Tolerance of cucumber to CGMMV

Abstract

The present invention relates to the resistance and / or tolerance of cucumber (preferably cucumber plant variant) plants to tobacco mosaic virus, in particular cucumber green mottle mosaic virus (CGMMV). The invention also relates to cucumbers, in particular to cultivated cucumbers, including genetic determinants that result in tolerance and / or resistance to CGMMV. The invention further relates to markers associated with genetic determinants and to the use of such markers to identify or select genetic determinants and to identify or select plants carrying such tolerance or resistance. The invention also relates to the seeds and progeny of such plants as well as to propagation material for obtaining such plants, and to different uses of these plants.

Description

Technical Field

[0001] The present invention relates to resistance and / or tolerance of cucumber (preferably cucumber cultivation variant, Cucumis sativus var. sativus) plants to tobacco mosaic virus, in particular cucumber green mottle mosaic virus (CGMMV). The present invention also relates to cucumbers, in particular cultivated cucumbers, including genetic determinants that lead to tolerance and / or resistance to CGMMV. The present invention further relates to markers associated with genetic determinants and the use of such markers to identify or select genetic determinants and to identify or select plants carrying such tolerance or resistance. The present invention also relates to seeds and progeny of such plants and propagation materials for obtaining such plants, as well as different uses of these plants. Background Art

[0002] Cucumber (Cucumis sativus L.2n=2x=14) belongs to the Cucurbitaceae family, which includes more than 800 species and is an annual vine plant. Cucumber is one of the most important and widely planted vegetable crops, originating from India, and China is widely considered to be its secondary origin. Although cucumber has significant morphological variability, cucumber shows a narrow genetic basis and has a relatively small genome size (350Mbp), which was sequenced in 2009 (Huang et al., 2009. Nat Genet. 2009 December; 41 (12): 1275-81). Cucumber has several plant varieties, including cultivated varieties (var. sativus), cultivated cucumbers (cultivated cucumbers) and wild, non-parasitic hard wickii varieties (var. hardwickii) (R.) Alef. (Kirkbride, 1993. Biosystematic monograph of the genus Cucumis (Cucurbitaceae). 84).

[0003] A variety of pathogens can affect the productivity of cucumber plants, including viruses, fungi, bacteria, nematodes and insects. Cucumbers are particularly susceptible to many viruses, so viral resistance is of great agricultural importance.

[0004] The genus Tobacco mosaic virus (family Virgaviridae) includes some of the most important plant viruses, causing severe damage to many economically important crops. Tobacco mosaic virus mainly infects vegetable crops, Solanaceae and Cucurbitaceae plants, ornamental plants, weeds and medicinal plants. In recent years, the spread of tobacco mosaic virus infecting two major cultivated vegetable crops (Solanaceae plants and Cucurbitaceae plants) has increased.

[0005] Tobacco mosaic virus consists of a group of plant viruses with single-stranded RNA, and the genome encodes four known proteins: short (126kDa or 129kDa) and long (183kDa or 186kDa) replicase-associated proteins. The long component is the result of translational read-through of the stop codon of the short component. In addition, a ≈30kDa movement protein (MP) and a ≈17kDa coat protein (CP) are translated from subgenomic RNA. The hypothetical fifth 54kDa protein is located between the two replicase-associated proteins (Smithd et al., 2018Aspect in Tobamovirus Management in intensive Agriculture. Plant Diseases, Chapter 3).

[0006] Cucumber green mottle mosaic virus (CGMMV) is a tobacco mosaic virus that can cause serious cucurbit diseases worldwide. CGMMV is a positive-strand RNA virus species of the genus Tobacco mosaic virus, which was separated from other cucurbits infected with tobacco mosaic virus to form a unique evolutionary branch. The close relatives of CGMMV are other cucurbit-infecting tobacco mosaic viruses, namely KGMMV, CFMMV and ZGMMV. In the complete genome sequence, CGMMV has 59.1-60.4% similarity with other cucurbit-infecting tobacco mosaic viruses, while the similarity with other tobacco mosaic virus species is only 46.0-49.3% (Mandal et al., 2008. Plant Viruses 2(1):25-34).

[0007] The main hosts of Cucumber Green Mottle Mosaic Virus (CGMMV) are crop species belonging to the Cucurbitaceae family, such as cucumber (Cucumis sativus), pumpkin (Cucurbita moschata) and watermelon (Citrullus lanatus) (Lovisolo, 1981 Acta Horticulturae 88, 33-82).

[0008] In 1935, Ainsworth first reported CGMMV in cucumber (Cucumis sativus) in the UK. In the past decade, its incidence has increased rapidly in other countries around the world. Subsequently, the virus has also been reported in several countries in Asia and Europe, such as China, Israel, Greece, Japan, India, South Korea, the Netherlands, Pakistan, Poland, Russia, Saudi Arabia, Spain and Ukraine (Mandal et al., 2008. Plant Viruses 2(1):25-34).

[0009] Cucumber green mottle mosaic virus (CGMMV) causes typical symptoms of leaf mottle and foliar variegation, plant stunting, flesh discoloration, surface mottle and fruit deformation. In some cucurbit crop species, fruit yield and quality losses can be serious, including watermelon and cucumber (Cucumis sativus) (Fletcher, JT et al., 1969. Plant Pathol 18: 16-22).

[0010] Cucumber green mottle mosaic virus (CGMMV) is seed-transmitted and highly contact-transmissible. CGMMV plant infection is transmitted through soil and irrigation water contaminated by infected plant debris. Seed transmission of CGMMV has also been described in gourd and cucumber. It has no known insect vectors, but recently bees (Apis mellifera) have been shown to spread CGMM during pollination (Darzi et al., 2017. Plant Pathology, 1365-3059). In addition, like other tobacco mosaic viruses, CGMMV can survive for a long time on plant debris of infected crops (Reingold et al., 2015. Plant pathology, 64: 245–255).

[0011] International patent application WO2015 / 150560 discloses a modified gene RDR1 located on chromosome 5, which confers increased resistance to potato viruses, such as potato virus and potyvirus, and Virgaviridae, which may include tobacco mosaic virus.

[0012] However, CGMMV is a tobacco mosaic virus, which is known to be able to overcome resistance (Luria et al., 2017. PloS One 12(1):e0170429).

[0013] Therefore, there is an urgent need in the art to identify other reliable sources of resistance and / or tolerance that can be used to obtain resistant commercial cucumber plants.

[0014] The present invention provides cultivated cucumber plants that exhibit resistance and / or tolerance to Cucumber Green Mottle Mosaic Virus (CGMMV), and methods for producing or determining cucumber plants that exhibit resistance and / or tolerance to CGMMV and possibly other tobacco mosaic viruses. The present invention also discloses molecular genetic markers, particularly SNPs, associated with genetic loci that confer resistance and / or tolerance to CGMMV. Summary of the invention

[0015] The inventors have identified cucumber plants that show tolerance and / or resistance to Cucumber Green Mottle Mosaic Virus (CGMMV), and they have been able to locate and identify the genetic determinants, hereinafter also referred to as QTLs (Quantitative Trait Loci), which lead to tolerance and / or resistance to CGMMV.

[0016] Tolerance and / or resistance according to the present invention are conferred by newly discovered genetic determinants, which can confer satisfactory levels of tolerance and / or resistance to Cucumber Green Mottle Mosaic Virus (CGMMV). Thus, the present invention provides these genetic determinants, also referred to herein as QTLs.

[0017] The present invention provides cultivated cucumber plants that exhibit tolerance and / or resistance to CGMMV, and methods for producing or identifying cucumber plants that exhibit tolerance and / or resistance to CGMMV. The present invention also discloses molecular genetic markers, particularly SNPs, associated with QTLs that lead to tolerance and / or resistance to CGMMV. Plants obtained by methods and uses of such molecular markers are also provided.

[0018] Furthermore, the resistance and / or tolerance is easily transferable to different genetic backgrounds and the invention also extends to different methods allowing the transfer or introgression of QTLs conferring the phenotype.

[0019] The present invention also provides several methods and uses of information associated with SNPs associated with QTLs that confer CGMMV resistance and / or tolerance, in particular, methods for identifying CGMMV-resistant and / or tolerant plants and methods for identifying other molecular markers associated with such resistance and / or tolerance, as well as methods for increasing cucumber yield in a CGMMV-infected environment and methods for protecting cucumber fields from CGMMV infection or spread.

[0020] definition

[0021] The term "resistance" is defined by the Vegetable and Ornamental Crops Division of the ISF (International Seed Federation) to describe the response of plants to pests or pathogens, as well as abiotic stresses in the vegetable seed industry. Specifically, resistance refers to the ability of a plant variety to limit the growth and development of a specific pest or pathogen and / or the damage caused by it, compared to susceptible plant varieties under similar environmental conditions and pest or pathogen pressure. Resistant varieties may develop some disease symptoms or damage under heavy pressure from pests or pathogens.

[0022] The term "tolerance" as used herein is used to refer to the phenotype of a plant, wherein at least some disease symptoms remain absent when the plant is exposed to an infectious dose of the virus, so that at least under certain culture conditions, the presence of systemic or local infection, viral proliferation, and at least the presence of viral genomic sequences and / or genomic integration thereof in the cells of the plant can be determined. Therefore, tolerant plants are resistant to symptom expression, except for asymptomatic carriers of the virus. Sometimes, viral sequences may exist or even propagate in the plant without causing disease symptoms. It should be understood that tolerant plants, although infected by the virus, are generally able to at least moderately restrict the growth and development of the virus. In addition, some plants may be tolerant under certain culture conditions and resistant under different conditions. Therefore, tolerance and resistance are not mutually exclusive. Symptoms of CGMMV infection generally include leaf mottling and leaf variegation, plant dwarfing, fruit skin discoloration, surface mottling, and fruit deformation. Susceptibility: The plant variety is unable to restrict the growth and development of a specific pest or pathogen; susceptible plants show harmful symptoms associated with viral infection, i.e. foliar lesions and fruit damage in the case of CGMMV infection.

[0023] "Cucumber" means the cucumber (Cucumis sativus) plant.

[0024] Cucumber plants susceptible to CGMMV, such as the commercially available Romi-F1 (Hazera). Prior to the present invention, all commercially available cucumber varieties to date were susceptible to CGMMV or did not provide a satisfactory level of resistance.

[0025] Thus, in the case of the Romi-F1 (Hazera) variety, and more generally in the case of most commercial varieties of cucumber, the plants according to the invention have at least increased tolerance or resistance to CGMMV.

[0026] As used herein, the term "offspring" or "progeny" refers to any plant of the offspring generation produced by asexual or sexual reproduction of one or more parent plants or their offspring. For example, the offspring plant can be obtained by cloning or selfing of a parent plant, or by crossing two parent plants, including selfing and F1 or F2 or more next generations. F1 is the first generation of offspring produced by at least one of the parents as a donor of a certain trait for the first time, while the second generation offspring (F2) or subsequent generations (F3, F4, etc.) are specimens produced by selfing of F1's, F2's, etc. Therefore, F1 can be (and usually is) a hybrid produced by crossing two true breeding parents (true inheritance is homozygous for a certain trait), while F2 can be (and usually is) the offspring produced by self-pollination of the F1 hybrid.

[0027] As used herein, the terms "cross," "crossing," "crosspollination," or "cross-breeding" refer to the process of applying pollen from a flower on one plant (artificially or naturally) to the ovules (stigma) of a flower on another plant.

