ ID NO: 7; and / or a molecular assay (e.g. PCR, sequencing, a molecular marker assay, etc.) which detects the presence of a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0309] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0310] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0311] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0312] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or a molecular assay (e.g. PCR, sequencing, a molecular marker assay, etc.) which detects the presence of the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11 and b) identifying and / or selecting a plant comprising the CC or CX genotype for SNP_01 at nucleotide 81 of SEQ ID NO: 1, and / or the CC or CX genotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or GG or GX genotype when referring to the complement strand), and / or the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, and / or the AA or AX genotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand), and / or the TT or TX genotype for SNP 05 at nucleotide 101 of SEQ ID NO: 5 (or AA or AX genotype when referring to the complement strand) and / or the AA or AX genotype for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or TT or TX genotype when referring to the complement strand), and / or the CC or CX genotype for SNP_07 in SEQ ID NO: 7; and / or identifying and / or selecting a plant comprising a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0313] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0314] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0315] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0316] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or identifying and / or selecting a plant comprising
[0317] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11.
[0318] A method of producing C. melo Fl hybrid plants comprising a ToLCNDV-ES resistance phenotype (especially resistance against resistance breaking strains) is provided comprising: a) crossing a first inbred melon plant comprising at least one recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment that confers ToLCNDV-ES resistance onto the first inbred melon plant when present in homozygous or heterozygous form (i.e. it comprises QTL5 / 7? in homozygous or heterozygous form) and wherein said introgression fragment is from a wild plant of the species Cucumis melo, with a second inbred melon plant with or without said at least one recombinant chromosome 5 or without QTL5 / 7? (but optionally with QTL5 instead) and b) collecting Fl hybrid seeds from said cross.
[0319] Further encompassed is a method for producing a melon plant comprising ToLCNDV-ES resistance on chromosome 5, said method comprising: a) screening a wild melon accession or several wild melon accessions using a molecular marker assay which detects at least one of the SNP marker selected from the group consisting of: SNP_01 in SEQ ID NO: 1, SNP_02 in SEQ ID NO: 2, SNP_03 in SEQ ID NO: 3, SNP 04 in SEQ ID NO: 4, SNP 05 in SEQ ID NO: 5, SNP 06 in SEQ ID NO: 6 and / or SNP_07 in SEQ ID NO: 7; and / or a molecular assay (e.g. PCR, sequencing, a molecular marker assay, etc.) which detects the presence of a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids
[0320] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0321] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0322] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0323] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or a molecular assay (e.g. PCR, sequencing, a molecular marker assay, etc.) which detects the presence of
[0324] - the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11; b) identifying and / or selecting a wild melon plant plant comprising the CC or CX genotype for SNP_01 at nucleotide 81 of SEQ ID NO: 1, and / or the CC or CX genotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or GG or GX genotype when referring to the complement strand), and / or the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, and / or the AA or AX genotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand), and / or the TT or TX genotype for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or AA or AX genotype when referring to the complement strand) and / or the AA or AX genotype for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or TT or TX genotype when referring to the complement strand), and / or the CC or CX genotype for SNP 07 in SEQ ID NO: 7; and / or identifying and / or selecting a wild melon plant comprising a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0325] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; - a methionine (M) at amino acid number 484 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0326] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0327] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8. or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or identifying and / or selecting a wild melon plant comprising the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11, c) optionally confirming ToLCNDV-ES resistance in a resistance assay, especially using a resistance breaking strain; d) and optionally introgressing said ToLCNDV-ES resistance from said wild accession into a cultivated melon plant.
[0328] A cultivated Cucumis melo plant, or part thereof, is provided comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment that confers ToLCNDV-ES resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: the CC or CX genotype for SNP_01 at nucleotide 81 of SEQ ID NO: 1, and / or the CC or CX genotype for SNP_02 at nucleotide 242 of SEQ ID NO: 2 (or GG or GX genotype when referring to the complement strand), and / or the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, and / or the AA or AX genotype for SNP_04 at nucleotide 101 ofSEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand), and / or the TT or TX genotype for SNP_05 at nucleotide 101 of SEQ ID NO: 5 (or AA or AX genotype when referring to the complement strand) and / or the AA or AX genotype for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 (or TT or TX genotype when referring to the complement strand), and / or the CC or CX genotype for SNP_07 in SEQ ID NO: 7, and optionally wherein said introgression fragment is, in one aspect, from a wild plant of the species Cucumis melo, said wild plant having an average ToLCNDV-ES disease score of at least 7.7, 7.8, 7.9, 8.0, preferably at least 9.0, on a scale of 1 = dead plant to 9 = no symptoms.
[0329] In one aspect the cultivated melon plant comprises at least the GG or GX genotype for the SNP_03 at nucleotide 81 of SEQ ID NO : 3 and / or the AA or AX genotype for SNP_04 at nucleotide 101 of SEQ ID NO: 4 (or TT or TX genotype when referring to the complement strand).
[0330] In one aspect the ToLCNDV-ES resistance QTL5 / 7? or the introgression fragment comprising the QTL5 / 7? is the obtainable from / can be obtained from / is as present in seeds of which a representative sample has been deposited under Accession Number NCIMB44139 or progeny thereof (whereby the progeny retain the ToLCNDV-ES resistance).
[0331] A cultivated Cucumis melo plant, or part thereof, is provided comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment that confers ToLCNDV-ES resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises: a gene encoding a protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0332] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0333] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0334] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8;
[0335] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; and / or the nucleotide sequence of SEQ ID NO: 11 or a sequence comprising at least 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 11; preferably encoding the above protein, and optionally wherein said introgression fragment is, in one aspect, from a wild plant of the species Cucumis melo, said wild plant having an average ToLCNDV-ES disease score of at least 7.7, 7.8, 7.9, 8.0, 8.5 preferably at least 9.0, on a scale of 1 = dead plant to 9 = no symptoms.
[0336] In one aspect the ToLCNDV-ES resistance QTL5 / A or the introgression fragment comprising the QTL5 / A is the obtainable from / can be obtained from / is as present in seeds of which a representative sample has been deposited under Accession Number NCIMB44139 or progeny thereof (whereby the progeny retain the ToLCNDV-ES resistance).
[0337] In a further aspect a melon plant (or plant part, e.g. cell) comprising QTL5 / A is generated de novo by random or targeted mutagenesis, by introducing one or more modifications into the susceptible gene on chromosome 5 at the same locus, in order to change the susceptible TIR-NBS-LRR protein into a resistant TIR-NBS-LRR protein.
[0338] In susceptible cultivated melon the locus on chromosome 5 comprises a gene which encodes the protein of SEQ ID NO: 10 (or a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% to SEQ ID NO: 10). This TIR-NBS-LRR protein is herein referred to as ‘susceptible protein’. In one aspect it can be changed into a ‘resistant protein’ by changing one or more (or all) of the four amino acid differences which are needed to make the protein a ‘resistant protein’, i.e. to confer resistance against ToLCNDV-ES. See Figure 2, where the four differences between the susceptible protein and the resistant protein are numbered from 1 to 4.
[0339] Either random mutagenesis, followed by selection (e.g. using TILLING) of the plant comprising the mutant allele, and / or targeted mutagenesis can be used to introduce one or more of changes 1 to 4 into a plant comprising the gene which encodes the susceptible protein of e.g. SEQ ID NO: 10, or a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% to SEQ ID NO: 10.
[0340] Therefore, in one aspect, a Cucumis melo plant, or part thereof, is provided comprising a modified allele of the gene encoding the TIR-NBS-LRR protein of SEQ ID NO: 10 (or a susceptible protein comprising at least 98%, 98.5%, 99.8% 99%, 99.2%, 99.5%, 99.8% identity to SEQ ID NO: 10), wherein the modified allele confers ToLCNDV-ES resistance, preferably ToLCNDV-ES resistance against resistance breaking strains, onto the Cucumis melo plant when the modified allele is present in homozygous or heterozygous form and wherein said modified allele encodes a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids
[0341] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 1 compared to the susceptible protein)
[0342] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 2 compared to the susceptible protein)
[0343] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 3 compared to the susceptible protein)
[0344] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8 (change number 4 compared to the susceptible protein). Thus, the modified allele encodes a modified protein comprises one or more or all of the following 4 amino acid changes compare to the susceptible protein of SEQ ID NO: 10, or to a susceptible protein comprising at least 98%, 98.5%, 99%, 99.5% or 99.8% to SEQ ID NO: 10:
[0345] 1. an insertion of two S (Serines) at the beginning of the protein, following the amino acid E9 (Glutamic acid number 9); i.e. the protein comprises 9 Serines (S) after E9, Serines are from amino acid 10 to 18 in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8 (while SEQ ID NO: 10 comprises only 7 Serines, from amino acid 10 to 16); see change number 1 of Figure 2;
[0346] 2. a change of amino acid V483 (Valine 483 of SEQ ID NO: 10) into M (Methionine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is M484; see change number 2 of Figure 2;
[0347] 3. a change of amino acid E628 (Glutamic acid 628 of SEQ ID NO: 10) into K (Lysine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is K629; see change number 3 of Figure 2;
[0348] 4. a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into H (Histidine) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is H679, see change number 4 of Figure 2; or a change of amino acid Y678 (Tyrosine 678 of SEQ ID NO: 10) into D (Aspartic acid) at the equivalent position in the protein which comprises at least 96%, 97%, 98% or 99% sequence identity to the protein of SEQ ID NO: 8; In SEQ ID NO: 8 the equivalent position is D679, see change number 4 of Figure 1 or Figure 2.
[0349] In one aspect the endogenous genomic sequence encoding the susceptible protein, is modified in the cultivated melon plant, so that the genomic sequence encodes a resistant protein instead of a susceptible protein and thus the genomic sequence encodes a protein comprising one or more of the four changes listed above.
[0350] For example, Figure 4 shows how SEQ ID NO: 36, encoding the susceptible protein of SEQ ID NO: 10, can be modified to convert it into a resistant protein.
[0351] For example, change number 1 is an insertion of two times the codon TCT, which encodes a Serine, resulting in two Serines being present in the resistant protein. Change number 2 is the change of codon GTG (Valine, V) to ATG (Methionine, M), change number 3 is the change of codon GAG (Glutamic Acid, E) to AAG (Lysine, K) and change number 4 is the change of codon TAT (Tyrosine, Y) to CAT (Histidine, H).
[0352] Therefore, in one aspect, a cultivated Cucumis melo plant, or part thereof (e.g. a cell or tissue or fruit or seed), is provided comprising an allele encoding a TIR-NBS-LRR protein, wherein the protein confers ToLCNDV-ES resistance, preferably ToLCNDV-ES resistance against resistance breaking strains, onto the Cucumis melo plant when the allele is present in homozygous or heterozygous form and wherein said allele encodes a protein comprising at least 96% , 97%, 98% or 99% sequence identity to SEQ ID NO: 8 and wherein said protein preferably comprises at least one, preferably at least two, three or all four of the following amino acids:
[0353] - nine Serines (S) from amino acid 10 to amino acid 18 of SEQ ID NO: 8, or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 1 compared to the susceptible protein)
[0354] - a methionine (M) at amino acid number 484 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 2 compared to the susceptible protein)
[0355] - a Lysine (K) at amino acid number 629 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8; (change number 3 compared to the susceptible protein)
[0356] - a Histidine (H) or Aspartic Acid (D) at amino acid number 679 of SEQ ID NO: 8 or at the equivalent position in a sequence comprising at 96% sequence identity to SEQ ID NO: 8 (change number 4 compared to the susceptible protein).
[0357] Therefore, in one aspect a cultivated melon plant or seed or plant part may comprise a mutant or modified TIR-NBS-LRR allele, wherein the mutant or modified allele (also referred to as modified allele herein) is produced by random mutagenesis or targeted mutagenesis, such as CRISPR based methods. Random mutagenesis may for example be chemical induced (e.g. EMS treatment) or radiation induced mutagenesis or other methods, whereby mutations are randomly induced in the genome and then plants or plant parts comprising mutations in the endogenous TIR-NBS-LRR gene can be screened for and identified. Targeted mutagenesis are methods whereby mutations are specifically introduced into a target gene, such as the TIR-NBS-LRR gene, using e.g. Crispr-Cas9, or Crispr-Cpfl or other known methods. It is noted that using such methods, the mutant alleles described herein can be generated without undue burden.
[0358] When referring herein to a melon plant this encompasses in one aspect a seed from which the plant can be grown, i.e. the embryo in the seed may comprise at least one copy (or two copies) of mutant allele as described.
[0359] In one aspect the melon plant comprising the mutant allele or modified allele is not produced exclusively by an essentially biological process, meaning that the mutant allele has at one point been generated by human intervention. If such a human generated mutant allele is transferred from one plant to another by crossing and selection, then the patent covers plants comprising the mutant allele, even if the plant itself has been generated solely by crossing and selection. Preferably in one aspect the plant is not transgenic, and e.g. any construct used to modify the endogenous gene, in case of e.g. targeted gene editing, has been removed from the genome. Also in one aspect the plant is not a transgenic plant in that the mutant allele has not been introduced from the outside and integrated anywhere in the plant genome using plant transformation techniques, but rather the mutant allele is an endogenous, TIR-NBS-LRR allele which has been mutated or modified (using e.g. targeted or random mutagenesis) at the locus on chromosome 5 in the genome where the TIR-NBS-LRR allele is located.
[0360] In one aspect, especially in respect of the European Patent Convention, the plant according to the invention is “not obtained exclusively by an essentially biological process”.
[0361] In one aspect the endogenous mutant or modified TIR-NBS-LRR allele is, thus, an induced mutant allele.
[0362] In one aspect the plant does not comprise any chimeric construct in its genome.
[0363] Detection and / or Selection methods
[0364] Provided is a method of selecting a Cucumis melo plant (especially a cultivated C. melo), or plant part, comprising a chromosome 5, said chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / 7? located in between a Cytosine for SNP O 1 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form, said method comprises selecting a plant or plant part comprising one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a) a Cytosine for SNP_02 at nucleotide 242 of SEQ ID NO: 2, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 2 (or a Guanine at nucleotide 242 in the complement sequence of SEQ ID NO: 2 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 2); b) a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; c) an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4 (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 4 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 4); d) a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5 (or an Adenine at nucleotide 101 in the complement sequence of SEQ ID NO: 5 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 5); e) an Adenine for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 6 (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 6 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 6).
[0365] In another aspect a method of selecting a Cucumis melo plant, or plant part, is provided, wherein said plant comprises a chromosome 5, said chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / A located in between a Cytosine for SNP 01 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form, said method comprises selecting a plant or plant part comprising one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a) a Cytosine for SNP_01 at nucleotide 81 of SEQ ID NO: 1, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 1; b) a Cytosine for SNP_02 at nucleotide 242 of SEQ ID NO: 2, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 2; (or a Guanine at nucleotide 242 in the complement sequence of SEQ ID NO: 2 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 2); c) a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; d) an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 4 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 4); e) a Thymine for SNP_05 at nucleotide 101 of SEQ ID NO: 5, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5; (or an Adenine at nucleotide 101 in the complement sequence of SEQ ID NO: 5 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 5); f) an Adenine for the SNP_06 at nucleotide 101 of SEQ ID NO : 6 or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 6; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 6 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 6). g) a Cytosine for SNP_07 at nucleotide 101 of SEQ ID NO: 7 or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 7.
[0366] For selection for example a KASP assay or other genotyping assay may be used, see e.g. Examples.
[0367] In one aspect, therefore, a genotyping assay is provided for genotyping melon plants, seeds, plant parts, cells or tissues, comprising the steps: a) providing genomic DNA of one or more melon plants or a population of plants (e.g. breeding population, F2 population, backcross population etc.), and b) carrying out a genotyping assay which detects the presence of one or more of the markers:
[0368] - a Cytosine for SNP_02 at nucleotide 242 of SEQ ID NO: 2, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 2; (or a Guanine at nucleotide 242 in the complement sequence of SEQ ID NO: 2 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 2);
[0369] - a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3;
[0370] - an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 4 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 4);
[0371] - a Thymine for SNP_05 at nucleotide 101 ofSEQ ID NO: 5, orthe equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5; (or an Adenine at nucleotide 101 in the complement sequence of SEQ ID NO: 5 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 5); an Adenine for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 6; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 6 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 6), and c) selecting a plant, seed, plant part, cell or tissue comprising one or more of the SNP nucleotides of step b).