[0028] As used herein, the term "genetic determinant" and / or "QTL" refers to any DNA segment associated with a biological function. Thus, QTL and / or genetic determinant include, but are not limited to, genes, coding sequences, and / or regulatory sequences required for their expression. QTL and / or genetic determinant may also include unexpressed DNA segments, for example, recognition sequences that form other proteins.

[0029] As used herein, the term "molecular marker" or "marker" refers to an indicator in a method for visualizing differences in nucleic acid sequence features. Examples of such indicators include restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPs), insertion mutations, microsatellite markers (SSRs), sequence-specific amplified regions (SCARs), polymorphic sequences amplified by enzyme digestion (CAPS) markers or isozyme markers or a combination of markers defining specific heredity and chromosomal positions described herein. The mapping of molecular markers near alleles is a process that those skilled in the art can easily perform using common molecular techniques.

[0030] It is worth noting in this regard that specific positions in chromosomes can indeed be defined based on markers (e.g., SNPs), as long as the flanking sequences of the markers are defined to unambiguously locate them on the genome. The inventors utilized SNP markers present in the cucumber genome, identified by their flanking sequences, to distinguish between introgressed sequences and endogenous resident sequences, and tracked introgressed sequences in the cucumber genome that confer resistance to CGMMV. Their positioning in the cucumber genome is referenced to v3, Chinese Long 9930", available at http: / / cucurbitgenomics.org / organism / 20 (based on Li et al., 2019 A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). Gigascience, Vol. 8, No. 6, June 2019, giz072). In the sequences associated with a specific SNP in the present application, such as SEQ ID NO: 44 of SNP CU-0002841, only one nucleotide in the sequence corresponds to the polymorphism: that is, the 36th nucleotide of SEQ ID NO: 44 corresponds to the polymorphic position of SNP CU-0002841, which can be A or G as shown in Table 8. Flanking sequences are used to locate SNPs in the genome, but are not part of this polymorphism.

[0031] As used herein, a "chromosomal region" or "chromosomal interval" defined by two markers (e.g., SNPs) X and Y refers to a portion of a chromosome that is located between the positions of the two markers and that includes the markers; therefore, the nucleotide sequence of the chromosomal region or interval begins with a nucleotide corresponding to marker X and ends with a nucleotide corresponding to marker Y, i.e., these markers are included in the region or interval defined by them. Therefore, the two markers define the boundaries of the chromosomal region or interval.

[0032] In the sense of the present invention, the SNPs defining the boundaries of the QTLs (see Table 5, Table 7 and Table 9) are used to precisely locate the chromosomal region containing the QTLs of the present invention (i.e., QTL1.2, QTL1.1 or QTL5) in the cucumber genome. Therefore, both allele versions of these SNPs defining the boundaries (i.e., Table 5, Table 7 and Table 9) can be used to define the boundaries.

[0033] Therefore, the chromosome region defined by the two SNPs A1 and A2 refers to the chromosome portion located between the positions of the two SNPs and containing the SNPs, and therefore, the nucleotide sequence of the chromosome region starts with the nucleotide corresponding to SNP A1 and ends with the nucleotide corresponding to SNP A2, i.e., according to the present invention, the above-mentioned SNPs are contained in the region defined by them.

[0034] It should also be noted that in the tables defining the boundaries of the QTLs of the present invention (i.e., Tables 5, 7, and 9), each SNP is classified as a group (X or Y). SNPs from group X are located on one side of the QTL and SNPs from group Y are located on the other side of the QTL. Therefore, each QTL of the present invention is located between SNPs from group X and group Y. Therefore, for each QTL, any SNP from group X can be combined with any SNP from group Y to define and delimit the QTL. For example, the chromosomal region of QTL1.2 can be delimited between CU-0006144 (SEQ ID NO 36, group X) and CU-0000049 (SEQ ID NO 38, group Y) or CU-0001483 (SEQ ID NO 39, group Y).

[0035] As used herein, the term "genotype" refers to the genetic constitution of a single cell, cell culture, tissue, organism (eg, plant), or group of organisms.

[0036] As used herein, the term "grafting" refers to the operation of grafting a stock to a scion. The main motivation for grafting is to avoid damage from soil-borne pests and pathogens when there are no available genetic or chemical methods for disease management. Grafting a susceptible scion onto a resistant stock can provide a resistant cultivar without breeding resistance into the cultivar. In addition, grafting can increase tolerance to abiotic stress, increase yield, and lead to more efficient water and nutrient utilization.

[0037] As used herein, the term "heterozygote" refers to a diploid or polyploid individual cell or plant having different alleles (forms of a given gene, genetic determinant, or sequence) present at least at one locus. As used herein, the term "heterozygote" refers to the presence of different alleles (forms of a given gene, genetic determinant, or sequence) at a specific locus.

[0038] As used herein, "homologous chromosomes" or "homologs" (or homologues) refer to a set of one maternal chromosome and one paternal chromosome that pair with each other during meiosis. The copies have identical genes at the same loci and the same centromere position.

[0039] As used herein, the term "homozygote" refers to an individual cell or plant that has identical alleles at one or more loci on all homologous chromosomes.

[0040] As used herein, the term "homozygous" refers to the presence of identical alleles at one or more loci in homologous chromosome segments.

[0041] As used herein, the term "hybrid" refers to any individual cell, tissue, or plant produced by a cross between parents that differ in one or more genes.

[0042] As used herein, the term "locus" (plural: "loci") refers to any genetically defined locus, which can be a single position (nucleotide) or a chromosomal region. A locus can be a gene, a genetic determinant, a portion of a gene, or a DNA sequence, and may be occupied by different sequences. A locus can also be defined by one SNP (single nucleotide polymorphism), multiple SNPs, or two flanking SNPs.

[0043] As used herein, the term "rootstock" is the lower part of the plant that is capable of receiving the scion during the grafting process.

[0044] As used herein, the term "scion" is the higher part of the plant that can be grafted onto a rootstock in the grafting process.

[0045] As used herein, the term "commercially acceptable fruit quality" refers to fruits of the Long European, Midi, Beit Alpha, Baby / Mini, Asian, Chinese parthenocarpic types, which may be parthenocarpic or non-parthenocarpic, 5 to 36 cm long, or / and 1 to 7 cm wide, with a light green to dark green or marbled peel, which may be bitter or non-bitter. Examples of fruits with commercially acceptable fruit quality may be fruits of ROMI-F1, Carmen or Kingstar varieties.

[0046] The present invention encompasses plants of different ploidy levels, whether diploid plants, triploid plants, tetraploid plants, etc.

[0047] In the context of the present invention, the assignment and positioning of DNA strands and alleles of SNP markers is performed according to the TOP / BOT method developed by Illumina (https: / / www.illumina.com / documents / products / technotes / technote_topbot.pdf). DETAILED DESCRIPTION

[0048] The present inventors have identified a major QTL on chromosome 1, when present in cucumber plants, which provides improved tolerance and / or resistance to these plants when infected or potentially infected with Cucumber Green Mottle Mosaic Virus (CGMMV). The QTL has been designated "QTL1.2".

[0049] The plants according to the invention are preferably cultivated cucumbers, ie plants of the cultivated cucumber variety (C. sativus var. sativus).

[0050] In most cases, the phenotype of the plants according to the present invention is best characterized as tolerance rather than resistance to CGMMV; however, in specific cases, the plants of the present invention exhibit resistance to CGMMV. In the following, reference is made to tolerance to CGMMV; however, in specific cases, this phenotype encompasses a resistance phenotype. Under certain conditions, the plants of the present invention may also behave as asymptomatic carriers. Therefore, in the following, any reference to tolerance or a tolerance phenotype may be replaced by a reference to resistance or by a reference to resistance and / or tolerance.

[0051] Tolerance according to the invention is preferably responsive to any type of infection, whether natural infection or mechanical inoculation in any case. It is at least tolerant to natural infection by CGMMV. As mentioned above, any reference to tolerance can be replaced by a reference to resistance or a reference to resistance and / or tolerance.

[0052] Preferably, tolerance according to the invention is characterized by the absence of all symptoms typically associated with CGMMV infection, in particular severe CGMMV, i.e. leaf mottling and mosaics on leaves, plant stunting, flesh discoloration, surface mottling and fruit deformation during exposure to the virus under natural infection conditions.

[0053] According to a first aspect, the present invention therefore relates to a cucumber plant resistant to Cucumber Green Mottle Mosaic Virus (CGMMV), the genome of which comprises a quantitative trait locus (QTL) on chromosome 1, wherein said QTL confers tolerance to CGMMV to said plant. The present invention also relates to cells or seeds of such a plant, comprising said QTL on chromosome 1 conferring tolerance to CGMMV.

[0054] According to an embodiment, according to the cucumber genome v2 map, the QTL on chromosome 1 that confers plant tolerance to CGMMV is not within the chromosomal region defined by 1723554 bp to 3791533 bp of chromosome 1.

[0055] In some embodiments, the QTL on chromosome 1 comprises at least QTL 1.2. The QTL 1.2 may be present in a heterozygous state or a homozygous state.

[0056] However, if QTL1.2 is homozygous, the level of CGMMV tolerance conferred by QTL1.2 will increase. Therefore, the present invention more specifically relates to a cucumber plant comprising in its genome QTL1.2 on chromosome 1, which confers tolerance to CGMMV, wherein the QTL is homozygous in the genome of the plant, seed or cell thereof, thereby conferring a higher level of tolerance to CGMMV.

[0057] In some embodiments, the QTL1.2 is located on chromosome 1, within the chromosomal region delineated by CU-0006144 (SEQ ID NO: 36) and CU-0001483 (SEQ ID NO: 39). Preferably, QTL1.2 is located on chromosome 1, within the chromosomal region delineated by CU-0008776 (SEQ ID NO: 37) and CU-0000049 (SEQ ID NO: 38).

[0058] The inventors have determined that QTL1.2 present in the genome of the plant, seed or cell of the invention and resulting in the phenotype of interest (ie improved tolerance to CGMMV) will be found within the above-mentioned chromosomal region by determining the presence of sequences at different loci along said region. The following 14 loci, defined by the following 14 SNPs, have been identified as associated with QTL1.2: CU-0006143 (SEQ ID NO:40), CU-0003007 (SEQ ID NO:41), CU-0001935 (SEQ ID NO:42), CU-0003410 (SEQ ID NO:43), CU-0002841 (SEQ ID NO:44), CU-0005159 (SEQ ID NO:45), CU-0003498 (SEQ ID NO:46), CU-0004638 (SEQ ID NO:47), CU-0000697 (SEQ ID NO:48), CU-0000649 (SEQ ID NO:49), CU-0003579 (SEQ ID NO:50), CU-0003759 (SEQ ID NO:51). ID NO:51), CU-0001719 (SEQ ID NO:52) and CU-0000987 (SEQ ID NO:53).

[0059] The alleles of the SNPs corresponding to QTL1.2, which confers CGMMV tolerance, are (see Table 8): Allele A of CU-0006143, Allele A of CU-0003007, Allele A of CU-0001935, Allele A of CU-0003410, Allele G of CU-0002841, Allele G of CU-0005159, Allele A of CU-0003498, Allele G of CU-0004638, Allele A of CU-0000697, Allele G of CU-0000649, Allele A of CU-0003579, Allele G of CU-0003759, Allele G of CU-0001719 and Allele A of CU-0000987.

[0060] Therefore, in some embodiments, the QTL1.2 can be detected by the presence of at least one of the above 14 loci. Preferred SNPs associated with QTL1.2 are CU-0003410 (SEQ ID NO: 43), CU-0002841 (SEQ ID NO: 44), CU-0005159 (SEQ ID NO: 45), CU-0003498 (SEQ ID NO: 46) and CU-0004638 (SEQ ID NO: 47). Therefore, the present invention more specifically relates to a cucumber plant, comprising in its genome QTL1.2 on chromosome 1, wherein QTL1.2 confers tolerance to CGMMV, wherein QTL1.2 comprises at least one of the following alleles: allele A of CU-0006143 consisting of SEQ ID NO:40, wherein the nucleotide at position 36 is A; allele A of CU-0003007 consisting of SEQ ID NO:41, wherein the nucleotide at position 36 is A; allele A of CU-0001935 consisting of SEQ ID NO:42, wherein the nucleotide at position 36 is A; allele A of CU-0003410 consisting of SEQ ID NO:43, wherein the nucleotide at position 36 is A; allele G of CU-0002841 consisting of SEQ ID NO:44, wherein the nucleotide at position 36 is G; allele G of CU-0005159 composed of SEQ ID NO:45, wherein the nucleotide at position 36 is G; allele A of CU-0003498 composed of SEQ ID NO:46, wherein the nucleotide at position 36 is A; allele G of CU-0004638 composed of SEQ ID NO:47, wherein the nucleotide at position 36 is G; allele A of CU-0000697 composed of SEQ ID NO:48, wherein the nucleotide at position 36 is A; allele G of CU-0000649 composed of SEQ ID NO:49, wherein the nucleotide at position 36 is G; allele A of CU-0003579 composed of SEQ ID NO:50, wherein the nucleotide at position 36 is A; allele G of CU-0003759 composed of SEQ ID NO:51, wherein the nucleotide at position 36 is G; Allele G of CU-0001719 composed of SEQ ID NO:52, wherein the nucleotide at position 36 is G; allele A of CU-0000987 composed of SEQ ID NO:53, wherein the nucleotide at position 36 is A.

[0061] In some embodiments, the cucumber plant, cell or seed of the present invention further comprises another QTL on chromosome 1, i.e., QTL1.1, and / or a QTL on chromosome 5, i.e., QTL5, which increases the tolerance level to CGMMV. Therefore, the present invention relates to a cucumber plant comprising QTL1.2 and preferably also QTL1.1 and / or QTL5 in its genome, wherein the QTL confers tolerance to CGMMV to the plant.

[0062] In some embodiments, the QTL1.1 is present in a heterozygous state or a homozygous state.

[0063] In some embodiments, the QTL5 is present in a heterozygous state or a homozygous state.

[0064] Preferably, the cucumber plant, cell or seed according to the present invention comprises any combination of QTLs as defined above. For example, the cucumber plant, cell or seed according to the present invention may comprise the following combination of QTLs associated with resistance to CGMMV:

[0065] QTL1.2 and QTL1.1 that confer tolerance to CGMMV, preferably one or both QTLs are present homozygously,

[0066] QTL1.2 and QTL5 conferring tolerance to CGMMV, preferably one or both QTLs are present homozygously, or

[0067] QTL1.2, QTL1.1 and QTL5 conferring tolerance to CGMMV, preferably one or two or three QTLs are present homozygously.

[0068] Individually, each QTL that confers tolerance to CGMMV provides a moderate but adequate level of tolerance to CGMMV in the case of CGMMV infection, regardless of the strain of CGMMV. As described above, the combination of at least two QTLs of the present invention confers a higher level of tolerance to CGMMV, regardless of the CGMMV strain infected.

[0069] Preferably, at least one QTL of the invention (i.e. QTL1.2 or QTL1.1 or QTL5) is present homozygously. More preferably, two QTLs of the invention are present homozygously. Even more preferably, three QTLs of the invention are present homozygously.

[0070] In some embodiments, the QTL1.1 is located on chromosome 1, within the chromosomal region delineated by CU-0001918 (SEQ ID NO: 1) and CU-0006297 (SEQ ID NO: 8). Preferably, QTL1.1 is located within the chromosomal region delineated by CU-0004565 (SEQ ID NO: 2) and CU-0004683 (SEQ ID NO: 7), more preferably within the chromosomal region delineated by CU-0001726 (SEQ ID NO: 3) and CU-0001398 (SEQ ID NO: 6), and even more preferably within the chromosomal region delineated by CU-0001212 (SEQ ID NO: 4) and CU-0001683 (SEQ ID NO: 5).

[0071] In some embodiments, the QTL5 is located on chromosome 5, within the chromosomal region delineated by CU-0005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57). Preferably, QTL5 is located on chromosome 5, within the chromosomal region delineated by CU-0007682 (SEQ ID NO: 55) and CU-0000521 (SEQ ID NO: 56).

[0072] The inventors have determined that QTL1.1 and QTL5 present in the genome of a plant, seed or cell of the invention, which contribute to the phenotype of interest, i.e. improved tolerance to CGMMV, can be found within the above-mentioned chromosomal region by determining the presence of sequences at different loci along said region:

[0073] The following 27 loci, defined by the following 27 SNPs, have been identified as associated with QTL1.1: CU-000760 (SEQ ID NO: 9), CU-0005918 (SEQ ID NO: 10), CU-0001201 (SEQ ID NO: 11), CU-0004609 (SEQ ID NO: 12), CU-0000028 (SEQ ID NO: 13), CU-0003841 (SEQ ID NO: 14), CU-0005952 (SEQ ID NO: 15), CU-0000131 (SEQ ID NO: 16), CU-0004274 (SEQ ID NO: 17), CU-0002804 (SEQ ID NO: 18), CU-0008736 (SEQ ID NO: 19), CU-0000648 (SEQ ID NO: 20). NQ:20), CU-0002063 (SEQ ID NO:21), CU-0008746 (SEQ ID NO:22), CU-0002751 (SEQ ID NO:23), CU-0002122 (SEQ ID NO:24), CU-0006155 (SEQ ID NO:25), CU-0001458 (SEQ ID NO:26), CU-0006165 (SEQ ID NO:27), CU-0006164 (SEQ ID NO:28), CU-0006180 (SEQ ID NO:29), CU-0000058 (SEQ ID NO:30), CU-0000848 (SEQ ID NO:31), CU-0001233 (SEQ ID NO:32), CU-0005032(SEQ ID NO:33), CU-0004710 (SEQ ID NO:34) and CU-0006247 (SEQ ID NO:35);

[0074] The following seven loci, defined by the following seven SNPs, have been identified as associated with QTL5: CU-0000533 (SEQ ID NO: 58), CU-0001575 (SEQ ID NO: 59), CU-0009561 (SEQ ID NO: 60), CU-0007750 (SEQ ID NO: 61), CU-0002973 (SEQ ID NO: 62), CU-0001079 (SEQ ID NO: 63), and CU-0005413 (SEQ ID NO: 64).

[0075] The alleles of the SNPs of the present invention corresponding to the QTLs conferring CGMMV tolerance are detailed as follows (see Tables 6 and 10):

[0076] The following 27 alleles are associated with QTL1.1: allele G of CU-000760 consisting of SEQ ID NO:9, wherein the nucleotide at position 36 is G; allele G of CU-0005918 consisting of SEQ ID NO:10, wherein the nucleotide at position 36 is G; allele G of CU-0001201 consisting of SEQ ID NO:11, wherein the nucleotide at position 36 is G; allele C of CU-0004609 consisting of SEQ ID NO:12, wherein the nucleotide at position 36 is C; allele G of CU-0000028 consisting of SEQ ID NO:13, wherein the nucleotide at position 36 is G; allele A of CU-0003841 consisting of SEQ ID NO:14, wherein the nucleotide at position 36 is A; allele A of CU-0005952 composed of SEQ ID NO:15, wherein the nucleotide at position 36 is A; allele G of CU-0000131 composed of SEQ ID NO:16, wherein the nucleotide at position 36 is G; allele G of CU-0004274 composed of SEQ ID NO:17, wherein the nucleotide at position 36 is G; allele G of CU-0002804 composed of SEQ ID NO:18, wherein the nucleotide at position 36 is G; allele A of CU-0008736 composed of SEQ ID NO:19, wherein the nucleotide at position 36 is A; allele G of CU-0000648 composed of SEQ ID NO:20, wherein the nucleotide at position 36 is G; allele A of CU-0002063 composed of SEQ ID NO:21, wherein the nucleotide at position 36 is A; allele G of CU-0008746 composed of SEQ ID NO:22, wherein the nucleotide at position 36 is G; allele A of CU-0002751 composed of SEQ ID NO:23, wherein the nucleotide at position 36 is A; allele A of CU-0002122 composed of SEQ ID NO:24, wherein the nucleotide at position 36 is A; allele C of CU-0006155 composed of SEQ ID NO:25, wherein the nucleotide at position 36 is C; allele G of CU-0001458 composed of SEQ ID NO:26, wherein the nucleotide at position 36 is G; allele G of CU-0006165 composed of SEQ ID NO:27, wherein the nucleotide at position 36 is G; allele G of CU-0006164 composed of SEQ ID NO:28, wherein the nucleotide at position 36 is G;allele A of CU-0006180 consisting of SEQ ID NO:29, wherein the nucleotide at position 36 is A; allele A of CU-0000058 consisting of SEQ ID NO:30, wherein the nucleotide at position 36 is A; allele C of CU-0000848 consisting of SEQ ID NO:31, wherein the nucleotide at position 36 is C; allele G of CU-0001233 consisting of SEQ ID NO:32, wherein the nucleotide at position 36 is G; allele C of CU-0005032 consisting of SEQ ID NO:33, wherein the nucleotide at position 36 is C; allele A of CU-0004710 consisting of SEQ ID NO:34, wherein the nucleotide at position 36 is A; and allele A of CU-0006247 consisting of SEQ ID NO:35, wherein the nucleotide at position 36 is A;

[0077] The following seven alleles are associated with QTL5: allele G of CU-0000533 consisting of SEQ ID NO:58, wherein the nucleotide at position 36 is G; allele G of CU-0001575 consisting of SEQ ID NO:59, wherein the nucleotide at position 36 is G; allele A of CU-0009561 consisting of SEQ ID NO:60, wherein the nucleotide at position 36 is A; allele G of CU-0007750 consisting of SEQ ID NO:61, wherein the nucleotide at position 36 is G; allele A of CU-0002973 consisting of SEQ ID NO:62, wherein the nucleotide at position 36 is A; allele G of CU-0001079 consisting of SEQ ID NO:63, wherein the nucleotide at position 36 is G; Allele A of CU-0005413 composed of NO:64, wherein the nucleotide at position 36 is A.

[0078] The presence of a QTL that confers tolerance to CGMMV can be revealed by the presence of the specific allele. Thus, the alleles of these SNPs can reflect the presence of the QTL of the present invention. At least one SNP will be checked to reflect the presence of QTL1.1 on chromosome 1. At least one SNP will be checked to reflect the presence of QTL1.2 on chromosome 1. At least one SNP will be checked to reflect the presence of QTL5 on chromosome 5.