[0372] The melon plants may be wild melon accessions or cultivated melon plants.
[0373] In another aspect, a genotyping assay genotyping melon plants, plant parts, cells or tissues, comprising the steps is provided, comprising the steps: a) providing genomic DNA of one or more melon plants or a population of plants (e.g. breeding population, F2 population, backcross population etc.), and b) carrying out a genotyping assay which detects the presence of one or more of
[0374] - a Cytosine for SNP_02 at nucleotide 242 of SEQ ID NO: 2, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 2; (or a Guanine at nucleotide 242 in the complement sequence of SEQ ID NO: 2 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 2);
[0375] - a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3;
[0376] - an Adenine for SNP_04 at nucleotide 101 of SEQ ID NO: 4, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 4 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 4);
[0377] - a Thymine for SNP_05 at nucleotide 101 ofSEQ ID NO: 5, orthe equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5; (or an Adenine at nucleotide 101 in the complement sequence of SEQ ID NO: 5 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 5);
[0378] - an Adenine for the SNP_06 at nucleotide 101 of SEQ ID NO: 6 or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 6; (or a Thymine at nucleotide 101 in the complement sequence of SEQ ID NO: 6 or at the equivalent nucleotide in a sequence comprising at least 95% sequence identity to the complement sequence of SEQ ID NO: 6), and optionally c) selecting a plant, seed, plant part, cell or tissue comprising one or more of the SNP nucleotides of step b) in homozygous form.
[0379] Step a) may comprise isolation of genomic DNA from the plant, seeds, plant part, cell or tissue to be analyzed in the genotyping assay. Often crude DNA extractions methods can be used, as known in the art.
[0380] Step b) preferably comprises a bi-allelic genotyping assay, which makes use of allele-specific primers and / or allele-specific probes.
[0381] In another aspect a method of selecting a Cucumis melo plant comprising a chromosome 5 is provided, said chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / 7? located in between a Cytosine for SNP 01 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form, said method comprises selecting a plant or plant part comprising a gene encoding the protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 located in between SNP_03 at nucleotide 81 of SEQ ID NO: 3, corresponding to nucleotide 25.956.264 of chromosome 5 of the melon genome and SNP_04 at nucleotide 101 of SEQ ID NO: 4 corresponding to nucleotide 26.040.072 of chromosome 5 of the melon genome.
[0382] In the above method the gene encodes in one aspect a protein comprising at least 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 8 and comprises one or more of the following amino acids: a) Amino acid number 10 to amino acid number 18 are Serines (S) b) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) c) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) d) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D). Various methods can be used to select the plant or plant part comprising the gene mentioned. Selection can be based on genotyping methods (e.g. KASP assay), sequencing of the gene, mRNA (or cDNA) analysis, etc.
[0383] In a further aspect a method is provided of modifying the endogenous gene on melon chromosome 5, encoding a protein of SEQ ID NO: 10 (or a susceptible protein comprising at least 98%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%, 99%, 99.5%, 99.8% sequence identity to SEQ ID NO: 10), by targeted gene editing or by induced by mutagenesis, such as induced by radiation or chemical mutagens, whereby the gene is modified so that the encoded protein comprising at least 96% sequence identity to SEQ ID NO: 8 and preferably comprises one or more of the following amino acid changes: a) Amino acid number 10 to amino acid number 18 are Serines (S) b) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) c) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) d) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).
[0384] In this method susceptible melon plants or seeds or plant parts, which comprise a TIR-NBS-LRR gene on chromosome 5 which encodes a ToLCNDV-ES susceptible protein, e.g. the protein of SEQ ID NO: 10 or a susceptible protein comprising at least 98%, 98.1%, 98.2%, 98.3%, 98.4%, 98.5%, 98.6%, 98.7%, 98.8%, 98.9%, 99%, 99.5%, 99.8% sequence identity to the susceptible protein of SEQ ID NO: 10, are e.g. treated with a mutagenic agent (e.g. radiation or chemical mutagen), or mutagenized plants, seeds or plant parts are provided, and mutant alleles in the gene are selected.
[0385] Alternatively, targeted gene editing is used to induce modifications in the gene encoding the susceptible protein. Thus, e.g. CRISPR based methods can be used to modify the endogenous TIR-NBS-LRR gene on chromosome 5.
[0386] A method for production of a cultivated melon plant comprising ToLCNDV-ES resistance is provided, comprising the steps of: a) introducing random or targeted mutations (e.g. using Crispr based methods) into one or more melon plants, plant parts or seeds; or providing a population of mutant plants or seeds (e.g. a TILLING population, e.g. M2, M3, M4 or further generation), b) selecting a plant comprises a mutant allele of a TIR-NBS-LRR gene on chromosome 5, e.g. a mutant allele whereby the allele is modified so that the encoded protein comprising at least 96% sequence identity to SEQ ID NO: 8 and preferably comprises one or more of the following amino acid changes: - Amino acid number 10 to amino acid number 18 are Serines (S)
[0387] - the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M)
[0388] - the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K)
[0389] - the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D), c) optionally removing any transgenic construct (e.g. CRISPR construct) from the plant, and / or d) optionally generating a plant homozygous for the mutant allele and analysing whether the plant is resistant against ToLCNDV-ES, especially resistance-breaking strains of ToLCNDV-ES.
[0390] Modified or mutated plants and plant parts obtained by or obtainable by any of the above methods are also encompassed herein, as are seeds from which such plants can be grown.
[0391] Transgenic plants
[0392] In another aspect, also transgenic plants are provided comprising a transgene which encodes a resistant TIR-NBS-LRR protein, e.g. the protein of SEQ ID NO: 8 or a protein comprising at least 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 8 preferably comprises one or more (or all) of the following amino acid: a) Amino acid number 10 to amino acid number 18 are Serines (S) b) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) c) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) d) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).
[0393] The transgenic plant may be of any species, in one aspect it is Cucumis melo, preferably cultivated melon.
[0394] The transgene may be inserted anywhere in the melon genome. As the gene is dominant, it does not matter that chromosome 5 comprises the gene encoding the susceptible TIR-NBS-LRR protein.
[0395] Seed deposit information
[0396] A representative sample of seeds of a ToLCNDV-ES resistant donor melon, designated Cucumis melo ToLQTL5RB, was deposited by Nunhems B.V. on 20 April 2023 at the NCIMB Ltd. (Ferguson Building, Craibstone Estate, Bucksbum Aberdeen, Scotland AB21 9YA, UK) according to the Budapest Treaty, under the Expert Solution (EPC 2000, Rule 32(1)). Seeds were given the following deposit numbers NCIMB 44139.
[0397] The Applicant requests that samples of the biological material and any material derived therefrom be only released to a designated Expert in accordance with Rule 32(1) EPC or related legislation of countries or treaties having similar rules and regulation, until the mention of the grant of the patent, or for 20 years from the date of fding if the application is refused, withdrawn or deemed to be withdrawn.
[0398] Access to the deposit will be available during the pendency of this application to persons determined by the Director of the U.S. Patent Office to be entitled thereto upon request. Subject to 37 C.F.R. § 1.808(b), all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of the patent. The deposit will be maintained for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent whichever is longer, and will be replaced if it ever becomes nonviable during that period. Applicant does not waive any rights granted under this patent on this application or under the Plant Variety Protection Act (7 USC 2321 et seq.).
[0399] Description of sequences
[0400] Characters other than G (Guanine), A (Adenine), T (Thymine) and C (Cytosine) have the following meaning in the SEQ ID NOs shown in the sequence listing:
[0401] R: G or A
[0402] Y: T or C
[0403] M: A or C
[0404] K: G or T
[0405] S: G or C
[0406] W: A or T
[0407] H: A or C or T
[0408] B: G or T or C
[0409] V: G or C or A
[0410] D: G or A or T
[0411] N: G or A or T or C In SEQ ID NO: 1 to SEQ ID NO: 7 the SNP nucleotide of the resistant donor is shown in bold, underlined. A SNP markers can be designed either to the forward strand (+ strand) of the double stranded DNA or to the reverse strand (- strand) of the DNA, which strands have been assigned as forward or reverse with respect to the reference genome sequence. For example, SEQ ID NO: 4 is, in the reference genome sequence of melon (found on melonomics.net, DHL92 version 4), the reverse strand, and the SNP_04 is ‘T’ on the reverse strand and is an ‘A’ on the forward strand (the forward strand is the complementary strand of SEQ ID NO: 4). The SNP haplotype or SNP donor nucleotide is preferably given in relation to the forward strand in the reference genome, irrespective of whether the sequence provided herein is the reverse strand.
[0412] SEQ ID NO 1 : Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_01.
[0413] SEQ ID NO: 1 (forward strand in reference genome):
[0414] TCAAAGGAGAGATTCTGATCTTCACTGCCAGGGCCAGCTTTCCTTTTTATTCGGTAGTATTT CTTTTGGTAATATTTGTACGGGCTGACTCTTTTAGATGATGAAGCTGCTTTATTAGCCGCAA ATTGTTCTATCCTTTCATTAATGCTGAGATTTTGTCT
[0415] SEQ ID NO 2: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_02.
[0416] SEQ ID NO: 2 (reverse strand in reference genome)
[0417] CATCCACCTTTACAACATTCCTGCACCATGAGATCAGTAAATAGTTATAAGTAATATATATT ATATGAATGAAATTAAATATACATGAGCTAGAGATAATGGTGAAGTCATGAGAAAGAGAT ATGGTACGCACCGCAGAATTACCACAAGATATGAAATCAGCTAAGTTGTCGGGAAATCTAG CCAATGATTTGCATCCTGCGGCACTCGTACAAATTACACCTTCTGGAACCTTTGAAATCTCT TCRAGCAACTCACAATCCATTGTATAAAGATATTTCAGGGATTTAAAATTAATAATACAYG AGGGTAKTCTACAAAAGTTGTTTTCGGACAAGTCCAACTCTTTCAAYGAAGGGGCAACATA AACAATTGTTTCTAAGAAATCCAAATTTGTTATCTTGCAACCTACAAGACGTAACTTGGTTA GGTAAAAAAGTGAGGAAGGTAAAGACGGATGAAGMCTCC
[0418] SEQ ID NO 3: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_03.
[0419] SEQ ID NO 3 (forward strand in reference genome)
[0420] TACAAGTGACAAAACCGAGTCGATCCGTAGTGAGCACGAAGATTTGTTTGTCAAAGTTAAT
[0421] TCTTTAGTTAATGAGATAAGTACGCGAAGATGGTAAAAAAGAACGAAAACAGGGACCCAC
[0422] ATCCTTTTGACTTGATTGCAGAGAGAAGATGAAAGAAATT
[0423] SEQ ID NO 4: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_04. SEQ ID NO 4 (reverse strand in reference genome)
[0424] TCTCATTTTCAATGCCATGTTTTTTTTACTCATTTATCAACGAGCACACTGTACAATTTTTAA
[0425] GATCCATTCTCTCTCAAGATGCCATTTAATTGTGTGTACATCATTCTTTAATTTTGATATGAT
[0426] TATGTACTTGACAACAGGAGGGAGGCTGATCTTATTTGAGATCTTGTTAAAGAAGTGTTAT
[0427] CTACAATAAATCGC
[0428] SEQ ID NO 5: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_05.
[0429] SEQ ID NO: 5 (reverse strand in reference genome)
[0430] CACTATAAACCTTATTCTTTTTAAGAAATCATGTTTCAAACCCAATAAAAGTAAGTTGATAC
[0431] ATTGTCCTTGTAGAAATTGTCAAAACTAAATACAGTAATAAACAACTTTAAAATTTTGTATC
[0432] ATGTTATATTACAATATGGCCCATCTCACGTTTTCCCAATTGTCTTGAGAATTCAATGATAT
[0433] TTCATTCCAATATAA
[0434] SEQ ID NO 6: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_06.
[0435] SEQ ID NO: 6 (reverse strand in reference genome)
[0436] CCCATCTTCCCTTTGCCACTCTAAAATAATAGAGGTTATCTTTTGTGTTTATTATTACATTTG
[0437] AGTAAACTTATCAAATAAAATTGGGGAGTAGGAGATCAACTGACGGAGAGAAATAAAGGG
[0438] GAGAAGAAGGAAAATCCAGAAGTGAAAATGGAGGAAAAGGAATGGAAAAAAATTAGAGG
[0439] GTAAAGAATGAGAAAACAA
[0440] SEQ ID NO 7: Sequence of the ToLCNDV-ES resistant donor plant comprising SNP_07.