[0079] Therefore, the present invention more specifically relates to plants, the genome of which comprises QTL1.2, wherein said QTL confers tolerance to CGMMV and said QTL1.2 is detectable by the presence of at least one of the above 14 loci. Preferably, said plants further comprise at least one additional QTL, namely QTL1.1 and / or QTL5. QTL1.1 is detectable by the presence of at least one of the above 27 loci. QTL5 is detectable by the presence of at least one of the above 7 loci. The preferred SNPs associated with QTL1.1 are CU-0000131 (SEQ ID NO: 16), CU-0004274 (SEQ ID NO: 17), CU-0002804 (SEQ ID NO: 18), CU-0008736 (SEQ ID NO: 19) and CU-0000648 (SEQ ID NO: 20), the preferred SNPs associated with QTL1.2 are CU-0003410 (SEQ ID NO: 43), CU-0002841 (SEQ ID NO: 44), CU-0005159 (SEQ ID NO: 45), CU-0003498 (SEQ ID NO: 46) and CU-0004638 (SEQ ID NO: 47), and the preferred SNPs associated with QTL5 are CU-0009561 (SEQ ID NO: 60), CU-0007750 (SEQ ID NO: 61). NO:61) and CU-0002973 (SEQ ID NO:62).

[0080] According to another aspect, the present invention also relates to a plant or a cell or seed thereof, comprising in its genome QTL1.1 or / and QTL1.2 on chromosome 1, which confers tolerance to CGMMV, wherein at least one of the QTLs is homozygous in the genome of the plant, seed or cell, thereby conferring a higher level of tolerance to CGMMV. Preferably, the plant, seed or cell further comprises a combination of QTL5 and QTL1.1 and / or QTL1.2 in its genome. More preferably, the QTL5 is homozygous.

[0081] The invention also relates to a hybrid plant of cucumber, which can be obtained by crossing a cucumber plant having an improved phenotype and carrying QTL1.2 and optionally carrying QTL1.1 and / or QTL5 with another cucumber plant. Preferably, the cucumber plant with an improved phenotype homozygously carries the three QTLs of the present invention. If the other cucumber hybrid partner lacks the QTL of the present invention, the hybrid produced by the hybridization will carry the QTL of the present invention in a heterozygous state, and the cucumber plant will also have a tolerant phenotype, although the level of tolerance to CGMMV will be moderate.

[0082] Preferably, the cucumber plant according to the present invention is a cultivated plant or strain, more preferably a commercial plant or strain or hybrid. Therefore, such plants or strains usually have 4 or fewer primary branches, usually less than 3, more preferably one primary branch.

[0083] Such commercial plants or lines also preferably show resistance to other viruses, especially resistance to Potato Virus Y. Preferably, the commercial plants are resistant to ZYMV (Zucchini Yellow Mosaic Virus) and / or CVYV (Cucumber Vein Yellowing Virus). Resistance to PRSV (Papaya Ringspot Virus) and WMV (Watermelon Mosaic Virus) and CMV (Cucumber Mosaic Virus) is also common in commercial plants. Thus, the plants of the present invention have advantageous resistance to at least powdery mildew and Potato Virus Y.

[0084] Other resistances or tolerances are also envisaged according to the invention, in particular resistance to downy mildew caused by Peronospora cucumeris, resistance to Fusarium caused by Fusarium solani or Fusarium oxysporum, resistance to scab caused by Venturia cucumeris, resistance to WMV, CYSDV and CCYV.

[0085] Advantageously, the plants of the present invention are also resistant to one or more arthropod pests, such as Franklineilla occidentalis, Bemisia tabaci, Trialeurodes vaporariorum and Meloidogyne incognita.

[0086] In some embodiments, the plant of the present invention is used as a scion or stock in a grafting process. Grafting is a process that has been used for many years in crops such as Cucurbitaceae. Grafting can be used to provide a certain degree of resistance to geopathogens (such as Phytophthora) or certain nematodes. Therefore, the grid is intended to prevent the plant or variety to be cultivated from contacting the infected soil. The variety of interest used as a graft or scion, optionally an F1 hybrid, is grafted onto a tolerant plant used as a stock. The tolerant stock remains healthy and provides normal support from the soil for the graft to protect it from disease.

[0087] The plants according to the invention are preferably pure female plants, or monoecious plants, which monoecious plants have at least 50% dioecious flowers, even more preferably at least 70% or 80% dioecious flowers. In addition, the commercial plants of the invention produce fruits under appropriate conditions, wherein 50% of the fruits are at least greater than 10 cm in length when fully mature, preferably greater than 15 cm or 20 cm in length when fully mature. The harvested fruits have a green skin color, and they preferably have an elongated shape.

[0088] As described above, the present invention relates to cucumber plants exhibiting CGMMV tolerance, and seeds producing these plants, as well as cells of these plants or seeds comprising tolerance QTLs.

[0089] The present invention relates to cucumber plants expressing CGMMV tolerance, as well as seeds producing these plants, and cells of these plants or seeds which comprise tolerance QTLs.

[0090] The present invention includes plants, seeds and cells of any ploidy level; it particularly includes diploid, triploid, tetraploid and / or allopolyploid plants, cells or seeds.

[0091] The plant or seed according to the invention may be a progeny or descendant of a plant grown from deposited seed CUC58.4 deposited at NCIMB under accession number NCIMB 43844. Plants grown from the deposited seed are indeed homozygous for the QTL of the invention conferring the improved phenotype and therefore contain in their genome the three QTLs of interest (QTL1.1, QTL1.2 and QTL5) on each homologue of chromosome 1 and chromosome 5. They can be used to transfer these sequences into another background by crossing and selfing and / or backcrossing.

[0092] The present invention also relates to deposited seeds of CUC58.4 (NCIMB 43844) and plants grown from one of these seeds. These seeds homozygously contain QTLs that confer a phenotype of interest. It is noteworthy that these seeds do not correspond to plant varieties, and except for the QTLs of the present invention, they are not homozygous for most genes; therefore, except for the tolerance of the present invention, their phenotypes are not fixed during reproduction; except for the CGMMV tolerance of the present invention, most of their phenotypic traits are separated during reproduction. The present invention also relates to plants or seeds as defined above, i.e., containing three QTLs of interest in a homozygous or heterozygous state, but most preferably at least one of the three QTLs is in a homozygous state, and the QTL confers CGMMV tolerance, wherein these plants or seeds can be obtained by transferring the QTL from a cucumber plant to another cucumber genetic background, and its representative seeds are deposited with NCIMB accession number NCIMB 43844; for example, by crossing the deposited plant with a second cucumber plant parent and selecting plants carrying the QTL responsible for the phenotype of interest. During this crossing process, QTL1.1, QTL1.2 and QTL5 can be transferred.

[0093] The QTL according to the present invention and conferring enhanced tolerance to CGMMV is preferably a QTL present in the seed genome of CUC58.4. A sample of seeds of this cucumber planting variety has been registered by Vilmorin & Cie, 4 quai de la Mégisserie 75001 Paris, FRANCE, in accordance with and in compliance with the requirements of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure (the "Budapest Treaty" and the National Collection of Industrial, Food and Marine Bacteria (NCIMB) (NCIMB, Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA, United Kingdom), effective August 16, 2021, with registration number NCIMB 43844.

[0094] It should be noted that the seeds or plants of the present invention can be obtained by different processes and are not entirely obtained by essentially biological processes.

[0095] According to such an aspect, the present invention relates to a cucumber plant or seed, preferably a non-naturally occurring cucumber plant or seed, such as a modified cucumber plant or seed, comprising one or more mutations in its genome which provide the plant with resistance to CGMMV, for example, the mutation is present in the genome of a plant, a representative sample of which is deposited in NCIMB under accession number NCIMB 43844.

[0096] In some embodiments, the present invention relates to a method for obtaining a modified cucumber plant or seed carrying one or more mutations in its genome, which provides the plant with resistance to CGMMV. This method may include:

[0097] a) treating M0 seeds of the CGMMV plant to be modified with a mutagen to obtain M1 seeds;

[0098] b) growing plants from the M1 seeds thus obtained to obtain M1 plants;

[0099] c) producing M2 seeds by self-fertilization of M1 plants; and

[0100] d) Optionally repeating step b) and step c) n times to obtain M1+n seeds.

[0101] The M1+n seeds are grown into plants and infected with CGMMV. Surviving plants or those with milder symptoms of CGMMV infection are propagated for one or more generations while continuing to be selected for their resistance to CGMMV.

[0102] In this method, the M1 seeds of step a) can be obtained by chemical mutagenesis (e.g., EMS mutagenesis). Other chemical mutagens include, but are not limited to, diethyl sulfate (des), ethyleneimine (ei), propane sultone, N-methyl-N-nitrosourea (mnu), N-nitroso-N-methylurea (NMU), N-ethyl-N-nitrosourea (enu), and sodium azide.

[0103] Alternatively, the mutations are induced by irradiation, for example selected from X-rays, fast neutrons, ultraviolet radiation.

[0104] In some embodiments of the invention, the above mutation is induced by genetic engineering. Such mutations include the integration of sequences that confer resistance to CGMMV, and the replacement of resident sequences with alternative sequences that confer resistance or tolerance to CGMMV. Preferably, the mutation is the integration of QTL1.2 with optional QTL1.1 and / or QTL5, as described above, to replace the homologous sequences of the cucumber plant. More preferably, the above mutation is to replace the sequence or fragment thereof contained in SNP CU-0006144 (SEQ ID NO: 36) and SNP CU-0001483 (SEQ ID NO: 39) on chromosome 1 of the cucumber genome with a homologous sequence present on chromosome 1 of the plant's genome, a representative sample of the plant is deposited in NCIMB with accession number NCIMB 43844, wherein the above sequence or fragment confers resistance to CGMMV. Optionally, the additional mutation is to replace the sequence or fragment thereof contained in SNP CU-0005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57) on chromosome 5 of the CGMMV genome with a homologous sequence on chromosome 5, and / or, the additional mutation is to replace the sequence or fragment thereof contained in SNP CU-0001918 (SEQ ID NO: 1) and SNP CU-0006292 (SEQ ID NO: 8) on chromosome 1 of the cucumber genome with a homologous sequence present on chromosome 1 of the plant genome, a representative sample of which is deposited in NCIMB under accession number NCIMB43844, wherein the sequence or fragment confers resistance to CGMMV.

[0105] Genetic engineering refers to the application of all such techniques that can be used, including the so-called new breeding techniques, which are various new technologies developed and / or used to create new characteristics in plants through genetic variation, for the purpose of targeted mutagenesis, targeted introduction of new genes or gene silencing (RdDM). Examples of such new breeding techniques include the use of zinc finger nuclease (ZFN) technology (ZFN-1, ZFN-2 and ZFN-3, see U.S. Patent No. 9145565), oligonucleotide-directed mutagenesis (ODM), syngenesis and endogenesis, grafting (on GM rootstock), reverse breeding, Agrobacterium infiltration (Agroinfiltration in the "strict sense", Agrobacterium inoculation, floral dip), transcription activator-like effector nucleases (TALENs, see U.S. Patent Nos. 8586363 and 91 81535), CRISPR / Cas systems (see U.S. Patent Nos. 8697359; 8771945; 8795965; 8865406; 8871445; 8889356; 8895308; 8906616; 8932814; 8945839; 8993233; and 8999641), engineered meganucleases, engineered homing endonucleases, DNA-guided genome editing (Gao et al., Nature Biotechnology (2016)), and synthetic genomics facilitate targeted sequence changes. A major part of targeted genome editing (another name for new breeding techniques) is the application of inducing DNA double-strand breaks (DSBs) at selected locations in the genome where modification is intended. Directed repair of DSBs allows targeted genome editing. Such applications can be used to generate mutations (e.g., targeted mutations or precise endogenous gene editing) as well as precise insertion of genes (e.g., cisgenes, ingenes, or transgenes). Applications that cause mutations are generally defined as site-directed nuclease (SDN) technologies, such as SDN1, SDN2 and SDN3. For SDN1, the result is a targeted, non-specific gene deletion mutation: the location of the DNA DSB is precisely selected, but the host cell's DNA repair is random, resulting in small nucleotide deletions, additions or substitutions. For SDN2, SDN is used to generate a targeted DSB, and a DNA repair template (a short DNA sequence that is identical to the target DSB DNA sequence except for one or a few nucleotide changes) is used to repair this DSB: this results in a targeted and predetermined point mutation in the desired target gene. For SDN3, SDN is used with a DNA repair template containing a new DNA sequence (e.g., a gene). The result of this technology is the integration of this DNA sequence into the plant genome. The most likely application that illustrates the use of SDN3 is the insertion of a cisgene, ingene or transgenic expression cassette at a selected genomic location. A full description of each of these technologies can be found in the 2011 report of the European Commission's Joint Research Center (JRC) entitled "New Plant Breeding Technologies - Current Status and Prospects for Commercial Development".

[0106] According to such aspect, the present invention relates to an improved cultivated cucumber plant or seed, preferably a non-naturally occurring cucumber plant or seed, which may include one or more mutations in its genome, which mutation makes the plant tolerant to CGMMV, for example, the mutation is present in the genome of the plant, a representative sample of which is deposited in NCIMB under accession number NCIMB43844.

[0107] In another embodiment, the present invention relates to a method for obtaining improved cucumber plants or seeds carrying one or more mutations in their genome, which provide the plants with tolerance to CGMMV.

[0108] The present invention also relates in another aspect to any plant that may be obtained from the seeds or plants of the present invention, and plant parts of such plants. Preferably, explants, scions, cuttings, seeds, fruits, roots, stock, pollen, ovules, embryos, protoplasts, leaves, anthers, stems, petioles and any other plant parts, wherein the plants, explants, scions, cuttings, seeds, fruits, roots, stock, pollen, ovules, embryos, protoplasts, leaves, anthers, stems, petioles and / or plant parts can be obtained from the seeds or plants according to the first aspect of the present invention, i.e., carry the QTL1.2 of the present invention in its genome in a homozygous or heterozygous manner, and optionally QTL1.1 and / or QTL5, wherein preferably at least one QTL is present homozygously. These plant parts, in particular explants, scions, cuttings, seeds, fruits, roots, stock, pollen, ovules, embryos, protoplasts, leaves, anthers, stems or petioles, comprise in their genome the QTL conferring the phenotype of interest, i.e. tolerance to CGMMV; therefore, they include cells containing the QTL.

[0109] According to a preferred embodiment, the present invention relates to a seed that can develop into a plant according to the present invention and is therefore tolerant to CGMMV infection. The QTL1.2 and optional QTL1.1 and / or QTL5 mentioned in this aspect of the present invention are those defined above in the context of the plant of the present invention. The different characteristics of the QTLs defined in relation to the plant of the present invention are applicable to this aspect of the present invention after appropriate modifications. Therefore, the above-mentioned QTLs are preferably QTLs present in the genome of a plant corresponding to the deposited material CUC58.4 (NCIMB accession number 43844). Each QTL is advantageously characterized by the presence of the following alleles:

[0110] QTL1.2 is preferably characterized by the presence of at least one of the following 14 alleles: allele A of CU-0006143, allele A of CU-0003007, allele A of CU-0001935, allele A of CU-0003410, allele G of CU-0002841, allele G of CU-0005159, allele A of CU-0003498, allele G of CU-0004638, allele A of CU-0000697, allele G of CU-0000649, allele A of CU-0003579, allele G of CU-0003759, allele G of CU-0001719, and allele A of CU-0000987;

[0111] QTL1.1 is preferably characterized by the presence of at least one of the following 27 alleles: allele G of CU-0000760, allele G of CU-0005918, allele G of CU-0001201, allele C of CU-0004609, allele G of CU-0000028, allele A of CU-0003841, allele A of CU-0005952, allele G of CU-0000131, allele G of CU-0004274, allele G of CU-0002804, allele A of CU-0008736, allele G of CU-0000648, allele C of CU-00020 allele A of CU-63, allele G of CU-0008746, allele A of CU-0002751, allele A of CU-0002122, allele C of CU-0006155, allele G of CU-0001458, allele G of CU-0006165, allele G of CU-0006164, allele A of CU-0006180, allele A of CU-0000058, allele C of CU-0000848, allele G of CU-0001233, allele C of CU-0005032, allele A of CU-0004710, and allele A of CU-0006247;

[0112] QTL5 is preferably characterized by the presence of at least one of the following seven alleles: allele G of CU-0000533, allele G of CU-0001575, allele A of CU-0009561, allele G of CU-0007750, allele A of CU-0002973, allele G of CU-0001079, and allele A of CU-0005413.

[0113] The present invention also relates to cells of cucumber plants, for example, these cells include in their genome the QTL1.2 of the present invention and optionally QTL1.1 and / or QTL5, QTL1.2 and optionally QTL1.1 and / or QTL5 confer tolerance to CGMMV on cucumber plants. QTL1.2 and optionally QTL1.1 and / or QTL5 are those already defined in the context of the present invention, and they are characterized by the same features and preferred embodiments of plants and seeds already disclosed according to the above aspects of the present invention. The presence of the above QTLs can be revealed by the above disclosed techniques and is well known to readers in the art. Among other things, it can be determined whether the QTL is homozygous or heterozygous in the genome of such cells of the present invention. The cell according to the present invention can be any type of cucumber cell carrying the QTL of the present invention, in particular an isolated cell and / or a cell capable of regenerating a whole cucumber plant.

[0114] In one embodiment, the above-mentioned cell is an isolated cell.

[0115] The present invention also relates to a tissue culture of non-renewable or renewable cells of the plant according to the present invention. The non-renewable or renewable cell comprises in its genome a QTL that confers CGMMV tolerance of the present invention, in particular QTL1.2, and optionally QTL1.1 and / or QTL5, preferably at least one QTL is homozygous. Preferably, the renewable cell is derived from the embryo, protoplast, meristem, callus, pollen, leaf, anther, stem, petiole, root, root tip, fruit, seed, flower, cotyledon and / or hypocotyl of the present invention, and the cell comprises in its genome a QTL of the present invention that confers tolerance to CGMMV, in particular when at least one QTL is homozygous.

[0116] The tissue culture is preferably capable of regenerating plants having the physiological and morphological characteristics of the above cucumber plants, as well as regenerated plants having substantially the same genotype as the above cucumber plants. The present invention also provides cucumber plants regenerated from the tissue culture of the present invention.

[0117] The present invention also provides protoplasts of the plant defined above, or protoplasts from tissue culture defined above, said protoplasts containing the QTL conferring the improved phenotype of the present invention.

[0118] According to another aspect, the present invention also relates to the use of the cucumber plant of the present invention, which comprises QTL1.2, and optionally further comprises QTL1.1 and / or QTL5, as a breeding partner for obtaining a cucumber plant with CGMMV tolerance in a breeding program. In fact, such a breeding partner preferably homozygous carries at least one QTL of the present invention that confers the target tolerance in its genome. By hybridizing the plant with a cucumber plant, in particular a cucumber line, the QTL of the present invention that confers the desired phenotype can be transferred to the offspring. Therefore, the plant according to the present invention can be used as a breeding partner for infiltrating the QTL that confers the desired CGMMV tolerance into a cucumber plant or germplasm. Although plants or seeds heterozygously carry the QTL of interest and can also be used as breeding partners as described in detail above, the separation of the phenotype can make the breeding program more complicated.

[0119] The improved phenotype of the present invention is resistant to CGMMV.

[0120] The introgressed QTL will be advantageously introduced into varieties containing other desirable genetic traits, such as resistance to other diseases or pests, early fruit maturity, drought tolerance, fruit shape, etc.

[0121] In some embodiments, the plant used is a plant or seed of CUC58.4, deposited at NCIMB under accession number NCIMB 43844. The plant is also suitable as an introgression partner in a breeding program aimed at conferring a desired phenotype to cucumber plants or germplasm.

[0122] In such breeding programs, selection of progeny displaying the desired phenotype or carrying a QTL associated with CGMMV tolerance can advantageously be performed based on the alleles of SNP markers, particularly the SNP markers of the present invention.

[0123] According to a preferred embodiment, the progeny of the plant are selected in the presence of:

[0124] at least one allele associated with QTL1.2: allele A of CU-0006143, allele A of CU-0003007, allele A of CU-0001935, allele A of CU-0003410, allele G of CU-0002841, allele G of CU-0005159, allele A of CU-0003498, allele G of CU-0004638, allele A of CU-0000697, allele G of CU-0000649, allele A of CU-0003579, allele G of CU-0003759, allele G of CU-0001719, and allele A of CU-0000987; and

[0125] Optionally at least one allele associated with QTL1.1: allele G of CU-0000760, allele G of CU-0005918, allele G of CU-0001201, allele C of CU-0004609, allele G of CU-0000028, allele A of CU-0003841, allele A of CU-0005952, allele G of CU-0000131, allele G of CU-0004274, allele G of CU-0002804, allele A of CU-0008736, allele G of CU-0000648, allele A of CU-0002063, allele C of CU-0008741. allele G of CU-746, allele A of CU-0002751, allele A of CU-0002122, allele C of CU-0006155, allele G of CU-0001458, allele G of CU-0006165, allele G of CU-0006164, allele A of CU-0006180, allele A of CU-0000058, allele C of CU-0000848, allele G of CU-0001233, allele C of CU-0005032, allele A of CU-0004710, allele A of CU-0006247, allele A of CU-0006247; and / or

[0126] Optionally at least one allele associated with QTL5: allele G of CU-0000533, allele G of CU-0001575, allele A of CU-0009561, allele G of CU-0007750, allele A of CU-0002973, allele G of CU-0001079, and allele A of CU-0005413.

[0127] Progeny of the above plants are preferably selected for the presence of identical alleles on both homologues of each chromosome, and for at least one SNP, are therefore homozygous for the presence of diploid plants.

[0128] Selection of progeny is preferably based on three or more SNPs, at least one SNP allele for QTL1.1, at least one SNP allele for QTL1.2 and at least one SNP allele for QTL5, wherein at least one SNP is homozygous.

[0129] This selection is made based on the presence of the target alleles in the sample of genetic material of the plant to be selected. The presence of these alleles indeed confirms the presence of the QTL of the present invention at the locus defined by the SNP. In addition, further to point mutation or recombination events, it is conceivable that at least 1 or 2 of these alleles are deleted, and the remaining part of the chromosome segment carrying the target QTL still confers the phenotype of interest.

[0130] Therefore, plants according to the invention or plants grown from seeds deposited under accession number NCIMB 43844 are particularly valuable for marker-assisted selection for obtaining commercial cucumber lines and varieties having the improved phenotype of the invention, ie CGMMV tolerance.

[0131] The invention also relates to the use of said plants in procedures aimed at identifying, sequencing and / or cloning gene sequences conferring a desired phenotype.