[0441] SEQ ID NO: 7 (forward strand in reference genome)
[0442] TTATCTTCTTGAACTGCCGAAGAAACTGCTTCTTTCTCCTTACCTTCATGTTCAGTCGAGAAC
[0443] TCTTCTACATTCCCCTCCGTTTTCTCTACATCAGACACACCTACTTCCTTCTCCTCACATTCA
[0444] GGCAAAGCAGAATCTGCTTCCATATTTGAATCTTG
[0445] SEQ ID NO 8: TIR-NBS-LRR protein of ToLCNDV-ES resistant donor of the instant application
[0446] MGSSALPVESSSSSSSSSPNFLYYYDYDVFFSFRGEDTRSSFISHLHMALRLKGVNVFID
[0447] DKLKRGDQISESLLKSIERSRLSLVIFSKNYASSTWCLDELVKIIEYKKSKSQAVLPVFY
[0448] KVDPSEVRKQTGGFGEALAKHEANKLLTNKIQPWKEALTFAAGLSGWDLANCKDEAELIQ
[0449] EIVKRVLSVLNPMQLLHVAKHPVGIDFRLRKIEELVSHIGSEGVNMVGMYGIGGIGKTTL AKALYNKIANQFEGCCFLQDVRREASKHGLVKLQETLLNDILKEDLKVVSRDRGINIIRS
[0450] RLCSKKVLIVLDDVDDREQLEALVGGRDWFGRGSKIIVTTRNDHLLSSHGFDKKHKIQEL
[0451] NQDHALELFSWHASKKSHPSSNYLCLSERATNYCKGLSLALVVLGSFLRGRDQAEWNCIL
[0452] DEFETSLRKDIKDVLQLSFDGLEDKAKDIFLDISCLLVGEEYNCAKKMLSACHLNIDFGI
[0453] MILMDLSLVIVETDRVQMHELIQQMGCSIVHNESSEPGKRSRLWLVQDIWEVFVNNSGTD
[0454] AVKAIKLDLPNPTKLNVDPQAFRSMKNLRLLIIRNAQFCRKIKYLPNSLKWIEWLGFAHR
[0455] SLPSCFITKNLVGLDLRHSSIKRFGKRLKGCERLKHVDLSYSTLLEQINDFSPASNLEEL
[0456] HLINCTNLGMIDKSVFSLHKLSVLNLDGCCNLQKLPRGYFMLSSLKELNLCYCKKLEKIP
[0457] DLSAASNLKRLYLQECTNLRVIHESVGSLDKLNHLDLRQCTKLVKLPSYLRLKSLSNLLL
[0458] SGCCKLESFPTIAENMKSLRELDMDFTAIKELPSSIGYLTNLSILKLNGCTNLISLPNTI
[0459] YLLRNLENLLLSGCSIFGMFPHTWDPTIPTIQQVCSPSNMMETASWSLEFPHLLVPNESL
[0460] CAHFTLLDLESCNISNAKFLELLCDVAPFLSDLRLSENKFSSLPSCLHKFMSLWNLELRN
[0461] CKFLQEIPNLPENIQKMDASGCESLARNPDNIVDIISKKQDLTLGEISREFLLTGIEIPE
[0462] WFSYKTTSNLVTASFRHYPDMERTLAACVSFKVNGDSSKRGAQISCSIFICSKLHSSFSR
[0463] PFLPSKSEYMWLVTTSLAWGSMEVNDWNKVLVWFEVHEAHGEVNVTITRYGVHVTEELHG
[0464] IQMDVKWPMVNYADFYQLEKLQSLDIEDLLLKSFLETVSCLSNSKAAMLHAGNYDPEAII
[0465] DSNIQPMIFPLHVTNNDGTYICGGMGGTALANSLCNKFKGMEGQCGEALDNSTSFFHIKR
[0466] RQLLSYSWSPAVHHRKCGDGERGTNITTHTISSKRYLILLREAKSYQDVHDWFYTHCWIK
[0467] ASYCSYDGRGDGVILIEGVDTSLL
[0468] SEQ ID NO 9: TIR-NBS-LRR protein of ToLCNDV-ES resistant donor of US11591611 / NCIMB42585
[0469] MGSSALPVESSSSSSSSSPNFLYYYDYDVFFSFRGEDTRSSFISHLHMALRLKGVNVFID
[0470] DKLKRGDQISESLLKSIERSRLSLVIFSKNYASSTWCLDELVKIIECMKPKGQLVLSVFY KVDPSVVWKQTGGFGEALAKHEATKLTTNKIKPWKEALTIAAGLSGWDLANCKDEAELIQ
[0471] EIVKRVLSVLNPMQLLHVAKHPVGIDFRLRKIEELVSHIGSEGVNMVGMYGIGGIGKTTL
[0472] AKALYNKIANQFEGSCFLQDVRREASKHGLVKLQETLLHDILKEDLKVVSRDRGINIIRS
[0473] RLCSKKVLIVLDDVDDREQLEALVGGRDWFGRGSKIIVTTRNEHLLFSHGFDDQKHKIQE
[0474] LNQDHALELFSWHAFKKSHPSSNYLGLSERATNYCKGLSLALVVLGSFLRGRDQAEWNCI
[0475] LDEFETSLRKDIKDVLQLSFDGLEDKAKEIFLDISCLLVGEEINCAKKMLSACHLNIDFE
[0476] IMILMDLSLVTIETDRVQMHELIQQMGRSIVHNESSEPGKRSRLWLVQDIWEVFVNNSGT
[0477] DAVKAIKLDLPNPTKLNVDPQAFRSMKNLRLLIIRNAQFCRKIKYLPNSLKWIEWRGFAH
[0478] RSLPSCFITKNLVGLDLRHSSIKRFGKRLKGCERLKHVDLSYSPLLEKIPNLSAASNLEQ
[0479] LYLINCKNLGMIDKSVFSLDKLNVLNLDGCCNLQKLPRGYFMLSSLRYLNLSYCKKLEKI
[0480] PDLSAASNLKRLYLQECTNLRVIHESVGSLDKLDHLDLRQCTKLVKLPSYLRLKSLEYLS
[0481] LSGCCKLESFPTIAENMKSLWGLDLDFTAIKELPSSIGYLTKLSILKLNGCTNLISLPNT
[0482] IYLLRNLENLLLSGCSIFGMFPHTWDPTIPTIQQVCSPSKMMETASWSLEFPDLLVPNES
[0483] LCAHFTLLDLESCNISNAKFLELLCDVAPFLSDLRLSENKFSSLPSCLHKFMSLWNLELR
[0484] NCKFLQEIPNLPENIQKMDASGCESLARNPDNIVDIISKKQDLTLGEISREFLLTGIEIP
[0485] EWFSYKTTSNLVTASFRHYPDMERTLAACVSFKVNGDSSKRGAQMSCSIFICSKLHSSFS
[0486] RPFLPSKSEYMWLVTTSLAWGSMEVNDWNKVLVWFEVHEAHSEVNATITRCGVHVTEELH
[0487] GIQMDVKWPMVNYADFYQLEKLQSLDIEDLLLKSFLETVSCLSNSKAAMLHAGNYDPEAI
[0488] IDSNIQPMIFPLHVTYNGETVICGMEGMGDTTLANSLCNKFKGMEGQCGEALDNSTSFFH
[0489] IKRRQLLSYSWSPAVHHRKCGDGERGTNITTHTISSKRYLILLREAKSYQDVHDWFYTHC
[0490] WIKASYCSYDGRGDGVFLIKGVDTSLL
[0491] SEQ ID NO 10: TIR-NBS-LRR protein of reference genome DHL92 MGSSALPVESSSSSSSPNFLYYYDYDVFFSFRGEDTRSSFISHLHMALRLKGVNVFID
[0492] DKLKRGDQISESLLKSIERSRLSLVIFSKNYASSTWCLDELVKIIEYKKSKSQAVLPVFY
[0493] KVDPSEVRKQTGGFGEALAKHEANKLLTNKIQPWKEALTFAAGLSGWDLANCKDEAELIQ
[0494] EIVKRVLSVLNPMQLLHVAKHPVGIDFRLRKIEELVSHIGSEGVNMVGMYGIGGIGKTTL
[0495] AKALYNKIANQFEGCCFLQDVRREASKHGLVKLQETLLNDILKEDLKVVSRDRGINIIRS
[0496] RLCSKKVLIVLDDVDDREQLEALVGGRDWFGRGSKIIVTTRNEHLLFSHGFDDQKHKIQE
[0497] LNQDHALELFSWHAFKKSHPSSNYLGLSERATNYCKGLSLALVVLGSFLRGRDQAEWNCI
[0498] LDEFETSLRKDIKDVLQLSFDGLEDKAKDIFLDISCLLVGEEYNCAKKMLSACHLNIDFG
[0499] IMILVDLSLVTIETDRVQMHELIQQMGRSIVHNESSEPGKRSRLWLVQDIWEVFVNNSGT
[0500] DAVKAIKLDLPNPTKLNVDPQAFRSMKNLRLLIIRNAQFCRKIKYLPNSLKWIEWRGFAH
[0501] RSLPSCFITKNLVGLDLRHSSIKRFGKRLEGCERLKHVDLSYSTLLEQINDFSPASNLEE
[0502] LHLINCTNLGMIDKSVFSLYKLSVLNLDGCCNLQKLPRGYFMLSSLKELNLCYCKKLEKI
[0503] PDLSAASNLKRLYLQECTNLRVIHESVGSLDKLNHLDLRQCTKLVKLPSYLRLKSLSNLL
[0504] LSGCCKLESFPTIAENMKSLRELDMDFTAIKELPSSIGYLTNLSILKLNGCTNLISLPNT
[0505] IYLLRNLENLLLSGCSIFGMFPHTWDPTIPTIQQVCSPSKMMETASWSLEFPHLLVPNES
[0506] LCAHFTLLDLESCNISNAKFLELLCDVAPFLSDLRLSENKFSSLPSCLHKFMSLWNLELR
[0507] NCKFLQEIPNLPENIQKMDASGCESLARNPDNIVDIISKKQDLTLGEISREFLLTGIEIP
[0508] EWFSYKTTSNLVTASFRHYPDMERTLAACVSFKVNGDSSKRGAQISCSIFICSKLHSSFS
[0509] RPFLPSKSEYMWLVTTSLAWGSMEVNDWNKVLVWFEVHEAHSEVNATITRCGVHVTEELH
[0510] GIQMDVKWPMVNYADFYQLEKLQSLDIEDLLLKSFLETVSCLSNSKAAMLHAGNYDPEAI
[0511] IDSNIQPMIFPLHVTNNDGTYICGGMGGTALANSLCNKFKGMEGQCGEALDNSTSFFHIK
[0512] RRQLLSYSWSPAVHHRKCGDGERGTNITTHTISSKRYLILLREAKSYQDVHDWFYTHCWI
[0513] KASYCSYDGRGDGVILIEGVDTSLL SEQ ID NO 11 : genomic DNA encoding the TIR-NBS-LRR protein of SEQ ID NO: 8 of the ToLCNDV-
[0514] ES resistant donor of the instant invention
[0515] ATGGGTTCTTCTGCTCTTCCAGTTGAATCTTCTTCT
[0516] TCTTCTTCTTCTTCTTCTCCCAACTTTCTCTATTACTACGATTATGATGTGTTTTTTAGT
[0517] TTCAGAGGAGAAGACACTCGCTCCAGTTTCATCAGTCATCTTCATATGGCCTTGCGTCTA
[0518] AAGGGAGTCAACGTCTTCATAGACGACAAACTCAAAAGGGGTGACCAAATCTCTGAGTCT
[0519] CTTCTCAAATCTATAGAGCGATCTAGACTTTCACTCGTTATTTTCTCTAAAAATTATGCA
[0520] TCTTCAACTTGGTGTTTGGATGAACTGGTGAAAATAATTGAGTATAAAAAATCCAAAAGT
[0521] CAAGCGGTTTTGCCGGTGTTCTACAAGGTGGATCCGTCCGAGGTTCGAAAACAAACCGGT
[0522] GGGTTTGGGGAAGCATTAGCCAAACATGAAGCTAATAAGTTATTGACCAACAAGATTCAA
[0523] CCATGGAAGGAAGCTTTGACTTTTGCTGCTGGTTTGTCTGGTTGGGATCTAGCAAATTGG
[0524] TATTTCTTTTTTTAATTTCCCAAGACTCATTGTCTAAGTGAAGTTTAAATTTATCTACTA
[0525] TTTCCTATTTTCATTTTTTTTTTTTGTATGATGTTACTTTACAACAGCAAGGATGAGGCT
[0526] GAACTTATCCAAGAAATTGTTAAACGAGTGTTGTCTGTATTAAATCCAATGCAATTACTA
[0527] CATGTAGCCAAGCATCCAGTTGGAATTGATTTTCGATTAAGGAAAATTGAGGAGTTGGTC
[0528] TCTCATATTGGGTCCGAGGGTGTTAACATGGTGGGGATGTATGGCATTGGAGGCATTGGT
[0529] AAGACCACTTTAGCTAAGGCTTTGTACAACAAAATTGCTAACCAATTTGAAGGATGTTGC
[0530] TTTCTACAAGATGTTAGACGAGAAGCTTCAAAGCATGGGCTCGTTAAACTACAAGAAACC
[0531] TTACTCAATGACATCTTAAAGGAGGATTTGAAGGTTGTCAGCCGTGATAGAGGAATTAAC
[0532] ATCATAAGGAGTAGACTGTGTTCAAAGAAAGTTCTTATAGTTCTTGATGATGTGGATGAT
[0533] CGTGAGCAATTAGAAGCACTGGTTGGTGGTCGTGATTGGTTTGGTCGAGGTAGCAAAATC
[0534] ATTGTGACGACAAGGAATGATCATTTACTTTCTAGCCATGGATTTGATAAAAAGCATAAA ATTCAAGAATTGAATCAAGATCATGCTCTTGAGCTTTTTAGTTGGCACGCTTCTAAGAAA
[0535] AGCCATCCATCAAGTAATTATCTATGCCTTTCAGAACGTGCTACAAATTATTGTAAAGGT
[0536] CTATCTTTGGCACTCGTTGTTTTGGGTTCTTTCCTTCGTGGCAGAGATCAAGCAGAATGG
[0537] AACTGTATATTAGATGAATTTGAAACCTCTTTGAGAAAAGATATTAAAGATGTTCTTCAA
[0538] TTAAGTTTTGATGGACTTGAAGACAAAGCAAAGGATATTTTCCTTGATATTTCTTGTTTA
[0539] CTTGTGGGAGAAGAATACAATTGTGCTAAAAAAATGTTGAGTGCATGCCATTTGAACATA
[0540] GATTTTGGAATTATGATACTCATGGATCTT CTCTTGTTATTGTTGAAACGGATAGAGTG
[0541] CAAATGCATGAGTTAATACAACAAATGGGTTGTAGCATAGTTCATAATGAATCATCTGAG
[0542] CCTGGAAAGAGGAGTAGGTTGTGGTTGGTGCAGGACATTTGGGAGGTGTTTGTTAATAAT
[0543] TCAGTGAGTAACTCCTACCTAAAGTATTTAATAATTTGGACTTCACCTGATAATATATAA
[0544] ATGTTTGTCAAAGTAATTAAATTGTCAGTAATGTTAAATTACTAAATATATGACTTTGTA
[0545] GGGAACAGATGCAGTTAAAGCCATAAAGTTGGACTTGCCTAATCCCACAAAGCTAAATGT
[0546] AGATCCACAAGCATTTAGAAGTATGAAAAATTTGAGATTGCTTATCATTCGAAATGCACA
[0547] ATTTTGTAGAAAGATTAAGTACCTACCTAATAGCTTAAAGTGGATTGAGTGGCTTGGATT
[0548] TGCTCATCGATCTTTGCCGTCATGCTTCATTACCAAAAATCTTGTTGGACTTGATTTGCG
[0549] ACATAGCTCCATCAAAAGATTTGGGAAAAGGCTCAAGGTAAAATATATTTCTTTTTGCAT
[0550] CTGTATTTGACTGGAGATTTCTTCATTGATTTTCTTAAAAAGTTTTAATGGGTAGCTTAA
[0551] CTGCACCGGAAAAAAAAAATCACAAATAGGTGATTTAGCAAAATTTAACATGGATTAACC
[0552] CGTGCTAATCACATATTTTTAAAGAATTTGCAAATTATATCAAAGTTTATTAATGATATA
[0553] GTGATCTATCGCACAACCATAGACTTATGCTAGTCATATGATCTATCATTAATATACTCC
[0554] TATTAGTGATATGATCTACATGGATTAATTCCAAGGGGTCTTTTGGGGAAAGGGTTGGAT
[0555] TATGGGAGTTAAGGTTATGATAAAACTAGTGTTATGACAAATCTAGGATTACGATAAAGA
[0556] TGTATTTAGTGGAAGGGTTATGGAGGAAGTATTATGATAAAATATGTTTGGGAGAAGGGT TATGTGGGTAGGGTTATGATAAATATATATATATATATATATATATATATATTAATTCAT
[0557] ATTATAAATCAAATACACAAATTTCGTATATTTAATTTACTAAATTGTCCTAGTTTTCAT
[0558] AAAATAATTTGCCTTAATTTATTTAACTACGTTATTCAATTTCAACATACACATTGTTTA
[0559] TTTTCAACATTTTTTAAGTATACGTTACGTTTCAATAATTTGGTTTTCATGAATATGACA
[0560] CACAACCTGTAAATATGTAAATAAGGGTAAATAACAATTGAAAATGCGAATTACCGAAAA
[0561] CAGAAAATAATAATCAACGCTTTTACAAACTCTAGTTTTGTTTTCTAGTGAAAAATTACA
[0562] ATGAATCTAGTTTTAGGTTTCTCTTCAATTTATTTTAGTCTACTTTTAAAATATTAACTT
[0563] TATTTTTTATTCTTTTTAACGGTGATTTATACTTTCAAAATATTTATTTTAGTCATTTTG
[0564] CAACAATTATTGGGTAAAAAATTCATGAATCTACCGCCTCTATAACAAAAAAATTTGTTA
[0565] TATTAATTTAACCAAGCTTAATTTAATAACCAAATTAACATTATGAAAGTGGGAAAATAT
[0566] AGACAAACTGCATCTAAATAATAGATTTGTTAAATTATAGCCCCACCAATTTTTAAATTA
[0567] TTCAAATAGTCCTTATGATTTTCTAATTGTTTTAATCAATTTATGGTAGTTTGTTAAAAT
[0568] TTTACCATTTTTTTTATTTAATTGATATTCCTTAGATATTTATCCTAGCTAACTAAAAAA
[0569] AAACAATGAGATTGAGATTTATATTAAAATTTTAATTTCATAAATATATTGATATGAATT
[0570] CAAACATAGAGTTGATTGAATGTAACTAAATTAAAAATTTAATTGTGAAATCACTATAAA
[0571] TTATCTAATTCAAGAGTAAAGGAAAAAATTTAAATTTTAATAATGTAATTATACCAAATT
[0572] CATAATTAAAAAACAAGCTGTGTTTTTAAAATAAAAAGATTAAAATGAACAAAACTCATA
[0573] AATATAAAAATTATAAATGAGAAAAAAATGAATTGAGGAAGGGTTGAAGAAAGGTTGAGG
[0574] GGATAAAACTAAGGTTATGATAACCCTATAATTAAAAAGACTAAACTACATTCTCATTCT
[0575] GTTTAAGGTATCAAATTAAATGGTTAGTTTACAATCTACTAAATTCAAGATAATATATTT
[0576] TAGGTATAATGGTTACTTTACAATAATATTAATTAATTAATTACTTATAAACTAAAATTT
[0577] AATTCAAAACTATGTTTAATTTAACTAATTCTCTCGTGCCTAAATTATATTTTTTTAAAC
[0578] TTTTGTATTAAGTTGCATTTTAAACTTATAAAACACACTTACTATCGATATGTATCAAAC TAATAGTTGTAAAAAGTGCATTGTTGCTAACATGAGTACAGCTGAACTGACATAATATTG
[0579] ATTAATGGTTATTATACAATTTCTTTTACCTATATTCTATATTTTTCTATATTTACGATT
[0580] GTTGTTTTAGCCACTATTTTATCTAAATTTTGTTTTGTATGGCAATTACATACCTCCTTT
[0581] TCCTTTTGGTTTTTTTTTTTCAATGTGTTTTAGGGTTGTGAAAGGTTGAAGCATGTTGAT
[0582] CTTAGCTACTCTACTTTATTAGAGCAAATTAATGATTTCTCTCCGGCATCAAATCTTGAA
[0583] GAATTGCATCTCATCAATTGCACAAATTTAGGAATGATAGATAAGTCTGTTTTTTCTCTC
[0584] CATAAGCTTAGTGTCCTAAACCTTGATGGTTGTTGTAACCTTCAAAAGCTTCCAAGAGGC
[0585] TATTTCATGTTAAGTTCTCTTAAAGAATTGAATCTCTGTTACTGCAAAAAGCTTGAAAAA
[0586] ATTCCAGACTTATCTGCAGCATCAAACCTTAAGAGATTGTATCTCCAAGAATGCACAAAT
[0587] TTAAGAGTGATTCATGAATCTGTTGGATCTTTGGATAAGCTTAATCATCTGGACCTTAGA
[0588] CAATGCACTAAACTGGTAAAGCTTCCAAGCTATCTCAGGTTAAAGTCTCTTTCCAATTTA
[0589] TTACTTTCTGGGTGTTGTAAGCTTGAAAGCTTCCCAACAATTGCTGAAAACATGAAATCT
[0590] TTAAGGGAATTGGATATGGATTTTACTGCCATAAAGGAGTTACCTTCATCAATTGGATAT
[0591] CTTACTAACCTTTCTATATTAAAACTTAACGGTTGCACAAACCTCATCTCCCTTCCCAAT
[0592] ACAATTTATTTGTTAAGGAATCTTGAGAATCTTCTTCTTAGTGGCTGTTCTATATTTGGA
[0593] ATGTTTCCCCATACATGGGACCCAACCATCCCAACCATCCAACAAGTATGCTCTCCTTCA
[0594] AATATGATGGAAACAGCTTCCTGGAGCTTAGAATTTCCCCATTTACTAGTACCAAATGAA
[0595] AGTTTATGTGCACATTTCACTTTGTTGGATCTTGAATCTTGCAACATATCAAATGCAAAA
[0596] TTTTTAGAATTATTATGTGATGTTGCCCCTTTCTTATCTGATCTACGCTTGTCTGAAAAC
[0597] AAATTCTCTAGTTTACCCTCATGTCTCCACAAGTTCATGTCCTTGTGGAATCTTGAATTA
[0598] AGGAATTGCAAGTTTCTTCAAGAAATTCCAAACCTTCCTGAGAATATACAAAAAATGGAT
[0599] GCCAGTGGTTGTGAATCGTTGGCTCGAAATCCAGATAACATTGTGGATATAATATCAAAA
[0600] AAACAGGTTCGCCTCTAATTTCCATTCAATTTATATTCTTATCTTGTAAACAATTTAATG CATTATGAATTCTTGTTCTCTATAGGACCTCACATTGGGTGAGATTTCAAGAGAGTTTTT
[0601] ATTAACGGGGATTGAGATTCCAGAATGGTTCAGCTATAAGACTACATCCAATTTAGTGAC
[0602] AGCTAGCTTTCGTCACTATCCAGACATGGAAAGAACTTTGGCTGCCTGTGTTAGTTTCAA
[0603] AGTGAATGGAGATTCATCTAAAAGAGGAGCCCAAATTTCATGTAGTATATTCATCTGCAG
[0604] TAAACTCCATTCTTCATTTTCAAGACCATTTCTTCCATCAAAATCAGAATATATGTGGTT
[0605] AGTAACAACTTCTCTAGCGTGGGGTTCCATGGAGGTGAATGATTGGAATAAAGTTTTAGT
[0606] ATGGTTTGAGGTTCATGAAGCACATGGTGAGGTTAATGTAACTATAACAAGGTATGGTGT
[0607] CCATGTCACTGAAGAGCTCCATGGGATACAAATGGATGTCAAGTGGCCGATGGTAAATTA
[0608] TGCTGATTTTTATCAACTGGAGAAATTGCAAAGTCTGTAAGTTGATTGTTAACTTGTTAT
[0609] TTATTTATTCTCTTTCTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTTTGGAGTGAAAGTA
[0610] TATAATAGATCTCAAAGGGGGAGATGAGTATGTTATGATTTTGTTTGTTTAATGGCATAG
[0611] GGATATTGAGGATCTTCTTCTCAAAAGCTTTTTAGAAACAGTCTCTTGCCTGTCAAATTC
[0612] CAAAGCAGCAATGTTACATGCAGGAAATTATGATCCAGAAGCAATAATTGATTCCAACAT
[0613] ACAACCTATGATATTTCCATTGCACGTAACAAATAATGATGGCACATATATATGTGGAGG
[0614] CATGGGAGGCACTGCACTTGCCAACTCTTTATGCAATAAATTTAAAGGGATGGAGGGCCA
[0615] ATGCGGTGAAGCTTTAGATAATTCTACAAGCTTTTTCCATATCAAAAGAAGACAACTCCT
[0616] GAGCTATTCCTGGTCGCCGGCGGTCCACCATCGTAAGTGTGGAGATGGTGAAAGAGGAAC
[0617] GAATATCACAACCCACACAATATCCTCCAAACGCTATTTGATACTCCTTCGTGAAGCCAA
[0618] GAGCTATCAGGATGTACATGACTGGTTTTATACACATTGTTGGATAAAAGCTTCATATTG
[0619] CAGTTATGACGGAAGAGGTGATGGTGTGATTCTGATTGAAGGGGTTGATACATCCTTGCT
[0620] CTGA
[0621] SEQ ID NO 12: cDNA (mRNA) of SEQ ID NO: 8 ATGGGTTCTTCTGCTCTTCCAGTTGAATCTTCTTCT
[0622] TCTTCTTCTTCTTCTTCTCCCAACTTTCTCTATTACTACGATTATGATGTGTTTTTTAGT
[0623] TTCAGAGGAGAAGACACTCGCTCCAGTTTCATCAGTCATCTTCATATGGCCTTGCGTCTA
[0624] AAGGGAGTCAACGTCTTCATAGACGACAAACTCAAAAGGGGTGACCAAATCTCTGAGTCT
[0625] CTTCTCAAATCTATAGAGCGATCTAGACTTTCACTCGTTATTTTCTCTAAAAATTATGCA
[0626] TCTTCAACTTGGTGTTTGGATGAACTGGTGAAAATAATTGAGTATAAAAAATCCAAAAGT
[0627] CAAGCGGTTTTGCCGGTGTTCTACAAGGTGGATCCGTCCGAGGTTCGAAAACAAACCGGT
[0628] GGGTTTGGGGAAGCATTAGCCAAACATGAAGCTAATAAGTTATTGACCAACAAGATTCAA
[0629] CCATGGAAGGAAGCTTTGACTTTTGCTGCTGGTTTGTCTGGTTGGGATCTAGCAAATTGC
[0630] AAGGATGAGGCTGAACTTATCCAAGAAATTGTTAAACGAGTGTTGTCTGTATTAAATCCA
[0631] ATGCAATTACTACATGTAGCCAAGCATCCAGTTGGAATTGATTTTCGATTAAGGAAAATT
[0632] GAGGAGTTGGTCTCTCATATTGGGTCCGAGGGTGTTAACATGGTGGGGATGTATGGCATT
[0633] GGAGGCATTGGTAAGACCACTTTAGCTAAGGCTTTGTACAACAAAATTGCTAACCAATTT
[0634] GAAGGATGTTGCTTTCTACAAGATGTTAGACGAGAAGCTTCAAAGCATGGGCTCGTTAAA
[0635] CTACAAGAAACCTTACTCAATGACATCTTAAAGGAGGATTTGAAGGTTGTCAGCCGTGAT
[0636] AGAGGAATTAACATCATAAGGAGTAGACTGTGTTCAAAGAAAGTTCTTATAGTTCTTGAT
[0637] GATGTGGATGATCGTGAGCAATTAGAAGCACTGGTTGGTGGTCGTGATTGGTTTGGTCGA
[0638] GGTAGCAAAATCATTGTGACGACAAGGAATGATCATTTACTTTCTAGCCATGGATTTGAT
[0639] AAAAAGCATAAAATTCAAGAATTGAATCAAGATCATGCTCTTGAGCTTTTTAGTTGGCAC
[0640] GCTTCTAAGAAAAGCCATCCATCAAGTAATTATCTATGCCTTTCAGAACGTGCTACAAAT
[0641] TATTGTAAAGGTCTATCTTTGGCACTCGTTGTTTTGGGTTCTTTCCTTCGTGGCAGAGAT
[0642] CAAGCAGAATGGAACTGTATATTAGATGAATTTGAAACCTCTTTGAGAAAAGATATTAAA
[0643] GATGTTCTTCAATTAAGTTTTGATGGACTTGAAGACAAAGCAAAGGATATTTTCCTTGAT ATTTCTTGTTTACTTGTGGGAGAAGAATACAATTGTGCTAAAAAAATGTTGAGTGCATGC
[0644] CATTTGAACATAGATTTTGGAATTATGATACTCATGGATCTTTCTCTTGTTATTGTTGAA
[0645] ACGGATAGAGTGCAAATGCATGAGTTAATACAACAAATGGGTTGTAGCATAGTTCATAAT
[0646] GAATCATCTGAGCCTGGAAAGAGGAGTAGGTTGTGGTTGGTGCAGGACATTTGGGAGGTG
[0647] TTTGTTAATAATTCAGGAACAGATGCAGTTAAAGCCATAAAGTTGGACTTGCCTAATCCC
[0648] ACAAAGCTAAATGTAGATCCACAAGCATTTAGAAGTATGAAAAATTTGAGATTGCTTATC
[0649] ATTCGAAATGCACAATTTTGTAGAAAGATTAAGTACCTACCTAATAGCTTAAAGTGGATT
[0650] GAGTGGCTTGGATTTGCTCATCGATCTTTGCCGTCATGCTTCATTACCAAAAATCTTGTT
[0651] GGACTTGATTTGCGACATAGCTCCATCAAAAGATTTGGGAAAAGGCTCAAGGGTTGTGAA
[0652] AGGTTGAAGCATGTTGATCTTAGCTACTCTACTTTATTAGAGCAAATTAATGATTTCTCT
[0653] CCGGCATCAAATCTTGAAGAATTGCATCTCATCAATTGCACAAATTTAGGAATGATAGAT
[0654] AAGTCTGTTTTTTCTCTCCATAAGCTTAGTGTCCTAAACCTTGATGGTTGTTGTAACCTT
[0655] CAAAAGCTTCCAAGAGGCTATTTCATGTTAAGTTCTCTTAAAGAATTGAATCTCTGTTAC
[0656] TGCAAAAAGCTTGAAAAAATTCCAGACTTATCTGCAGCATCAAACCTTAAGAGATTGTAT
[0657] CTCCAAGAATGCACAAATTTAAGAGTGATTCATGAATCTGTTGGATCTTTGGATAAGCTT
[0658] AATCATCTGGACCTTAGACAATGCACTAAACTGGTAAAGCTTCCAAGCTATCTCAGGTTA
[0659] AAGTCTCTTTCCAATTTATTACTTTCTGGGTGTTGTAAGCTTGAAAGCTTCCCAACAATT
[0660] GCTGAAAACATGAAATCTTTAAGGGAATTGGATATGGATTTTACTGCCATAAAGGAGTTA
[0661] CCTTCATCAATTGGATATCTTACTAACCTTTCTATATTAAAACTTAACGGTTGCACAAAC
[0662] CTCATCTCCCTTCCCAATACAATTTATTTGTTAAGGAATCTTGAGAATCTTCTTCTTAGT
[0663] GGCTGTTCTATATTTGGAATGTTTCCCCATACATGGGACCCAACCATCCCAACCATCCAA
[0664] CAAGTATGCTCTCCTTCAAATATGATGGAAACAGCTTCCTGGAGCTTAGAATTTCCCCAT
[0665] TTACTAGTACCAAATGAAAGTTTATGTGCACATTTCACTTTGTTGGATCTTGAATCTTGC AACATATCAAATGCAAAATTTTTAGAATTATTATGTGATGTTGCCCCTTTCTTATCTGAT
[0666] CTACGCTTGTCTGAAAACAAATTCTCTAGTTTACCCTCATGTCTCCACAAGTTCATGTCC
[0667] TTGTGGAATCTTGAATTAAGGAATTGCAAGTTTCTTCAAGAAATTCCAAACCTTCCTGAG
[0668] AATATACAAAAAATGGATGCCAGTGGTTGTGAATCGTTGGCTCGAAATCCAGATAACATT
[0669] GTGGATATAATATCAAAAAAACAGGACCTCACATTGGGTGAGATTTCAAGAGAGTTTTTA
[0670] TTAACGGGGATTGAGATTCCAGAATGGTTCAGCTATAAGACTACATCCAATTTAGTGACA
[0671] GCTAGCTTTCGTCACTATCCAGACATGGAAAGAACTTTGGCTGCCTGTGTTAGTTTCAAA
[0672] GTGAATGGAGATTCATCTAAAAGAGGAGCCCAAATTTCATGTAGTATATTCATCTGCAGT
[0673] AAACTCCATTCTTCATTTTCAAGACCATTTCTTCCATCAAAATCAGAATATATGTGGTTA
[0674] GTAACAACTTCTCTAGCGTGGGGTTCCATGGAGGTGAATGATTGGAATAAAGTTTTAGTA
[0675] TGGTTTGAGGTTCATGAAGCACATGGTGAGGTTAATGTAACTATAACAAGGTATGGTGTC
[0676] CATGTCACTGAAGAGCTCCATGGGATACAAATGGATGTCAAGTGGCCGATGGTAAATTAT
[0677] GCTGATTTTTATCAACTGGAGAAATTGCAAAGTCTGGATATTGAGGATCTTCTTCTCAAA
[0678] AGCTTTTTAGAAACAGTCTCTTGCCTGTCAAATTCCAAAGCAGCAATGTTACATGCAGGA
[0679] AATTATGATCCAGAAGCAATAATTGATTCCAACATACAACCTATGATATTTCCATTGCAC
[0680] GTAACAAATAATGATGGCACATATATATGTGGAGGCATGGGAGGCACTGCACTTGCCAAC
[0681] TCTTTATGCAATAAATTTAAAGGGATGGAGGGCCAATGCGGTGAAGCTTTAGATAATTCT
[0682] ACAAGCTTTTTCCATATCAAAAGAAGACAACTCCTGAGCTATTCCTGGTCGCCGGCGGTC
[0683] CACCATCGTAAGTGTGGAGATGGTGAAAGAGGAACGAATATCACAACCCACACAATATCC
[0684] TCCAAACGCTATTTGATACTCCTTCGTGAAGCCAAGAGCTATCAGGATGTACATGACTGG
[0685] TTTTATACACATTGTTGGATAAAAGCTTCATAT GCAGTTATGACGGAAGAGGTGATGGT
[0686] GTGATTCTGATTGAAGGGGTTGATACATCCTTGCTC SEQ ID NO 13: genomic DNA encoding SEQ ID NO: 9
[0687] ATGGGTTCTTCTGCTCTTCCAGTTGAATCTTCTTCT
[0688] TCTTCTTCTTCTTCTTCTCCCAACTTTCTCTATTACTACGATTATGATGTGTTTTTTAGT
[0689] TTCAGAGGAGAAGACACTCGCTCCAGTTTCATCAGTCATCTTCATATGGCCTTGCGTCTA
[0690] AAGGGAGTCAACGTCTTCATAGACGACAAACTCAAAAGGGGTGACCAAATCTCTGAGTCT
[0691] CTTCTCAAATCTATAGAGCGATCTAGACTTTCACTCGTTATTTTCTCTAAAAATTATGCA
[0692] TCTTCAACTTGGTGTTTGGATGAACTGGTGAAAATAATTGAGTGTATGAAACCCAAAGGA
[0693] CAGCTAGTTTTGTCTGTCTTCTACAAGGTGGATCCGTCCGTGGTTTGGAAACAAACAGGT
[0694] GGGTTTGGTGAAGCATTGGCCAAACATGAGGCTACTAAGTTAACAACCAACAAGATTAAA
[0695] CCATGGAAGGAAGCTTTGACTATTGCTGCTGGTTTGTCTGGTTGGGATCTAGCAAATTGG