[0132] Any of the specific embodiments described for the previous aspects of the invention also apply to this aspect of the invention, particularly with respect to the characterization of the QTL that confers the phenotype of interest.

[0133] According to another aspect, the present invention also relates to a method or process for producing cucumber plants, especially cucumber planting variant plants, especially cultivated cucumbers, with a desired phenotype, especially commercial plants and self-pollinated parent lines. The present invention indeed also relates to transferring the QTL (QTL1.2, and optionally QTL1.1 and / or QTL5) of the present invention, which confers CGMMV tolerance and is preferably homozygous, to other cucumber varieties, or other species or self-pollinated parent lines, and facilitates the production of new types and varieties of cucumbers.

[0134] A method or process for producing a plant having these characteristics may include the following steps:

[0135] a) crossing plants grown from plants carrying QTL1.2 and optionally QTL1.1 and / or QTL5, preferably at least one of which is homozygously present, with initial cucumber plants (preferably without said QTLs), QTL1.2 and optionally QTL1.1 and / or QTL5 conferring CGMMV tolerance;

[0136] b) selecting a plant among the progeny thus obtained, which plant carries the QTL1.2 of the present invention and optionally QTL1.1 and / or QTL5;

[0137] c) optionally self-pollinating the plants obtained in step b) one or more times and selecting in the subsequent generations, thereby obtaining plants tolerant to CGMMV.

[0138] Alternatively, the method or process may not include step a), but may include the following steps:

[0139] a1) crossing plants conferring CGMMV tolerance grown from plants carrying QTL1.2 and optionally QTL1.1 and / or QTL5, or their progeny, with initial cucumber plants (preferably without the QTL);

[0140] a2) Increase the F1 hybrids by selfing to produce F2 populations.

[0141] In the above methods or processes, SNP markers are preferably used in step b) and / or step c) to select plants carrying sequences conferring the tolerance phenotype of interest.

[0142] The SNP markers used are preferably the markers of the present invention, including all the combinations mentioned in other parts of this application, in particular:

[0143] At least one SNP associated with QTL1.2, and

[0144] Optionally, at least one SNP associated with QTL1.1, and / or at least one SNP associated with QTL5.

[0145] By selecting plants based on the alleles of one or more SNPs, it can be understood that when the allele of the SNP is the allele corresponding to the allele of the tolerant parent of the SNP, rather than the allele corresponding to the initial cucumber plant, the plant is selected to be tolerant to CGMMV, or to have QTL1.2 and optionally QTL1.1 and / or QTL5. Those alleles of the 48 SNPs of the present invention have been described in detail in the present application.

[0146] Preferably, the cucumber plants of step a) are elite lines for obtaining plants having commercially desirable traits or desirable horticultural traits.

[0147] The method or process as described above may advantageously include a backcrossing step, preferably after step c), to obtain plants having all the characteristic features of cucumber plants, in particular cucumber planting variety plants. Therefore, the method or process for the production of plants having these characteristics may also include the following additional steps:

[0148] d) backcrossing the tolerant plants selected in step b) or step c) with cucumber plants;

[0149] e) selecting plants carrying QTL1.2 and optionally QTL1.1 and / or QTL5 of the invention.

[0150] The plant used in step a), ie any plant according to the first aspect of the invention; it may preferably be a plant grown from deposited seeds, homozygously carrying the three QTLs of the invention conferring the phenotype of interest.

[0151] In step e), the SNP marker can be used to select plants with improved tolerance to CGMMV relative to the initial plants.The SNP marker is a marker of the present invention, as described in the previous sections.

[0152] According to a preferred embodiment, the method or process of the invention is performed as follows, for at least one of the selection steps, ie b), c) and / or e), the selection is based on the detection of at least one tolerance allele reported in Tables 6, 8 and 10.

[0153] Note that when plants have an improved phenotype and carry QTL1.2 and optionally QTL1.1 and / or QTL5, selection will be based on the presence of one or more SNPs of the invention, representative alleles of the QTL (ie the alleles found in the tolerant parent).

[0154] The plants selected in step e) are preferably cultivated plants or commercial plants, in particular plants with marketable fruits under normal cultivation conditions, for example, 50% of the fruits are at least greater than 10 cm in length when fully mature, preferably greater than 15 cm or 20 cm in length when fully mature. The harvested fruits have a green skin color, and they preferably have an elongated shape.

[0155] Preferably, step d) and step e) are repeated at least twice, preferably three times, not necessarily using the same cucumber plants. The cucumber plants are preferably breeding lines.

[0156] In each selection step of the above process, additional selection may be made for resistance to potato virus Y and / or powdery mildew.

[0157] Furthermore, the selection may also take into account the proportion of gynecological flowers, wherein gynecological plants or monoecious plants having at least 50%, preferably at least 70% or 80% gynecological flowers are selected.

[0158] It is also preferred that the selected plants have 4 or less primary branches, more preferably 3 or less, such as 2, most preferably only one primary branch.

[0159] The selfing and backcrossing steps may be performed in any order and may be inserted, for example, backcrossing may be performed before and after one or more selfings, and selfing may conceivably be performed before and after one or more backcrossings.

[0160] Selection of progeny with the desired improved phenotype can also be performed based on comparison of CGMMV tolerance from cucumber parents by the protocols specifically disclosed in the Examples.

[0161] The method for allele detection may be based on any technique that allows distinguishing between two different alleles of a SNP on a specific chromosome.

[0162] The invention also relates to a plant obtained or obtainable by this method. Such a plant is indeed a cucumber plant having a modified phenotype according to the first aspect of the invention.

[0163] The present invention also relates to a method for obtaining a cultivated cucumber plant or a commercial cucumber plant or an inbred parental line thereof having a desired improved phenotype corresponding to an improved tolerance to CGMMV relative to the initial commercial cucumber plant, the method comprising the following steps:

[0164] a) backcrossing plants carrying QTL1.2 and optionally QTL1.1 and / or QTL5 conferring CGMMV tolerance with commercial cucumber plants,

[0165] b) Selecting plants carrying QTL1.2 and optionally QTL1.1 and / or QTL5.

[0166] Preferably, the plant of step a) is obtained by germinating the deposited seed CUC58.4 with NCIMB accession number 43844 or its progeny, and the plant carries QTL1.1, QTL1.2 and QTL5.

[0167] Preferably, the selection is based on the presence of at least one of the 14 SNPs associated with QTL1.2, and optionally, (i) at least one of the 27 SNPs associated with QTL1.1, and / or (ii) at least one of the 7 SNPs associated with QTL5. According to a preferred embodiment, the offspring carrying QTL1.2 and optionally QTL1.1 and / or QTL5 contain at least one of the above SNPs in a homozygous state.

[0168] The invention also relates to cucumber plants and seeds obtainable by any of the methods and processes described above. Such cucumber seeds are preferably coated or granulated with a single or combined active substance, such as a plant nutrient, an enhancing microorganism, or a product for disinfecting the seed and the plant environment. These substances and chemicals may be products that promote plant growth, such as hormones, or products that increase their resistance to environmental stress, such as defense stimulants, or stabilize the pH of the substrate and its intermediate environment, or may be a nutrient.

[0169] They can also be products for preventing agents that are detrimental to the growth of seedlings, including viruses and pathogenic microorganisms in this context, such as fungicidal, bactericidal, hemicide (hematicidal), insecticidal or herbicidal products that act by contact, ingestion or gas diffusion; for example, it is any suitable essential oil, such as thyme extract. All these products enhance the resistance response of the plant, and / or disinfect or regulate the environment of the plant. They can also be living biological materials, such as non-pathogenic microorganisms, such as at least one fungus, bacterium or virus, if necessary, and with a medium that ensures its viability; such microorganisms, such as Pseudomonas, Bacillus, Trichoderma, Capsular Fungi, Fusarium, Rhizobium and other types stimulate the growth of plants, or protect plants from pathogens.

[0170] In all previous methods and processes, the determination of plants carrying QTLs for enhanced tolerance to CGMMV can be accomplished by detecting at least one allele associated with each QTL, and can also be accomplished by combining the absence of other allelic forms of the SNP of the present invention to confirm the homozygous state of at least one QTL. Therefore, the determination of plants homozygously carrying QTL1.2 in the present invention will be based on the determination of allele A of CU-0006143, allele A of CU-0003007, allele A of CU-0001935, allele A of CU-0003410, allele G of CU-0002841, allele G of CU-0005159, allele A of CU-0003498, allele G of CU-0004638, allele A of CU-0000697, allele G of CU-0000649, allele A of CU-0003579, allele G of CU-0003759, allele G of CU-0001719 and allele A of CU-0000987, as well as the absence of other alleles of these SNPs. Similarly, the determination of plants homozygously carrying QTL1.1 in the present invention will be based on the alleles: allele G of CU-0000760, allele G of CU-0005918, allele G of CU-0001201, allele C of CU-0004609, allele G of CU-0000028, allele A of CU-0003841, allele A of CU-0005952, allele G of CU-0000131, allele G of CU-0004274, allele G of CU-0002804, allele A of CU-0008736, allele G of CU-0000648, allele A of CU-0002063, allele C of CU-0000028. The determination of allele G of CU-0008746, allele A of CU-0002751, allele A of CU-0002122, allele C of CU-0006155, allele G of CU-0001458, allele G of CU-0006165, allele G of CU-0006164, allele A of CU-0006180, allele A of CU-0000058, allele C of CU-0000848, allele G of CU-0001233, allele C of CU-0005032, allele A of CU-0004710 and allele A of CU-0006247, as well as the absence of other alleles of these SNPs.The determination of plants homozygously carrying QTL5 in the present invention will be based on the determination of allele G of CU-0000533, allele G of CU-0001575, allele A of CU-0009561, allele G of CU-0007750, allele A of CU-0002973, allele G of CU-0001079 and allele A of CU-0005413, as well as the absence of other alleles of these SNPs.

[0171] The present invention also relates to the use of the information provided herein by the inventors, namely the three QTLs present in the deposited seed CUC58.4 (NCIMB accession number 43844) and conferring an improved phenotype to cucumber plants and the disclosure of molecular markers associated with these QTLs. This knowledge is particularly useful for accurately mapping QTLs, defining their sequences, determining cucumber plants containing QTLs that confer improved phenotypes, and determining other markers or alternative markers associated with the QTLs. Such other markers are characterized by their location, i.e., proximity to the 48 markers disclosed in the present invention, and their association with the phenotype of interest disclosed by the present invention, i.e., tolerance to CGMMV.