[0696] TATTTCTTTTTTTAATTTCCCAAGACTCATTGTCTAAGTGAAGTTTAAATTTATCTACTA
[0697] TTTCTTATTTTCATTTTTTTTTTTGTATGATGTTACTTTACAACAGCAAGGATGAGGCTG
[0698] AACTTATCCAAGAAATTGTTAAACGAGTGTTGTCTGTATTAAATCCAATGCAATTACTAC
[0699] ATGTAGCCAAGCATCCAGTTGGAATTGATTTTCGATTAAGGAAAATTGAGGAGTTGGTCT
[0700] CTCATATTGGGTCCGAGGGTGTTAACATGGTGGGGATGTATGGCATTGGAGGCATTGGTA
[0701] AGACCACTTTGGCTAAGGCTTTGTACAACAAAATTGCTAACCAATTTGAAGGATCTTGCT
[0702] TTCTACAAGATGTTAGACGAGAAGCTTCAAAGCATGGGCTCGTTAAACTACAAGAAACCT
[0703] TACTCCATGACATCTTAAAGGAGGATTTGAAGGTTGTCAGCCGTGATAGAGGAATTAACA
[0704] TCATAAGGAGTAGACTGTGTTCAAAGAAAGTTCTTATAGTTCTTGATGATGTGGATGATC
[0705] GTGAGCAATTAGAAGCACTGGTTGGTGGTCGTGATTGGTTTGGTCGAGGTAGCAAAATCA
[0706] TTGTGACGACAAGGAATGAGCATTTACTTTTTAGCCATGGATTTGATGATCAAAAGCATA
[0707] AAATTCAAGAATTGAATCAAGATCATGCTCTTGAGCTTTTTAGTTGGCACGCTTTTAAGA
[0708] AAAGCCATCCATCAAGTAATTATCTAGGCCTTTCAGAACGTGCTACAAATTATTGTAAAG GTCTATCTTTGGCACTCGTTGTTTTGGGTTCTTTCCTTCGTGGCAGAGATCAAGCAGAAT
[0709] GGAACTGTATATTAGATGAATTTGAAACCTCTTTGAGAAAAGATATTAAAGATGTTCTTC
[0710] AATTAAGTTTTGATGGACTTGAAGACAAAGCAAAGGAAATTTTCCTTGATATTTCTTGTT
[0711] TACTCGTGGGAGAAGAAATCAATTGTGCTAAAAAGATGTTGAGTGCATGCCATTTGAACA
[0712] TAGATTTTGAAATTATGATACTCATGGATCTTTCACTTGTTACTATTGAAACGGATAGAG
[0713] TGCAAATGCATGAGTTAATACAACAAATGGGTCGTAGCATAGTTCATAATGAATCATCTG
[0714] AGCCTGGAAAGAGGAGTAGGTTGTGGTTGGTGCAGGACATTTGGGAGGTGTTTGTTAATA
[0715] ATTCAGTGAGTAACTCCTACCTAAAGTATTTAATAATTTGGACTTCACCTGATAATATAT
[0716] AAATGTTTGTCAAAGTAATTAAATTGTCAGTAATGTTAAATTACTAAATATATGACTTTG
[0717] TAGGGAACAGATGCAGTTAAAGCCATAAAGTTGGACTTGCCTAATCCCACAAAGCTAAAT
[0718] GTAGATCCACAAGCATTTAGAAGTATGAAAAATTTGAGATTGCTTATCATTCGAAATGCA
[0719] CAATTTTGTAGAAAGATTAAGTACCTACCTAATAGCTTAAAGTGGATTGAGTGGCGTGGA
[0720] TTTGCTCATCGATCTTTGCCGTCATGCTTCATTACCAAAAATCTTGTTGGACTTGATTTG
[0721] CGACATAGCTCCATCAAAAGATTTGGGAAAAGGCTCAAGGTAAAATATATTTCTTTTTGC
[0722] ATCTGTATTTGACTGGAGATTTCTTCATTGATTTTCTTAAAAAGTTTTAATGGGTAGCTT
[0723] AACTGCACCGGAAAAAAAAAATCACAAATAGGTGATTTAGCAAAATTTAACATGGATTAA
[0724] CCCGTGCTAATCACATATTTTTAAAGAATTTGCAAATTATATCAAAGTTTATTAATGATA
[0725] TAGTGATCTATCGCACAACCATAGACTTATGCTAGTCATATGATCTATCATTAATATACT
[0726] CCTATTAGTGATATGATCTACATGGATTAATTCCAAGGGGTCTTTTGGGGAAAGGGTTGG
[0727] ATTATGGGAGTTAAGGTTATGATAAAACTAGTGTTATGACAAATCTAGGATTACGATAAA
[0728] GATGTATTTAGTGGAAGGGTTATGGAGGAAGTATTATGATAAAATATGTTTGGGAGAAGG
[0729] GTTATGTGGGTAGGGTTATGATAAATATATATATATATTAATTCATATTATAAATCAAAT
[0730] ACACAAATTTCGTATATTTAATTTACTAAATTGTCCTAGTTTTCATAAAATAATTTGCCT TAATTTATTTAACTACGTTATTCAATTTCAACATACACATTGTTTATTTTCAACATTTTT
[0731] TAAGTATACGTTACGTTTCAATAATTTGGTTTTCATGAATATGACACACAACCTGTAAAT
[0732] ATGTAAATAAGGGTAAATAACAATTGAAAATGCGAATTACCGAAAACAGAAAATAATAAT
[0733] CAACGCTTTTACAAACTCTAGTTTTGTTTTCTAGTGAAAAATTACAATGAATCTAGTTTT
[0734] AGGTTTCTCTTCAATTTATTTTAGTCTACTTTTAAAATATTAACTTTATTTTTTATTCTT
[0735] TTTAACGGTGATTTATACTTTCAAAATATTTATTTTAGTCATTTTGCAACAATTATTGGG
[0736] TAAAAAATTCATGAATCTACCGCCTCTATAACAAAAAAATTTGTTATATTAATTTAACCA
[0737] AGCTTAATTTAATAACCAAATTAACATTATGAAAGTGGGAAAATATAGACAAACTGCATC
[0738] TAAATAATAGATTTGTTAAATTATAGCCCCACCAATTTTTAAATTATTCAAATAGTCCTT
[0739] ATGATTTTCTAATTGTTTTAATCAATTTATGGTAGTTTGTTAAAATTTTACCATTTTTTT
[0740] TATTTAATTGATATTCCTTAGATATTTATCCTAGCTAACTAAAAAAAAACAATGAGATTG
[0741] AGATTTATATTAAAATTTTAATTTCATAAATATATTGATATGAATTCAAACATAGAGTTG
[0742] ATTGAATGTAACTAAATTAAAAATTTAATTGTGAAATCACTATAAATTATCTAATTCAAG
[0743] AGTAAAGGAAAAAATTTAAATTTTAATAATGTAATTATACCAAATTCATAATTAAAAAAC
[0744] AAGCTGTGTTTTTAAAATAAAAAGATTAAAATGAACAAAACTCATAAATATAAAAATTAT
[0745] AAATGAGAAAAAAATGAATTGAGGAAGGGTTGAAGAAAGGTTGAGGGGATAAAACTAAG G
[0746] TTATGATAACCCTATAATTAAAAAGACTAAACTACATTCTCATTCTGTTTAAGGTATCAA
[0747] ATTAAATGTTTAGTTTACAATCTACTAAATTCAAGATAATATATTTTAGGTATAATGGTT
[0748] ACTTCACAATAATATTAATTAATTAATTACTTATAAACTAAAATTTAATTCAAAACTATG
[0749] TTTAATTTAACCAATTCTCTCGTGCCTAAATTATATCTTTTTAAACTTTTGTATTAAGTT
[0750] GCATTTTAAACTTATAAAACACATTCAATACACATATTATCGATGTGTATCAAACTAATA
[0751] GTCGTAAAAAGTGCATTGTTGCCAACATGAGTACAGCTGAACTGACATAATATTTGTATA TATGAAGTTCTATTAATGTGCCTAAATATTGATTAATGGTTATTATACAATTTCTTTTAC
[0752] CTATATTCTATATTTTTCTATATTTACGATTGTTGTTTTAGCCACTATTTTATCTAAATT
[0753] TTGTTTTGTATGGCAATTACATACCCCCTTTTCCTTTTGGTTTTTTTTTTTTTCAATGTG
[0754] TTTTAGGGTTGTGAAAGGTTGAAGCATGTTGATCTTAGCTACTCTCCGTTATTAGAGAAA
[0755] ATTCCTAATTTGTCTGCAGCATCAAACCTTGAACAGTTGTATCTCATAAATTGCAAAAAT
[0756] TTAGGAATGATAGATAAGTCTGTTTTTTCTCTCGATAAGCTTAATGTCCTAAACCTTGAT
[0757] GGTTGTTGTAACCTTCAAAAGCTTCCAAGAGGCTATTTCATGTTAAGTTCTCTTCGGTAT
[0758] TTGAATCTCTCTTACTGCAAAAAGCTTGAAAAAATTCCAGACTTATCTGCAGCATCAAAC
[0759] CTTAAAAGATTGTATCTCCAAGAATGCACAAATTTAAGAGTGATTCATGAATCTGTTGGA
[0760] TCTTTGGATAAGCTTGATCATCTGGACCTTAGACAATGCACTAAACTGGTAAAGCTTCCA
[0761] AGCTATCTCAGGTTAAAGTCTCTTGAATATTTATCACTTTCTGGGTGTTGTAAGCTTGAA
[0762] AGCTTCCCAACAATTGCTGAAAACATGAAATCTTTATGGGGATTGGATTTGGATTTTACT
[0763] GCCATAAAGGAGTTACCTTCATCAATTGGATATCTTACTAAGCTTTCTATATTAAAACTT
[0764] AACGGTTGCACAAACCTCATCTCCCTTCCCAATACAATTTATTTGTTAAGGAATCTTGAG
[0765] AATCTTCTTCTTAGTGGCTGTTCTATATTTGGAATGTTTCCCCATACATGGGACCCAACC
[0766] ATCCCAACCATCCAACAAGTATGCTCTCCTTCAAAAATGATGGAAACAGCTTCCTGGAGC
[0767] TTAGAATTTCCCGATTTACTAGTACCAAATGAAAGTTTATGTGCACATTTCACTTTGTTG
[0768] GATCTTGAATCTTGCAACATATCAAATGCAAAATTTTTAGAATTATTGTGTGATGTTGCC
[0769] CCTTTCTTATCTGATCTACGCTTGTCTGAAAACAAATTCTCTAGTTTACCCTCATGTCTC
[0770] CACAAGTTCATGTCCTTGTGGAATCTTGAATTAAGGAATTGCAAGTTTCTTCAAGAAATT
[0771] CCAAACCTTCCTGAGAATATACAAAAAATGGATGCCAGTGGTTGTGAATCGTTGGCTCGA
[0772] AATCCAGATAACATTGTGGATATAATATCAAAAAAACAGGTTCGCCTCTAATTTCCATTC
[0773] AATTTATATTCTTATCTTGTAAACAATTTAATGCATTATGAATTCTTGTTCTCTATAGGA CCTCACATTGGGTGAGATTTCAAGAGAGTTTTTATTAACGGGGATTGAGATTCCAGAATG
[0774] GTTCAGCTATAAGACTACATCCAATTTAGTGACAGCTAGCTTTCGTCACTATCCAGACAT
[0775] GGAAAGAACTTTGGCTGCCTGTGTTAGTTTCAAAGTGAATGGAGATTCATCTAAAAGAGG
[0776] AGCCCAAATGTCATGTAGTATATTCATCTGCAGTAAACTCCATTCTTCATTTTCAAGACC
[0777] ATTTCTTCCATCAAAATCAGAATATATGTGGTTAGTAACAACTTCTCTAGCGTGGGGTTC
[0778] CATGGAGGTGAATGATTGGAATAAAGTTTTGGTCTGGTTTGAGGTTCATGAAGCACATAG
[0779] TGAGGTTAATGCAACTATAACAAGGTGTGGTGTTCATGTCACTGAAGAGCTCCATGGGAT
[0780] ACAAATGGATGTCAAGTGGCCGATGGTAAATTATGCTGATTTTTATCAACTGGAGAAATT
[0781] GCAAAGTCTGTAAGTTGATTGTTTACTTGTTATTTATTTAGTCTCTTTCTTTTTCTTTTT
[0782] TTTTTTTTTTTTTTTTTTTGGAGTGAAAGTATATAATAGATCTCAAAGGGGGAGATGAGT
[0783] ATGTTATGATTTTGTTTGTTTAATGGCATAGGGATATTGAGGATCTTCTTCTCAAAAGCT
[0784] TTTTAGAAACAGTCTCTTGCCTGTCAAATTCCAAAGCAGCAATGTTACATGCAGGAAATT
[0785] ATGATCCAGAAGCAATAATTGATTCCAACATACAACCTATGATTTTCCCATTGCACGTAA
[0786] CATATAATGGTGAAACAGTGATATGTGGAATGGAAGGCATGGGAGATACTACACTCGCCA
[0787] ACTCTTTATGCAATAAATTTAAAGGGATGGAGGGCCAATGCGGTGAAGCTTTAGATAATT
[0788] CTACAAGCTTTTTCCATATCAAAAGAAGACAACTCCTGAGCTATTCCTGGTCGCCGGCGG
[0789] TCCACCATCGTAAGTGTGGAGATGGTGAAAGAGGAACGAATATCACAACCCACACAATAT
[0790] CCTCCAAACGCTATTTGATACTCCTTCGTGAAGCCAAGAGCTATCAGGATGTACATGACT
[0791] GGTTTTATACACATTGTTGGATAAAAGCTTCATATTGCAGTTATGACGGAAGAGGTGATG
[0792] GTGTGTTTCTGATTAAAGGGGTTGATACATCCTTGCTCTGA
[0793] SEQ ID NO 14: cDNA (mRNA) encoding SEQ ID No: 9
[0794] ATGGGTTCTTCTGCTCTTCCAGTTGAATCTTCTTCT TCTTCTTCTTCTTCTTCTCCCAACTTTCTCTATTACTACGATTATGATGTGTTTTTTAGT
[0795] TTCAGAGGAGAAGACACTCGCTCCAGTTTCATCAGTCATCTTCATATGGCCTTGCGTCTA
[0796] AAGGGAGTCAACGTCTTCATAGACGACAAACTCAAAAGGGGTGACCAAATCTCTGAGTCT
[0797] CTTCTCAAATCTATAGAGCGATCTAGACTTTCACTCGTTATTTTCTCTAAAAATTATGCA
[0798] TCTTCAACTTGGTGTTTGGATGAACTGGTGAAAATAATTGAGTGTATGAAACCCAAAGGA
[0799] CAGCTAGTTTTGTCTGTCTTCTACAAGGTGGATCCGTCCGTGGTTTGGAAACAAACAGGT
[0800] GGGTTTGGTGAAGCATTGGCCAAACATGAGGCTACTAAGTTAACAACCAACAAGATTAAA
[0801] CCATGGAAGGAAGCTTTGACTATTGCTGCTGGTTTGTCTGGTTGGGATCTAGCAAATTGC
[0802] AAGGATGAGGCTGAACTTATCCAAGAAATTGTTAAACGAGTGTTGTCTGTATTAAATCCA
[0803] ATGCAATTACTACATGTAGCCAAGCATCCAGTTGGAATTGATTTTCGATTAAGGAAAATT
[0804] GAGGAGTTGGTCTCTCATATTGGGTCCGAGGGTGTTAACATGGTGGGGATGTATGGCATT
[0805] GGAGGCATTGGTAAGACCACTTTGGCTAAGGCTTTGTACAACAAAATTGCTAACCAATTT
[0806] GAAGGATCTTGCTTTCTACAAGATGTTAGACGAGAAGCTTCAAAGCATGGGCTCGTTAAA
[0807] CTACAAGAAACCTTACTCCATGACATCTTAAAGGAGGATTTGAAGGTTGTCAGCCGTGAT
[0808] AGAGGAATTAACATCATAAGGAGTAGACTGTGTTCAAAGAAAGTTCTTATAGTTCTTGAT
[0809] GATGTGGATGATCGTGAGCAATTAGAAGCACTGGTTGGTGGTCGTGATTGGTTTGGTCGA
[0810] GGTAGCAAAATCATTGTGACGACAAGGAATGAGCATTTACTTTTTAGCCATGGATTTGAT
[0811] GATCAAAAGCATAAAATTCAAGAATTGAATCAAGATCATGCTCTTGAGCTTTTTAGTTGG
[0812] CACGCTTTTAAGAAAAGCCATCCATCAAGTAATTATCTAGGCCTTTCAGAACGTGCTACA
[0813] AATTATTGTAAAGGTCTATCTTTGGCACTCGTTGTTTTGGGTTCTTTCCTTCGTGGCAGA
[0814] GATCAAGCAGAATGGAACTGTATATTAGATGAATTTGAAACCTCTTTGAGAAAAGATATT
[0815] AAAGATGTTCTTCAATTAAGTTTTGATGGACTTGAAGACAAAGCAAAGGAAATTTTCCTT
[0816] GATATTTCTTGTTTACTCGTGGGAGAAGAAATCAATTGTGCTAAAAAGATGTTGAGTGCA TGCCATTTGAACATAGATTTTGAAATTATGATACTCATGGATCTTTCACTTGTTACTATT
[0817] GAAACGGATAGAGTGCAAATGCATGAGTTAATACAACAAATGGGTCGTAGCATAGTTCAT
[0818] AATGAATCATCTGAGCCTGGAAAGAGGAGTAGGTTGTGGTTGGTGCAGGACATTTGGGAG
[0819] GTGTTTGTTAATAATTCAGGAACAGATGCAGTTAAAGCCATAAAGTTGGACTTGCCTAAT
[0820] CCCACAAAGCTAAATGTAGATCCACAAGCATTTAGAAGTATGAAAAATTTGAGATTGCTT
[0821] ATCATTCGAAATGCACAATTTTGTAGAAAGATTAAGTACCTACCTAATAGCTTAAAGTGG