[0172] Therefore, the present invention also relates to a method for detecting and / or selecting cucumber plants having a QTL according to the invention (i.e. QTL1.2 and optionally QTL1.1 and / or QTL5) which confers improved CGMMV tolerance relative to corresponding plants lacking said QTL, the method comprising in a sample of the genetic material of the plant to be identified and / or selected:

[0173] Detection of at least one of the following markers: allele A of CU-0006143, allele A of CU-0003007, allele A of CU-0001935, allele A of CU-0003410, allele G of CU-0002841, allele G of CU-0005159, allele A of CU-0003498, allele G of CU-0004638, allele A of CU-0000697, allele G of CU-0000649, allele A of CU-0003579, allele G of CU-0003759, allele G of CU-0001719, and allele A of CU-0000987 of QTL1.2 on chromosome 1, and

[0174] Optionally, detection of at least one of the following markers: allele G of CU-0000760, allele G of CU-0005918, allele G of CU-0001201, allele C of CU-0004609, allele G of CU-0000028, allele A of CU-0003841, allele A of CU-0005952, allele G of CU-0000131, allele G of CU-0004274, allele G of CU-0002804, allele A of CU-0008736, allele G of CU-0000648, allele A of CU-0002063, allele C of CU-0008741. allele G of CU-46, allele A of CU-0002751, allele A of CU-0002122, allele C of CU-0006155, allele G of CU-0001458, allele G of CU-0006165, allele G of CU-0006164, allele A of CU-0006180, allele A of CU-0000058, allele C of CU-0000848, allele G of CU-0001233, allele C of CU-0005032, allele A of CU-0004710, and allele A of CU-0006247 of QTL1.1 on chromosome 1, and / or

[0175] Optionally, detection of at least one of the following markers: allele G of CU-0000533, allele G of CU-0001575, allele A of CU-0009561, allele G of CU-0007750, allele A of CU-0002973, allele G of CU-0001079, and allele A of CU-0005413 of QTL5 on chromosome 5,

[0176] The method is particularly suitable for breeding programs with CUC58.4 (NCIMB Accession No. 43844) as the original parent or its progeny, including the three QTLs of the present invention that confer CGMMV tolerance, wherein the detection and / or selection is preferably carried out under conditions involving CGMMV infection.

[0177] The present invention also relates to a method for detecting and / or selecting cucumber plants having three QTLs of the present invention that confer the improved phenotype, the method being based on allele detection of at least one of the 27 SNPs of QTL1.1, at least one of the 14 SNPs of QTL1.2, and at least one of the 7 SNPs of QTL5. If at least one (preferably at least 2, 3, 5, 8, 10 or 29 SNPs) of QTL1.1 has an allele representative of CGMMV tolerance, plants are selected for the presence of QTL1.1. If at least one (preferably at least 2, 3, 5, 8, 10, 12 or 15 SNPs) of QTL1.2 has an allele representative of CGMMV tolerance, plants are selected for the presence of QTL1.2. If at least one (preferably at least 2, 3, 5, 8, 10, 12 or 15 SNPs) of QTL5 has an allele representative of CGMMV tolerance, plants are selected for the presence of QTL5.

[0178] The present invention further relates to a method for detecting and / or selecting cucumber plants (particularly cucumber planting varieties, especially cultivated cucumbers) which have the QTL1.2 of the present invention which confers an improved phenotype, and optionally QTL1.1 and / or QTL5, the method being based on the detection of any molecular marker which reveals the presence of the QTL. In fact, now that the QTL of the present invention has been determined by the inventors, the determination and use of molecular markers in addition to the 48 SNPs of the present invention can be accomplished by a person skilled in the art. The above-mentioned QTLs themselves can be characterized by the presence of at least one of the 48 SNPs of the present invention (Table 6 listed for QTL1.1, Table 8 listed for QTL1.2 and Table 10 listed for QTL5), but they can also be identified by using different alternative markers. Therefore, the present invention also includes methods and uses of any such molecular markers for identifying one or two or three QTLs of the present invention in the cucumber genome, wherein the QTL confers improved tolerance to CGMMV relative to corresponding plants lacking the QTL, wherein the QTL is independently characterized by the presence of at least one SNP listed in Table 8 for QTL1.2, preferably at least one SNP listed in Table 6 for QTL1.1 and / or at least one SNP listed in Table 10 for QTL5.

[0179] Also included are methods and uses of any such alternative molecular markers for identifying a QTL of the present invention in the cucumber genome, wherein the QTL confers tolerance to CGMMV, wherein QTL1.2 is characterized by the presence of at least one of the 14 tolerance alleles of the 14 SNPs in Table 8, and preferably, wherein (i) QTL1.1 is characterized by the presence of at least one of the 27 tolerance alleles of the 27 SNPs in Table 6, and / or (ii) QTL5 is characterized by the presence of at least one of the 7 tolerance alleles of the 7 SNPs in Table 10.

[0180] The present invention also relates to a method for detecting and / or selecting cucumber plants having QTL1.2 and optionally QTL1.1 and / or QTL5 as described above, which confer tolerance to CGMMV, the method comprising:

[0181] a) detecting the presence of at least one genetic marker genetically associated with QTL1.2 involved in tolerance to CGMMV in cucumber plants, and optionally, (i) at least one genetic marker genetically associated with QTL1.1, and / or (ii) at least one genetic marker genetically associated with QTL5,

[0182] b) selecting plants containing genetic markers associated with QTL1.2 and optionally QTL1.1 and / or QTL5 involved in tolerance to CGMMV, wherein the QTL1.2 is located on chromosome 1, within the chromosomal region delineated by CU-0006144 (SEQ ID NO:36) and CU-0001483 (SEQ ID NO:39), the QTL1.1 is located on chromosome 1, within the chromosomal region delineated by CU-0001918 (SEQ ID NO:1) and CU-0006297 (SEQ ID NO:8), and the QTL5 is located on chromosome 5, within the chromosomal region delineated by CU-0005234 (SEQ ID NO:54) and CU-0007979 (SEQ ID NO:57).

[0183] By association or genetic association, more specifically genetic linkage, it is understood that a genetic polymorphism of a marker (i.e. a particular allele of a SNP marker) and a phenotype of interest co-occur, i.e. are inherited together, more frequently than expected by chance, i.e. there is a non-random association of the allele and the gene sequence responsible for the phenotype because they are adjacent on the same chromosome.

[0184] Screening for genetic markers that are genetically associated with a specific QTL is considered a routine practice for technicians. It generally includes, but is not limited to, collecting F1 offspring of cucumbers with a specific QTL and measuring the occurrence of specific polymorphisms of genetic markers and the occurrence of specific QTLs. When the probability of co-occurrence is higher than the expected probability, the marker is considered to be genetically associated. Sampling, phenotyping, genotyping, genotypic data analysis and linkage map generation, SNP detection and marker selection can be performed by methods that the operator deems preferred. Genotyping libraries and alignment software can be used. The probability of a specific QTL and a marker occurring simultaneously is usually tested using one-way analysis of variance, chi-square test or Student's test.

[0185] The molecular marker of the invention, one of the 48 markers disclosed above or a surrogate marker, is inherited with the phenotype of interest in preferably more than 90% of the meioses, preferably more than 95%, 96%, 98% or 99% of the meioses.

[0186] Thus, the present invention relates to the use of one or more molecular markers for fine mapping or determining QTLs in the cucumber genome, said QTLs being involved in the improved phenotype of the present invention, wherein said one or more markers are located in one of the following chromosomal regions:

[0187] For QTL1.1, within the chromosomal region delineated by CU-0001918 (SEQ ID NO: 1) and CU-0006297 (SEQ ID NO: 2) on chromosome 1,

[0188] For QTL1.2, within the chromosomal region delineated by CU-0006144 (SEQ ID NO:36) and CU-0001483 (SEQ ID NO:39) on chromosome 1,

[0189] For QTL5, within the chromosomal region delineated by CU-0005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57) on chromosome 5,

[0190] The distance from the locus of one of the 48 SNP markers of the present invention is less than 2 megabase units.

[0191] According to a preferred embodiment, the alternative marker is located in the chromosomal region delimited by CU-0004565 (SEQ ID NO: 2) and CU-0004683 (SEQ ID NO: 7) on chromosome 1, preferably by CU-0001726 (SEQ ID NO: 3) and CU-0001398 (SEQ ID NO: 6), more preferably by CU-0001212 (SEQ ID NO: 4) and CU-0001683 (SEQ ID NO: 5) for QTL1.1, or by CU-0008776 (SEQ ID NO: 37) and SNP CU-0000049 (SEQ ID NO: 38) on chromosome 1 for QTL1.2, or by CU-0007682 (SEQ ID NO: 55) and SNP CU-0000521 (SEQ ID NO: 56) on chromosome 5 for QTL5.

[0192] Furthermore, the one or more molecular markers are preferably associated with at least one of the following SNPs of the present invention with a p-value of 0.05 or less. More preferably, the p-value is preferably less than 0.01.

[0193] The molecular marker is preferably a SNP marker. It is more preferably located less than 1 megabase away from the locus of at least one of the 48 SNPs of the present invention.

[0194] Said QTL can be found in the seed deposit NCIMB 43844.

[0195] The present invention also relates to the use of at least one of the 48 SNPs of the present invention, which are associated with QTL1.1 (SEQ ID No: 11-35) on chromosome 1 and QTL1.2 (SEQ ID No: 40-53) on chromosome 1 and QTL5 (SEQ ID No: 58-64) on chromosome 5 that confer CGMMV tolerance, for identifying alternative molecular markers associated with the QTLs, wherein the alternative molecular markers are:

[0196] For QTL1.1, within the chromosomal region delineated by CU-0001918 (SED ID NO: 1) and CU-0006297 (SEQ ID NO: 2) on chromosome 1,

[0197] For QTL1.2, within the chromosomal region delineated by CU-0006144 (SEQ IS NO: 36) and CU-0001483 (SEQ ID NO: 39) on chromosome 1,

[0198] For QTL5, within the chromosomal region delineated by CU-0005234 (SEQ ID NO:54) and CU-0007979 (SEQ ID NO:57) on chromosome 5, or

[0199] At less than 2 megabase units from the locus of one of the 48 SNP markers of the present invention.

[0200] According to a preferred embodiment, the alternative marker is located in the chromosomal region delimited by CU-0004565 (SEQ ID NO: 2) and CU-0004683 (SEQ ID NO: 7) on chromosome 1, preferably by CU-0001726 (SEQ ID NO: 3) and CU-0001398 (SEQ ID NO: 6), more preferably by CU-0001212 (SEQ ID NO: 4) and CU-0001683 (SEQ ID NO: 5) for QTL1.1, or by CU-0008776 (SEQ ID NO: 37) and SNP CU-0000049 (SEQ ID NO: 38) on chromosome 1 for QTL1.2, or by CU-0007682 (SEQ ID NO: 55) and SNP CU-0000521 (SEQ ID NO: 56) on chromosome 5 for QTL5.

[0201] The surrogate molecular marker is preferably associated with said QTL with a p-value of 0.05 or less, preferably less than 0.01. The above QTL can be found in deposited seeds NCIMB 43844. The above QTL conferring CGMMV tolerance according to the present invention is the QTL present in CUC58.4 (NCIMB 43844).

[0202] Genetic association or linkage is as defined above; preferably, the association or linkage has a p-value preferably less than 0.05, and most preferably less than 0.01 or even less. The molecular marker and the tolerance phenotype are preferably inherited together in more than 90% of the meioses, preferably in more than 95% of the meioses.

[0203] The molecular markers according to this aspect of the invention are most preferably SNPs. They are more preferably located less than 1 megabase, preferably less than 0.5 megabase, from the locus of at least one of the 48 SNPs of the invention.

[0204] The present invention also includes a method for identifying molecular markers associated with QTLs involved in tolerance to CGMMV in cucumber, as described herein, comprising the following steps:

[0205] identifying a genetic marker within the chromosomal region delineated by SNP markers CU-0001918 (SEQ ID NO: 1) and CU-0006297 (SEQ ID NO: 2) on chromosome 1, or within the chromosomal region delineated by CU-0006144 (SEQ ID NO: 36) and CU-0001483 (SEQ ID NO: 39) on chromosome 1, or within the chromosomal region delineated by CU-0005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57) on chromosome 5,

[0206] Determine whether the allele or state of the molecular marker is associated with the phenotype of resistance to CGMMV virus in a segregating population generated from plants that exhibit resistance to CGMMV virus, such as in a segregating population generated from plants corresponding to deposited seeds.