[0822] ATTGAGTGGCGTGGATTTGCTCATCGATCTTTGCCGTCATGCTTCATTACCAAAAATCTT
[0823] GTTGGACTTGATTTGCGACATAGCTCCATCAAAAGATTTGGGAAAAGGCTCAAGGGTTGT
[0824] GAAAGGTTGAAGCATGTTGATCTTAGCTACTCTCCGTTATTAGAGAAAATTCCTAATTTG
[0825] TCTGCAGCATCAAACCTTGAACAGTTGTATCTCATAAATTGCAAAAATTTAGGAATGATA
[0826] GATAAGTCTGTTTTTTCTCTCGATAAGCTTAATGTCCTAAACCTTGATGGTTGTTGTAAC
[0827] CTTCAAAAGCTTCCAAGAGGCTATTTCATGTTAAGTTCTCTTCGGTATTTGAATCTCTCT
[0828] TACTGCAAAAAGCTTGAAAAAATTCCAGACTTATCTGCAGCATCAAACCTTAAAAGATTG
[0829] TATCTCCAAGAATGCACAAATTTAAGAGTGATTCATGAATCTGTTGGATCTTTGGATAAG
[0830] CTTGATCATCTGGACCTTAGACAATGCACTAAACTGGTAAAGCTTCCAAGCTATCTCAGG
[0831] TTAAAGTCTCTTGAATATTTATCACTTTCTGGGTGTTGTAAGCTTGAAAGCTTCCCAACA
[0832] ATTGCTGAAAACATGAAATCTTTATGGGGATTGGATTTGGATTTTACTGCCATAAAGGAG
[0833] TTACCTTCATCAATTGGATATCTTACTAAGCTTTCTATATTAAAACTTAACGGTTGCACA
[0834] AACCTCATCTCCCTTCCCAATACAATTTATTTGTTAAGGAATCTTGAGAATCTTCTTCTT
[0835] AGTGGCTGTTCTATATTTGGAATGTTTCCCCATACATGGGACCCAACCATCCCAACCATC
[0836] CAACAAGTATGCTCTCCTTCAAAAATGATGGAAACAGCTTCCTGGAGCTTAGAATTTCCC
[0837] GATTTACTAGTACCAAATGAAAGTTTATGTGCACATTTCACTTTGTTGGATCTTGAATCT
[0838] TGCAACATATCAAATGCAAAATTTTTAGAATTATTGTGTGATGTTGCCCCTTTCTTATCT GATCTACGCTTGTCTGAAAACAAATTCTCTAGTTTACCCTCATGTCTCCACAAGTTCATG
[0839] TCCTTGTGGAATCTTGAATTAAGGAATTGCAAGTTTCTTCAAGAAATTCCAAACCTTCCT
[0840] GAGAATATACAAAAAATGGATGCCAGTGGTTGTGAATCGTTGGCTCGAAATCCAGATAAC
[0841] ATTGTGGATATAATATCAAAAAAACAGGACCTCACATTGGGTGAGATTTCAAGAGAGTTT
[0842] TTATTAACGGGGATTGAGATTCCAGAATGGTTCAGCTATAAGACTACATCCAATTTAGTG
[0843] ACAGCTAGCTTTCGTCACTATCCAGACATGGAAAGAACTTTGGCTGCCTGTGTTAGTTTC
[0844] AAAGTGAATGGAGATTCATCTAAAAGAGGAGCCCAAATGTCATGTAGTATATTCATCTGC
[0845] AGTAAACTCCATTCTTCATTTTCAAGACCATTTCTTCCATCAAAATCAGAATATATGTGG
[0846] TTAGTAACAACTTCTCTAGCGTGGGGTTCCATGGAGGTGAATGATTGGAATAAAGTTTTG
[0847] GTCTGGTTTGAGGTTCATGAAGCACATAGTGAGGTTAATGCAACTATAACAAGGTGTGGT
[0848] GTTCATGTCACTGAAGAGCTCCATGGGATACAAATGGATGTCAAGTGGCCGATGGTAAAT
[0849] TATGCTGATTTTTATCAACTGGAGAAATTGCAAAGTCTGGATATTGAGGATCTTCTTCTC
[0850] AAAAGCTTTTTAGAAACAGTCTCTTGCCTGTCAAATTCCAAAGCAGCAATGTTACATGCA
[0851] GGAAATTATGATCCAGAAGCAATAATTGATTCCAACATACAACCTATGATTTTCCCATTG
[0852] CACGTAACATATAATGGTGAAACAGTGATATGTGGAATGGAAGGCATGGGAGATACTACA
[0853] CTCGCCAACTCTTTATGCAATAAATTTAAAGGGATGGAGGGCCAATGCGGTGAAGCTTTA
[0854] GATAATTCTACAAGCTTTTTCCATATCAAAAGAAGACAACTCCTGAGCTATTCCTGGTCG
[0855] CCGGCGGTCCACCATCGTAAGTGTGGAGATGGTGAAAGAGGAACGAATATCACAACCCAC
[0856] ACAATATCCTCCAAACGCTATTTGATACTCCTTCGTGAAGCCAAGAGCTATCAGGATGTA
[0857] CATGACTGGTTTTATACACATTGTTGGATAAAAGCTTCATATTGCAGTTATGACGGAAGA
[0858] GGTGATGGTGTGTTTCTGATTAAAGGGGTTGATACATCCTTGCTC
[0859] SEQ ID NO 15: FAM primer for KASP assay of SNP_01 GAAGGTGACCAAGTTCATGCTCGGTAGTATTTCTTTTGGTAATATTTGTAC
[0860] SEQ ID NO 16: VIC primer for KASP assay of SNP 01
[0861] GAAGGTCGGAGTCAACGGATTCGGTAGTATTTCTTTTGGTAATATTTGTAT
[0862] SEQ ID NO 17: Common primer for KASP assay of SNP 01
[0863] CGGCTAATAAAGCAGCTTCATCATCTAAA
[0864] SEQ ID NO 18: FAM primer for KASP assay of SNP_02
[0865] GAAGGTGACCAAGTTCATGCTAAATTACACCTTCTGGAACCTTTGAAATT
[0866] SEQ ID NO 19: VIC primer for KASP assay of SNP_02
[0867] GAAGGTCGGAGTCAACGGATTACACCTTCTGGAACCTTTGAAATC
[0868] SEQ ID NO 20: Common primer for KASP assay of SNP_02
[0869] CTTTATACAATGGATTGTGAGTTGCTYGAA
[0870] SEQ ID NO 21: FAM primer for KASP assay of SNP_03
[0871] GAAGGTGACCAAGTTCATGCTGTCAAAGTTAATTCTTTAGTTAATGAGATAAA
[0872] SEQ ID NO 22: VIC primer for KASP assay of SNP_03
[0873] GAAGGTCGGAGTCAACGGATTGTCAAAGTTAATTCTTTAGTTAATGAGATAAG
[0874] SEQ ID NO 23: Common primer for KASP assay of SNP_03
[0875] GATGTGGGTCCCTGTTTTCGTTCTT
[0876] SEQ ID NO 24: FAM primer for KASP assay of SNP_04
[0877] GAAGGTGACCAAGTTCATGCTCTCAAGATGCCATTTAATTGTGTGTA
[0878] SEQ ID NO 25: VIC primer for KASP assay of SNP_04
[0879] GAAGGTCGGAGTCAACGGATTCTCAAGATGCCATTTAATTGTGTGTG
[0880] SEQ ID NO 26: Common primer for KASP assay of SNP 04
[0881] CCCTCCTGTTGTCAAGTACATAATCATAT SEQ ID NO 27: FAM primer for KASP assay of SNP_05
[0882] GAAGGTGACCAAGTTCATGCTTGTAGAAATTGTCAAAACTAAATACAGTAAT
[0883] SEQ ID NO 28: VIC primer for KASP assay of SNP_05
[0884] GAAGGTCGGAGTCAACGGATTGTAGAAATTGTCAAAACTAAATACAGTAAC
[0885] SEQ ID NO 29: Common primer for KASP assay of SNP 05
[0886] CGTGAGATGGGCCATATTGTAATATAACAT
[0887] SEQ ID NO 30: FAM primer for KASP assay of SNP_06
[0888] GAAGGTGACCAAGTTCATGCTCCCTTTATTTCTCTCCGTCAGTC
[0889] SEQ ID NO 31 : VIC primer for KASP assay of SNP 06
[0890] GAAGGTCGGAGTCAACGGATTCCCCTTTATTTCTCTCCGTCAGTT
[0891] SEQ ID NO 32: Common primer for KASP assay of SNP_06
[0892] CTTATCAAATAAAATTGGGGAGTAGGAGAT
[0893] SEQ ID NO 33: FAM primer for KASP assay of SNP_07
[0894] GAAGGTGACCAAGTTCATGCTAGAACTCTTCTACATTCCCCTCC
[0895] SEQ ID NO 34: VIC primer for KASP assay of SNP_07
[0896] GAAGGTCGGAGTCAACGGATTGAGAACTCTTCTACATTCCCCTCT
[0897] SEQ ID NO 35: Common primer for KASP assay of SNP_07
[0898] GGAGAAGGAAGTAGGTGTGTCTGAT
[0899] SEQ ID NO 36: genomic DNA encoding the susceptible protein of SEQ ID NO: 10
[0900] ATGGGTTCTTCTGCTCTTCCAGTTGAATCTTCTTCT
[0901] TCTTCTTCTTCTCCCAACTTTCTCTATTACTACGATTATGATGTGTTTTTTAGTTTCAGA
[0902] GGAGAAGACACTCGCTCCAGTTTCATCAGTCATCTTCATATGGCCTTGCGTCTAAAGGGA
[0903] GTCAACGTCTTCATAGACGACAAACTCAAAAGGGGTGACCAAATCTCTGAGTCTCTTCTC AAATCTATAGAGCGATCTAGACTTTCACTCGTTATTTTCTCTAAAAATTATGCATCTTCA
[0904] ACTTGGTGTTTGGATGAACTGGTGAAAATAATTGAGTATAAAAAATCCAAAAGTCAAGCG
[0905] GTTTTGCCGGTGTTCTACAAGGTGGATCCGTCCGAGGTTCGAAAACAAACCGGTGGGTTT
[0906] GGGGAAGCATTAGCCAAACATGAAGCTAATAAGTTATTGACCAACAAGATTCAACCATGG
[0907] AAGGAAGCTTTGACTTTTGCTGCTGGTTTGTCTGGTTGGGATCTAGCAAATTGGTATTTC
[0908] TTTTTTTAATTTCCCAAGACTCATTGTCTAAGTGAAGTTTAAATTTATCTACTATTTCCT
[0909] ATTTTCATTTTTTTTTTTGTATGATGTTACTTTACAACAGCAAGGATGAGGCTGAACTTA
[0910] TCCAAGAAATTGTTAAACGAGTGTTGTCTGTATTAAATCCAATGCAATTACTACATGTAG
[0911] CCAAGCATCCAGTTGGAATTGATTTTCGATTAAGGAAAATTGAGGAGTTGGTCTCTCATA
[0912] TTGGGTCCGAGGGTGTTAACATGGTGGGGATGTATGGCATTGGAGGCATTGGTAAGACCA
[0913] CTTTAGCTAAGGCTTTGTACAACAAAATTGCTAACCAATTTGAAGGATGTTGCTTTCTAC
[0914] AAGATGTTAGACGAGAAGCTTCAAAGCATGGGCTCGTTAAACTACAAGAAACCTTACTCA
[0915] ATGACATCTTAAAGGAGGATTTGAAGGTTGTCAGCCGTGATAGAGGAATTAACATCATAA
[0916] GGAGTAGACTGTGTTCAAAGAAAGTTCTTATAGTTCTTGATGATGTGGATGATCGTGAGC
[0917] AATTAGAAGCACTGGTTGGTGGTCGTGATTGGTTTGGTCGAGGTAGCAAAATCATTGTGA
[0918] CGACAAGGAATGAGCATTTACTTTTTAGCCATGGATTTGATGATCAAAAGCATAAAATTC
[0919] AAGAATTGAATCAAGATCATGCTCTTGAACTTTTTAGTTGGCACGCTTTTAAGAAAAGCC
[0920] ATCCATCAAGTAATTATCTAGGCCTTTCAGAACGTGCTACAAATTATTGTAAAGGTCTAT
[0921] CTTTGGCACTCGTTGTTTTGGGTTCTTTCCTTCGTGGCAGAGATCAAGCAGAATGGAACT
[0922] GTATATTAGATGAATTTGAAACCTCTTTGAGAAAAGATATTAAAGATGTTCTTCAATTAA
[0923] GTTTTGATGGACTTGAAGACAAAGCAAAGGATATTTTCCTTGATATTTCTTGTTTACTTG
[0924] TGGGAGAAGAATACAATTGTGCTAAAAAAATGTTGAGTGCATGCCATTTGAACATAGATT
[0925] TTGGAATTATGATACTCGTGGATCTTTCACTTGTTACTATTGAAACGGATAGAGTGCAAA TGCATGAGTTAATACAACAAATGGGTCGTAGCATAGTTCATAATGAATCATCTGAGCCTG
[0926] GAAAGAGGAGTAGGTTGTGGTTGGTGCAGGACATTTGGGAGGTGTTTGTTAATAATTCAG
[0927] TGAGTAACTCCTACCTAAAGTATTTAATAATTTGGACTTCACCTGATAATATATAAATGT
[0928] TTGTCAAAGTAATTAAATTGTCAGTAATGTTAAATTACTAAATATATGACTTTGTAGGGA
[0929] ACAGATGCAGTTAAAGCCATAAAGTTGGACTTGCCTAATCCCACAAAGCTAAATGTAGAT
[0930] CCACAAGCATTTAGAAGCATGAAAAATTTGAGATTGCTTATCATTCGAAATGCACAATTT
[0931] TGTAGAAAGATTAAGTACCTACCTAATAGCTTAAAGTGGATTGAGTGGCGTGGATTTGCT
[0932] CATCGATCTTTGCCGTCATGCTTCATTACCAAAAATCTTGTTGGACTTGATTTGCGACAT
[0933] AGCTCCATCAAAAGATTTGGGAAAAGGCTCGAGGTAAAATATATTTCTTTTTGCATCTGT
[0934] ATTTGACTGGAGATTTCTTCATTGATTTTCTTAAAAAGTTTTAATGGGTAGCTTAACTGC
[0935] ACCGGAAAAAAAAAATCACAAATAGGTGATTTAGCAAAATTTAACATGGATTAACCCGTG
[0936] CTAATCACATACTTTTAAAGAATTTGCAAATTATATCAAAGTTTATTAATGATATAGTGA
[0937] TCTATCGCACAACCATAGACTTATGCTAGTCATATGATCTATCATTAATATACTCCTATT
[0938] AGTGATATGATCTACATGGATTAATTCCAAGGGGTCTTTTGGGGAAAGGGTTGGATTATG
[0939] GGAGTTAAGGTTATGATAAAACTAGTGTTATGACAAATCTAGGATTACGATAAAGATGTA
[0940] TTTAGTGGAAGGGTTATGGAGGAAGTATTATGATAAAATATGTTTGGGAGAAGGGTTATG
[0941] TGGGTAGGGTTATGATAAATATATATATATATATATATATATATATATATATATATATAT
[0942] ATATTAATTCATATTATAAATCAAATACACAAATTTCGTATATTTAATTTACTAAATTGT
[0943] CCTAGTTTTCATAAAATAATTTGCCTTAATTTATTTAACTACGTTATTCAATTTCAACAT
[0944] ACACATTGTTTATTTTCAACATTTTTTAAGTATACGTTACGTTTCAATAATTTGGTTTTC
[0945] ATGAATATGACACACAACCTGTAAATATGTAAATAAGGGTAAATAACAATTGAAAATGCG
[0946] AATTACCGAAAACAGAAAATAATAATCAACGCTTTTACAAACTCTAGTTTTGTTTTCTAG
[0947] TGAAAAATTACGATGAATCTAGTTTTAGGTTTCTCTTCAATTTATTTTAGTCTACTTTTA AAATATTAACTTTATTTTTTATTCTTTTTAACGGTGATTTATACTTTCAAAATATTTATT
[0948] TTAGTCATTTTGCAACAATTATTGGGTAAAAAATTCATGAATCTACCGCCTCTATAACAA
[0949] AAAAATTTGTTATATTAATTTAACCAAGCTTAATTTAATAACCAAATTAACATTATGAAA
[0950] GTGGGAAAATATAGACAAACTGCATCTAAATAATAGATTTGTTAAATTATAGCCCCACCA
[0951] ATTTTTAAATTATTCAAATAGTCCTTATGATTTTCTAATTGTTTTAATCAATTTATGGTA
[0952] GTTTGTTAAAATTTTACCATTTTTTTTATTTAATTGATATTCCTTAGATATTTATCCTAG
[0953] CTAACTAAAAAAAAACAATGAGATTGAGATTTATATTAAAATTTTAATTTCATAAATATA
[0954] TTGATATGAATTCAAACATAGAGTTGATTGAATGTAACTAAATTAAAAATTTAATTGTGA
[0955] AATCACTATAAATTATCTAATTCAAGAGTAAAGGAAAAAATTTAAATTTTAATAATGTAA
[0956] TTATACCAAATTCATAATTAAAAAACAAGCTGTGTTTTTAAAATAAAAAGATTAAAATGA
[0957] ACAAAACTCATAAATATAAAAATTATAAATGAGAAAAAAATGAATTGAGGAAGGGTTGAA
[0958] GAAAGGTTGAGGGGATAAAACTAAGGTTATGATAACCCTATAATTAAAAAGACTAAACTA
[0959] CATTCTCATTCTGTTTAAGGTATCAAATTAAATGGTTAGTTTACAATCTACTAAATTCAA
[0960] GATAATATATTTTAGGTATAATGGTTACTTTACAATAATATTAATTAATTAATTACTTAT
[0961] AAACTAAAATTTAATTCAAAACTATGTTTAATTTAACTAATTCTCTCGTGCCTAAATTAT
[0962] ATTTTTTTAAACTTTTGTATTAAGTTGCATTTTAAACTTATAAAACACACTTACTATCGA
[0963] TATGTATCAAACTAATAGTTGTAAAAAGTGCATTGTTGCTAACATGAGTACAGCTGAACT
[0964] GACATAATATTGATTAATGGTTATTATACAATTTCTTTTACCTATATTCTATATTTTTCT
[0965] ATATTTACGATTGTTGTTTTAGCCACTATTTTATCTAAATTTTGTTTTGTATGGCAATTA
[0966] CATACCTCCTTTTCCTTTTGGTTTTTTTTTTTTCAATGTGTTTTAGGGTTGTGAAAGGTT
[0967] GAAGCATGTTGATCTTAGCTACTCTACTTTATTAGAGCAAATTAATGATTTCTCTCCGGC
[0968] ATCAAATCTTGAAGAATTGCATCTCATCAATTGCACAAATTTAGGAATGATAGATAAGTC
[0969] TGTTTTTTCTCTCTATAAGCTTAGTGTCCTAAACCTTGATGGTTGTTGTAACCTTCAAAA GCTTCCAAGAGGCTATTTCATGTTAAGTTCTCTTAAAGAATTGAATCTCTGTTACTGCAA
[0970] AAAGCTTGAAAAAATTCCAGACTTATCTGCAGCATCAAACCTTAAGAGATTGTATCTCCA
[0971] AGAATGCACAAATTTAAGAGTGATTCATGAATCTGTTGGATCTTTGGATAAGCTTAATCA
[0972] TCTGGACCTTAGACAATGCACTAAACTGGTAAAGCTTCCAAGCTATCTCAGGTTAAAGTC
[0973] TCTTTCCAATTTATTACTTTCTGGGTGTTGTAAGCTTGAAAGCTTCCCAACAATTGCTGA
[0974] AAACATGAAATCTTTAAGGGAATTGGATATGGATTTTACTGCCATAAAGGAGTTACCTTC
[0975] ATCAATTGGATATCTTACTAACCTTTCTATATTAAAACTTAACGGTTGCACAAACCTCAT
[0976] CTCCCTTCCCAATACAATTTATTTGTTAAGGAATCTTGAGAATCTTCTTCTTAGTGGCTG
[0977] TTCTATATTTGGAATGTTTCCCCATACATGGGACCCAACCATCCCAACCATCCAACAAGT
[0978] ATGCTCTCCTTCAAAAATGATGGAAACAGCTTCCTGGAGCTTAGAATTTCCCCATTTACT
[0979] AGTACCAAATGAAAGTTTATGTGCCCATTTCACTTTGTTGGATCTTGAATCTTGCAACAT
[0980] ATCAAATGCAAAATTTTTAGAATTATTATGTGATGTTGCCCCTTTCTTATCTGATCTACG
[0981] CTTGTCTGAAAACAAATTCTCTAGTTTACCCTCATGTCTCCACAAGTTCATGTCCTTGTG
[0982] GAATCTTGAATTAAGGAATTGCAAGTTTCTTCAAGAAATTCCAAACCTTCCTGAGAATAT
[0983] ACAAAAAATGGATGCCAGTGGTTGTGAATCGTTGGCTCGAAATCCAGATAACATTGTGGA
[0984] TATAATATCAAAAAAACAGGTTCGCCTCTAATTTCCATTCAATTTATATTCTTATCTTGT
[0985] AAACAATTTAATGCATTATGAATTCTTGTTCTCTATAGGACCTCACATTGGGTGAGATTT
[0986] CAAGAGAGTTTTTATTAACGGGGATTGAGATTCCAGAATGGTTCAGCTATAAGACTACAT
[0987] CCAATTTAGTGACAGCTAGCTTTCGTCACTATCCAGACATGGAAAGAACTTTGGCTGCCT
[0988] GTGTTAGTTTCAAAGTGAATGGAGATTCATCTAAAAGAGGAGCCCAAATTTCATGTAGTA
[0989] TATTCATCTGCAGTAAACTCCATTCTTCATTTTCAAGACCATTTCTTCCATCAAAATCAG
[0990] AATATATGTGGTTAGTAACAACTTCTCTAGCGTGGGGTTCCATGGAGGTGAATGATTGGA
[0991] ATAAAGTTTTGGTCTGGTTTGAGGTTCATGAAGCACATAGTGAGGTTAATGCAACTATAA CAAGGTGTGGTGTTCATGTCACTGAAGAGCTCCATGGGATACAAATGGATGTCAAGTGGC
[0992] CGATGGTAAATTATGCTGATTTTTATCAACTGGAGAAATTGCAAAGTCTGTAAGTTGATT
[0993] GTTAACTTGTTATTTATTTATTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
[0994] GAGTGAGAGTATATAATAGATCTCAAAGGGGGAGATGAGTATGTTATGATTTTGTTTGTT
[0995] TAATGGCATAGGGATATTGAGGATCTTCTTCTCAAAAGCTTTTTAGAAACAGTCTCTTGC
[0996] CTGTCAAATTCCAAAGCAGCAATGTTACATGCAGGAAATTATGATCCAGAAGCAATAATT
[0997] GATTCCAACATACAACCTATGATATTTCCATTGCACGTAACAAATAATGATGGCACATAT
[0998] ATATGTGGAGGCATGGGAGGCACTGCACTTGCCAACTCTTTATGCAATAAATTTAAAGGG
[0999] ATGGAGGGCCAATGCGGTGAAGCTTTAGATAATTCTACAAGCTTTTTCCATATCAAAAGA
[1000] AGACAACTCCTGAGCTATTCCTGGTCGCCGGCGGTCCACCATCGTAAGTGTGGAGATGGT
[1001] GAAAGAGGAACGAATATCACAACCCACACAATATCCTCCAAACGCTATTTGATACTCCTT
[1002] CGTGAAGCCAAGAGCTATCAGGATGTACATGACTGGTTTTATACACATTGTTGGATAAAA
[1003] GCTTCATATTGCAGTTATGACGGAAGAGGTGATGGTGTGATTCTGATTGAAGGGGTTGAT
[1004] ACATCCTTGCTCTGA
[1005] General Methods
[1006] 1. Determination of symptom level on ToLCNDV-ES infected plants
[1007] 1. 1 Plants and pathogens (vims)
[1008] A melon plant (Cucumis me lo) infecting strain of ToLCNDV-ES is used for infection of melon plants. In the present invention an aggressive ToLCNDV-ES isolate named MU_13_002 isolated in Almeria, Spain, was used as inoculum.
[1009] 1.2 ToLCNDV-ES propagation
[1010] The ToLCNDV-ES inoculum source is maintained on living infected melon plants. It must be ensured, that pure vims isolates are used and that neither the vims source, nor the whiteflies are contaminated with other diseases, in particular with other vimses (e.g. CGMMV, CYSDV, CYVY SqMV). For pre- multiplication of the ToLCNDV-ES inoculum whiteflies (Bemisia tabaci) are fed on ToLCNDV-ES sensitive (susceptible), infected melon plants in an insect proven cage. Before infection of test plants, put ToLCNDV-ES infected plants into an insect proven cage, release whiteflies to the same cage and allow the whiteflies to feed for approximately 3 days on the ToLCNDV-ES infected plants.
[1011] 1.3 Inoculation of plants to be tested
[1012] For each genotype of melon plants to be analysed 18 plants were grown until the first true leaf is expanded (normally 12 - 15 days after sowing), 15 of which were infected and 3 were mock infected. Also 15 plants of susceptible varieties were included, in this experiment susceptible variety Vedantrais and a susceptible Galia and Piel de Sapo. The 15 plants per genotype to be tested on ToLCNDV-ES resistance were put into an insect proof cage, infected whiteflies obtained as described under 1.2 above, were released into the cage to infect the plants. It has to be ensured that at least 5 -10 whiteflies are available for each test plant in the cage. Whiteflies and test plants are kept in the cage for approximately 48 hours, before the whiteflies are eliminated with an appropriate insecticide. Also three plant per genotype were mock infected, i.e. they were treated in the same manner as the test plants apart from that the whiteflies used for infection were free of ToLCNDV-ES. The experiment was set up in 3 replicates of 5 plants inoculated per genotype and 1 mock inoculated.
[1013] 1.4 Growing infected test plants
[1014] Infected test plants obtained as described under 1.3 were transplanted to bigger pots, transferred into a greenhouse with cooling equipment. The plants were grown at approximately 18°C night temperature and approximately 25°C day temperature in a timeframe of 14 to 16 hours daylight. The infected plants for each infected genotype were grown in three replicates, each of which comprises 5 ToLCNDV infected plants and 1 mock infected plant. The plots are randomized in respect to the growing area.
[1015] 1.5. Scoring the symptom level of ToLCNDV-ES infection
[1016] The scoring of the symptom level may already be done approximately 25 days post infection (dpi) with ToLCNDV-ES but is preferably done approximately 30 or 40 days post infection (dpi) with ToLCNDV- ES, or later. In case plants are present which show recovery from the virus infection, a further scoring of the symptom may be done approximately 45 or 55 days post infection (dpi) with ToLCNDV-ES.
[1017] The following symptom levels are to be used according to the phenotypes indicated in the following:
[1018] Symptom level Observed phenotype
[1019] 1.6 Optional additional tests
[1020] It is recommended to use at least one genotype highly resistant to ToLCNDV-ES (symptom level 8 - 9) and one genotype highly sensitive to ToLCNDV-ES (symptom level 1) in each experimental setup. It is further recommended to also include a genotype being intermediate resistant to ToLCNDV-ES infection in each test setup. Best results are obtained when the just mentioned genotypes are included and the symptom levels of each genotype is scored relative to the results obtained for the highly resistant, highly sensitive and intermediate resistant genotypes. These genotypes also give a clear indication on the amount of infection of melon plants with ToLCNDV-ES by the whiteflies. Furthermore, it is advisable to check infection and spreading of ToLCNDV-ES in infected plants and control plants. This can be done by checking for the presence and amount of virus DNA in upper parts of the plants. A suitable way to check for the presence and amount of ToLCNDV-ES DNA in upper plant parts is hybridization of plant material with a probe hybridizing with the DNA of the ToLCNDV-ES strain used. Various hybridization techniques are well known in the art. A simple so called Dot Blot analysis is sufficient for obtaining valuable results. Likewise PCR or quantitative PCR techniques can be used. I l l
[1021] Examples
[1022] Example 1 - Selection of ToLCNDV-ES resistant donor plants
[1023] The symptom level of wild accessions of melon plants were tested for ToLCNDV-ES resistance according to the test described under “General Methods”. A wild donor plant (belonging to the species Cucumis melo ssp. melo according to the source) was identified which has a high resistance to ToLCNDV-ES infection. The accession was not fixed for the resistance so several seed lots were tested to fix and confirm the resistance. The fixed accession had a resistance level of 9 (as seen further below the average disease score was 9, while the susceptible plant had an average score of around 2 to 3). See Figure 5 and below. Also qPCR was done, showing that very little virus is in the resistant accession, see Figure 6 and below.
[1024] Example 2 - Identification of genomic location of ToLCNDV resistance
[1025] An F2 mapping population was generated between the resistant donor accession and a susceptible breeding line. QTL mapping was done with 200 individuals of the F2 population. A peak marker has been revealed at 94.2 cM of chromosome 5, which explained 99,17% of the variation, allocated in the phy pos. ranged from 25,283,538 to 26,983,782 Mbp of chromosome 5. After a fine-mapping, this interval was further reduced. In the region there were around 80 genes. The inheritance of the trait was evaluated and found to behave as monogenic dominant.
[1026] Example 3 - ToLCNDV-ES resistance levels
[1027] ToLCNDV-ES symptom level are given in the following Table and in Figure 5. The symptom levels have been determined 40 days post infection (dpi) according to the method described herein under “General Methods”.
[1028] AVG disease score on scale 1-9 at 40dpi: average value of tested genotype (N=15), STDV: standard deviation; dpi = days post inoculation / infection
[1029] Also a qPCRtest was carried out. The result is shown in Figure 6, which shows the average of q-PCR (ct values) at 55 dpi for 10 plants per genotype (N=10).
[1030] Thus, qPCR (quantitative PCR) was carried out on the upper leaves of the infected donor plants and a susceptible control line after 55 dpi. No ToLCNDV-ES virus was detected in the donor tissue at 55 dpi, while ToLCNDV-ES virus was detected in the susceptible control. (Note that a low Ct-value indicates a high virus titer, while a high Ct-value indicates a low amount of virus).
[1031] The results show that the ToLCNDV-ES virus particles are very low (e.g. average Ct-value of at least 30 or more) or not detectable in the upper leaves of the donor plant NCIMB 44139 following infection. Example 4 - SNP markers linked to the QTL5 / 7?
[1032] The fine-mapping resulted in 7 SNP markers which were closely linked to QTL5 / 7?.
[1033] Table 2
[1034] It is noted that the DNA sequences for SNP_02, SNP_04, SNP_05 and SNP_06 are the reverse strand (- strand) with respect of the reference genome sequence found on the world wide web at melonomics.net for melon (DHL92) V4. This can be seen by Blast analysis of the sequence against the reference genome database, resulting in an alignment with either the forward strand (wherein nucleotide numbering is counting upwards) or with the reverse strand / complement strand whereby nucleotide numbering is counting downwards. It is understood that this is just a matter of naming. So a nucleotide G for SNP_02 at nucleotide 242 in SEQ ID NO: 2 corresponds to the nucleotide C for SNP_02 at nucleotide 242 of the complementary sequence of SEQ ID NO: 2. When referring to the donor SNP nucleotide in a reverse strand sequence, such reference thus also comprises a reference to the complement donor SNP nucleotide in the complement / forward strand of the sequence (and vice versa, reference to a donor nucleotide in a forward strand sequence can also be referred to by referring to the complement donor nucleotide in the complement strand).
[1035] The donor nucleotide of any of the SNP markers herein may be present in the SEQ ID NO: mentioned, or at the equivalent (or corresponding) nucleotide of a sequence comprising at least 94% (or at least 95%, 96%, 97%, 98%, 99%) sequence identity to the given sequence. This applies to all SNP markers. The ‘equivalent nucleotide’ can be easily identified by pairwise alignment using e.g. Emboss-Needle pairwise alignment (using default parameters).
[1036] Below the SNP haplotype forthe donor of QTL5 / 7? and forthe QTL5 of US11,591,611 is given. It is noted that for SNP_02, SNP_04, SNP_05 and SNP_06, the assay was based on detection of the SNP nucleotide in the reverse strand, which was converted into the SNP nucleotide in the complementary (forward) strand in the data presented below.
[1037] Table 3
[1038] As can be seen, the SNP haplotype is different between the markers linked to QTL5 / 7? and QTL5 of US11591611.
[1039] Example 5 - KASP assay Development of a KASP-assay for detecting and / or selecting plant with QTL5 / A
[1040] A KASP-assay was developed for identifying the SNPs linked to the QTL5 / 7). The SNPs linked to the QTL5 / 7? can be determined by use of the following primers in a KASP-assay:
[1041] SNP FAM allele VIC allele Common Primer
[1042] SNP_01 SEQ ID NO 15 SEQ ID NO 16 SEQ ID NO 17 SNP_02 SEQ ID NO 18 SEQ ID NO 19 SEQ ID NO 20
[1043] SNP_03 SEQ ID NO 21 SEQ ID NO 22 SEQ ID NO 23 SNP 04 SEQ ID NO 24 SEQ ID NO 25 SEQ ID NO 26
[1044] SNP 05 SEQ ID NO 27 SEQ ID NO 28 SEQ ID NO 29
[1045] SNP 06 SEQ ID NO 30 SEQ ID NO 31 SEQ ID NO 32
[1046] SNP 07 SEQ ID NO 33 SEQ ID NO 34 SEQ ID NO 35
[1047] Example 6 - identification of the causal gene underlying QTL5 / 7?
[1048] The region ranging from 25,283,538 to 26,983,782 bp of melon chromosome 5 was linked to a ToLCNDV resistance observed in the donor. This region contained numerous TIR-NBS-LRR genes.
[1049] An inventory of the TIR-NBS-LRR genes in the QTL / 7? region was made, which resulted in a list of 22 candidate TIR-NBS-LRR genes.
[1050] Next, Illumina short-read sequencing data of the wild donor was used to find structural variants in the QTL / 7) region that are unique to donor (when compared to sequencing data of the melon reference genome and a Vedrantais negative control. This uncovered several large deletions colocalized or in close vicinity with or to several of the candidate TIR-NBS-LRR genes. The largest deletion is 79,597 bp in size and results in the deletion of five TIR-NBS-LRR genes. This reduced the list of candidate genes to 17. During structural variant analysis it became clear that the QTL5 / 7? region is a highly repetitive region, and that as a result the integrated gene annotation of the reference genome DHL92 (v4) contains many errors in this region. Thus, RNAseq data was used to manually curate the list of 17 remaining candidate genes, which reduced the number of candidate genes to 7.
[1051] The same Illumina short-read sequencing data as mentioned above was then used again to look for SNPs or InDeis unique to the donor. By applying the manually curated annotation of the 7 remaining TIR-NBS- LRR genes it could subsequently determine which of these variants resulted in changes in the protein sequences or the expression of these genes. This led to the identification of one gene, which is the causal gene underlying the QTL / 7?.
[1052] The gene encoded a TIR-NBS-LRR protein (SEQ ID NO: 8). The protein of the QTL5 donor of US11591611 was analyzed (SEQ ID NO: 9) and both proteins were compared to the proteins of the reference genome DHL92 v4 (SEQ ID NO: 10) and of the susceptible variety Vedrantais. Both DHL92v4 and Vedrantais had identical proteins.
[1053] Figure 1 shows a multiple sequence alignment of SEQ ID NO: 8 (protein of QTL5 / 7?). SEQ ID NO: 9 (protein of QTL5 of US11591611) and SEQ ID NOTO (protein of ToLCNDV-ES susceptible varieties DHL92v4 and Vedrantais). In Figure 1, there were four amino acid changes that accounted for differences between the two proteins of the QTL5 and QTL5 / 7? plants and the two susceptible plants. These are indicated in black squares with solid lines. These are: a) Change 1 : an insertion of two S (Serines) at the beginning of the protein; b) Change 2: a change from amino acid V (Valine) into M (Methionine) c) Change 3 : A change of amino acid E (Glutamic acid) into K (Lysine) d) Change 4: A change of amino acid Y (Tyrosine) into either H, Histidine (SEQ ID NO: 8) or D, Aspartic Acid (SEQ ID NO: 9).
[1054] These 4 changes are also shown in Figure 2. And in Figure 4 the underlying changes in the genomic sequence are shown.
[1055] The last two of these changes are in the Leucine Rich Repeats, which are indicated in black squares with dotted lines.
[1056] One or more of these four differences (changes 1 to 4) between the ‘resistant proteins’ and the ‘susceptible proteins’ is, therefore, believed to be responsible for the resistance against ToLCNDV-ES.
[1057] The resistant protein underlying QTL5 / 7). therefore, preferably comprises one or more or all of the following amino acids: a) Amino acid number 10 to amino acid number 18 are Serines (S) b) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) c) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) d) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).
[1058] These four changes are also shown in Figure 2. Further, in Figure 4 the underlying mutations in the genomic sequence are shown.
[1059] The gene encoding the protein is expressed in at least leaves and roots of the melon plants.
[1060] As shown in Figure 3, the location of the gene is in-between SNP_03 and SNP_04 on chromosome 5.
[1061] Example 7 - backcross lines with QTL5rb
[1062] The QTL5rb locus was backcrossed into Galia, Honey Dew, Piel de Sapo, Cantaloupe and Ananas backgrounds. A greenhouse trial of various backcross lines was carried out in Spain, together with the suitable controls.
[1063] The Experimental design was as follows:
[1064] Date of Sowing : 13 / 02 / 2024
[1065] Date of inoculation: 04 / 03 / 2024 Date of transplant: 11 / 03 / 2024
[1066] Dates of scoring: 01 / 04 / 2024 / 17 / 04 / 2024 / 14 / 05 / 2024
[1067] Plants were grown in the greenhouse in peat. The backcross lines were tested in a randomized block design (randomized at sowing) with two replicates, with 5 infected plants and one mock inoculated plant per replicate. For the controls 8 replicates were sown, 1 resistant control and 5 susceptible controls in each sowing tray.
[1068] Inoculation was with viruliferus Bemisia tabaci (15-25 insect per plant at the time of infection during 48h) as described further above. The most aggressive ToLCNDV-ES isolate was used, as described above.
[1069] All plants of the backcross lines had a ToLCNDV-ES score of 9.0, except one plant of the BC2F2 Honeydew background.
[1070] The backcross lines were also genotyped for the SNP markers of the QTL5rb donor. All backcross lines had the SNP haplotype of the QTL5rb donor for SNP_03, SNP_04 and SNP_05. However, for SNP_01 and SNP_02, as well as for SNP_06 and SNP_07, the donor SNP nucleotide was not present in the backcross lines. It is, therefore, in one aspect sufficient for the plants which comprise QTL5rb to comprise the donor SNP nucleotide for SNP_03, SNP_04 and / or SNP_05.
Claims
CLAIMS1. A cultivated Cucumis melo plant, or part thereof, comprising a recombinant chromosome 5, the recombinant chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / 7? located in between a Cytosine for SNP O 1 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form and wherein said introgression fragment comprises one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; an Adenine for SNP 04 at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5.
2. The Cucumis melo plant according to claim 1, wherein the QTL5 / 7? is located in between SNP_03 at nucleotide 81 of SEQ ID NO: 3, corresponding to nucleotide 25.956.264 of chromosome 5 of the melon genome and SNP_04 at nucleotide 101 of SEQ ID NO: 4 corresponding to nucleotide 26.040.072 of chromosome 5 of the melon genome.
3. The Cucumis melo plant according to claim 1 or 2, comprising a gene encoding the protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 located in between SNP_03 at nucleotide 81 of SEQ ID NO: 3, corresponding to nucleotide 25.956.264 of chromosome 5 of the melon genome and SNP_04 at nucleotide 101 of SEQ ID NO: 4 corresponding to nucleotide 26.040.072 of chromosome 5 of the melon genome.
4. The Cucumis melo plant, or part thereof, according to claim 1, wherein the QTL5 / 7? is obtainable from seeds, a representative sample of which has been deposited under accession number NCIMB 44139 or from another wild Cucumis melo donor which comprises the following SNP marker haplotype:a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; an Adenine for SNP 04 at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5.
5. Seeds from which a plant according to claim 1 to claim 4 can be grown.
6. The Cucumis melo plant according to claim 4, wherein the wild Cucumis melo donor is of the species Cucumis melo subspecies melo.
7. A Cucumis melo plant, or part thereof, comprising a chromosome 5 comprising a gene encoding the protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8, wherein said gene confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form.
8. The plant, or plant part, according to claim 7, wherein the protein comprising at least 96% sequence identity to SEQ ID NO: 8 comprises one or more of the following amino acid changes:Amino acid number 10 to amino acid number 18 are Serines (S) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).
9. The plant, or plant part, according to claim 8, wherein the changes in the gene encoding the protein comprising at least 96% sequence identity to SEQ ID NO: 8 are made using targeted gene editing of the endogenous gene encoding the protein of SEQ ID NO: 10 or are induced by mutagenesis, such as induced by radiation or chemical mutagens.
10. A method of selecting a Cucumis melo plant comprising a chromosome 5, said chromosome 5comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / 7? located in between a Cytosine for SNP_01 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form, said method comprises selecting a plant or plant part comprising one or more or all of the Single Nucleotide Polymorphism (SNP) markers of the group: a Guanine for the SNP_03 at nucleotide 81 of SEQ ID NO: 3, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 3; an Adenine for SNP 04 at nucleotide 101 of SEQ ID NO: 4 or a Thymine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 4; a Thymine for SNP 05 at nucleotide 101 of SEQ ID NO: 5 or an Adenine in the complementary strand, or the equivalent nucleotide in a sequence comprising at least 95% sequence identity to SEQ ID NO: 5.
11. A method of selecting a Cucumis melo plant comprising a chromosome 5, said chromosome 5 comprising an introgression fragment comprises a Quantitative Trait Locus (QTL) named QTL5 / A located in between a Cytosine for SNP_01 at nucleotide 81 of SEQ ID NO: 1, corresponding to nucleotide 25.456.098 of chromosome 5 of the melon genome, and a Cytosine for SNP_07 at nucleotide 81 of SEQ ID NO: 7, corresponding to nucleotide 26.390.451 of chromosome 5 of the melon genome, said QTL5 / 7? confers Tomato Leaf Curl New Delhi virus (ToLCNDV-ES) resistance onto the Cucumis melo plant when present in homozygous or heterozygous form, said method comprises selecting a plant or plant part comprising a gene encoding the protein of SEQ ID NO: 8 or a gene encoding a protein comprising at least 96% sequence identity to SEQ ID NO: 8 located in between SNP_03 at nucleotide 81 of SEQ ID NO: 3, corresponding to nucleotide 25.956.264 of chromosome 5 of the melon genome and SNP_04 at nucleotide 101 of SEQ ID NO: 4 corresponding to nucleotide 26.040.072 of chromosome 5 of the melon genome.
12. The method according to claim 11, wherein the gene encodes a protein comprising at least 96% sequence identity to SEQ ID NO: 8 and comprises one or more of the following amino acids:Amino acid number 10 to amino acid number 18 are Serines (S)the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).
13. A method of modifying the endogenous gene on melon chromosome 5, encoding a protein of SEQ ID NO: 10, by targeted gene editing or by induced by mutagenesis, such as induced by radiation or chemical mutagens, whereby the gene is modified so that the encoded protein comprising at least 96% sequence identity to SEQ ID NO: 8 comprises one or more of the following amino acid changes:Amino acid number 10 to amino acid number 18 are Serines (S) the amino acid at the equivalent position of amino acid 484 of SEQ ID NO: 8 is a Methionine (M) the amino acid at the equivalent position of amino acid 629 of SEQ ID NO: 8 is a Lysine (K) the amino acid at the equivalent position of amino acid 679 of SEQ ID NO: 8 is a Histidine (H) or an Aspartic Acid (D).