[0207] The present invention also relates to the use of one or more molecular markers to identify or select cucumber plants, which contain in their genome a QTL that confers tolerance to CGMMV in cucumber plants (particularly cucumber planting variety plants), wherein the marker is located:

[0208] For QTL1.2, within the chromosomal region delineated by SNPs CU-0006144 and CU-0001483 on chromosome 1, and

[0209] Optionally for QTL1.1, within the chromosomal region delineated by SNP markers CU-0001918 and CU-0006297 on chromosome 1, and / or

[0210] Optionally for QTL5, within the chromosomal region on chromosome 5 delineated by SNPs CU-0005234 and CU-0007979.

[0211] Alternatively, the use of one or more molecular markers for identifying or selecting cucumber plants, which contain in their genome a QTL that confers tolerance to CGMMV on cucumber plants (particularly cucumber planting variety plants), wherein the marker is located less than 2 megabase units from the locus of at least one of the 48 SNP markers of the present invention; and wherein the molecular marker is associated with at least one of the SNPs of the present invention (i.e., Tables 6, 8 and 10).

[0212] The above-mentioned molecular markers to be used according to the present embodiment can be obtained in particular by the above-mentioned method for identifying other molecular markers or alternative molecular markers. The molecular markers are preferably SNP markers. They are more preferably located at less than 1 megabase of the locus of at least one of the 48 SNPs of the present invention.

[0213] According to a further aspect, the present invention also relates to a method for genotyping plants, preferably cucumber plants or cucumber germplasm, for the presence of at least one genetic marker associated with tolerance to CGMMV infection, wherein the method comprises the determination or detection of a nucleic acid in the genome of the tested plant, the nucleic acid comprising at least one of the markers of the invention, or comprising at least one of the alternative molecular markers as described above. Preferably, the method comprises the following steps: as already disclosed, identifying a specific sequence associated with tolerance to CGMMV in a sample of the tested plant, identifying a specific sequence associated with tolerance to CGMMV in a nucleic acid comprising at least one allele of a SNP of the invention.

[0214] Detection of a specific allele of a SNP can be performed by any method known to the reader in the art.

[0215] In view of the ability of the tolerant plants of the present invention to limit the damage caused by CGMMV infection, they are advantageously grown in environments that are infested or potentially infested or infected by CGMMV; under these conditions, the resistant or tolerant plants of the present invention produce more marketable cucumbers than susceptible plants. Therefore, the present invention also relates to a method for increasing the yield of cucumber plants in an environment infested by CGMMV, the method comprising planting cucumber plants comprising in their genome QTL1.2 on chromosome 1, optionally in combination with QTL1.1 on chromosome 1 and / or QTL5 on chromosome 5, wherein the QTL is defined according to the previous aspects of the present invention, conferring tolerance to CGMMV to the plant. Preferably, at least one of the three QTLs is present homozygously. Further preferably, two QTLs are present homozygously. More preferably, all QTLs are present homozygously.

[0216] Preferably, the above method comprises a first step of selecting or picking cucumber plants having the QTL of interest. The method can also be defined as a method for improving the productivity of cucumber fields, tunnels, greenhouses or glasshouses.

[0217] The present invention also relates to a method for reducing cucumber yield loss under CGMMV infection or infection conditions, comprising planting the cucumber plants as described above.

[0218] These methods are particularly valuable for populations of cucumber plants grown in the field, tunnels, greenhouses or glasshouses.

[0219] Alternatively, the method for increasing yield or reducing yield loss in cucumber may include a first step of identifying a CGMMV-resistant cucumber plant comprising QTL1.2 on chromosome 1 in its genome, and optionally combined with QTL1.1 on chromosome 1 and / or QTL5 on chromosome 5, conferring tolerance to CGMMV on the plant, and then planting the tolerant plant in an environment infected or potentially infected by the virus.

[0220] Therefore, the present invention relates to a method for increasing the yield of cucumber plants in an environment infected by CGMMV, the method comprising:

[0221] Identifying a CGMMV-resistant cucumber plant comprising in its genome QTL1.2, and optionally further comprising QTL1.1 and / or QTL5, wherein said QTL confers tolerance to CGMMV, and

[0222] The resistant cucumber plants are planted in the infested environment.

[0223] In this way, if the yield of the cucumber plants is increased, it is possible in particular to harvest more marketable cucumbers, or to produce more commercial cucumbers, or to obtain more seeds.

[0224] The tolerant plants of the present invention can also at least partially limit the growth of CGMMV, thereby limiting the infection of other plants and the reproduction of the virus. Therefore, the present invention also relates to a method for protecting fields, arch sheds, greenhouses or glass houses or any other type of plantation from CGMMV infection, or at least limiting the degree of infection of the fields, arch sheds, greenhouses or glass houses by CGMMV, or limiting the spread of CGMMV in fields, arch sheds, greenhouses or glass houses (especially in glass houses). This method preferably includes the step of planting the tolerant plants of the present invention, i.e., plants containing QTL1.2, and optionally QTL1.1 and / or QTL5 in their genome, QTL1.2 and optionally QTL1.1 and / or QTL5 conferring tolerance to CGMMV to the plants.

[0225] The present invention also relates to the use of a CGMMV-resistant plant for controlling CGMMV infection or infestation in fields, arch sheds, greenhouses or glasshouses, or other plantations; such a plant is a plant of the present invention, which contains QTL1.2 in its genome as described above, and optionally QTL1.1 and / or QTL5. According to this use, the plant of the present invention is therefore used to protect fields, arch sheds, greenhouses or glasshouses from CGMMV infection.

[0226] The present invention is further illustrated by the following figures and examples. BRIEF DESCRIPTION OF THE DRAWINGS

[0227] Figure 1 : Correlation between the QTLs and the tolerance or resistance phenotype (each QTL individually) based on the alleles of one SNP for each QTL, namely CU-0002804 for QTL1.1, CU6-0005119 for QTL1.2 and CU0007750 for QTL5.

[0228] Figure 2 : Correlation between the QTLs and the tolerance or resistance phenotype for all QTL combinations, based on the alleles of one SNP for each QTL, namely CU-0002804 for QTL1.1, CU6-0005119 for QTL1.2 and CU0007750 for QTL5.

[0229] Example

[0230] Example 1: Phenotyping scheme and screening of resistant plants

[0231] Between 2013 and 2016, trials were conducted aimed at discovering CGMMV resistance leads in cucumber. After screening potential leads, 60 genotypes (landraces) were selected. Additional commercial hybrids (S-hybrid) and breeding lines (S-Breeding line) were tested as susceptible controls based on previous observations in the breeding program. The selected genotypes are shown in Table 1.

[0232] Table 1: Selected cucumber genotypes

[0233]

[0234]

[0235] The test was a mechanical infection. The inoculation process was as follows:

[0236] Screening was done by sowing seeds in seedling trays (33 to 48 seeds per row). Each plant was scored individually. The plants for this test were transplanted to the greenhouse at 21 days after infection (dpi).

[0237] Cucumber leaves containing CGMMV were used as the inoculum source.

[0238] Inoculum preparation: Cucumber leaves containing CGMV were dried and stored frozen (-80°C) until used for mechanical inoculation. On the day of inoculation, the frozen tissue was manually ground with cold water and silicon carbide powder. Mechanical inoculation was performed by rubbing the plants at the cotyledon stage or at the beginning of the development of the first true leaf.

[0239] The propagation of the isolate was carried out on a susceptible variety called Romi-F1.

[0240] Phenotypic evaluation is performed based on 4 disease indicators:

[0241] 1. Very susceptible: strong mottled pattern, all the way to the top

[0242] 2. Susceptible: Strong piebaldness, but not at the top or slightly at the top

[0243] 3. Medium: Weaker variegation, but on a few lower and middle leaves

[0244] 4. Resistance: Completely clean or unclear spots

[0245] During the season, evaluation of symptom levels was performed 4 times, at 21 days, 30 days, 45 days, and 60 days after infection (dpi). All data presented in Tables 2 to 4 correspond to evaluations performed at 60 dpi. However, if plants were evaluated as very susceptible (scored as 1) during the first evaluation, they were removed from the trial and explicitly marked as 1 (i.e., very susceptible).

[0246] Table 2: Phenotypic assessments during spring 2013

[0247]

[0248]

[0249]

[0250] Table 3: Phenotypic assessments during spring 2015

[0251]

[0252] Further testing led to the discovery of two leads, Cuc58 and Cuc60. In the same year, 2016, Cuc58 and Cuc60 were self-bred and their offspring were evaluated to identify the best lead.

[0253] Table 4: Phenotypic assessments during spring 2016

[0254]

[0255]

[0256] Cuc58 was confirmed to be the best lead, and the Cuc58.4 plant and the progeny of Cuc58 were selected for further studies.

[0257] Example 2: Creation of an F2 mapping population derived from Cuc58.4 x Cuc61.

[0258] An F2 mapping population was created with the susceptible breeding line as the susceptible parent, namely Cuc58.4 (R parent)*Cuc61 (S parent).

[0259] To obtain more accurate phenotypic data, the mapping population was phenotyped using the following levels: 1 = very susceptible, 3 = susceptible, 5 = intermediate resistance (IR), 7 = more resistant than IR but not resistant, 9 = resistant.

[0260] Five different evaluations of the phenotype were performed starting from 3 weeks post infection (1st evaluation) to 10 weeks post infection (5th evaluation). The 1st evaluation was at the seedling stage in trays, and the 2nd to 5th evaluations were performed at 34, 40, 53 and 67 DPI (days post inoculation) after transplanting to the greenhouse.

[0261] Example 3: QTL analysis of F2 mapping population derived from Cuc58.4 x Cuc61.

[0262] Complete QTL analysis was performed using available SNPs.

[0263] A first selection of potential SNPs was performed based on their allelic variation between Cuc58.4 and Cuc61. The F2 mapping population was screened using a custom Affymetrix array (a set of 3312 SNPs) covering all chromosomes.

[0264] Genotypic analysis revealed three QTLs associated with resistance:

[0265] The QTL interval at the origin of chromosome 1 is between CU-0001726 (pos.450655) and CU-0001233 (pos.2603822), with LOD=17.

[0266] The QTL interval at the end of chromosome 1 is between CU-0006143 (pos.23286654) and CU-0000987 (pos.24850252), with LOD=40.

[0267] The third QTL was detected on chromosome 5, located between CU-0000533 (pos.9205026) and CU-0005413 (pos.12603711), with LOD=15.

[0268] The sequences of the SNPs on chromosomes 1 and 5, including the surrounding sequences, and the positions in the cucumber genome (according to the reference genome 9930v3 (Li et al., 2019)) are given in Tables 5 to 10. Table 11 gives the results of the QTL analysis, i.e., the lod value and the heritability value (% var). The Lod parameter does indicate the correlation with the tolerance phenotype (the highest value indicates the highest correlation), and the heritability value (% var) indicates the effect of the marker on the disease tolerance phenotype (the highest value indicates the highest effect on the tolerance phenotype).

[0269] Figure 1 The correlation between the QTL and the tolerance or resistance phenotype is shown for each QTL in Figure 2 All QTLs combined are shown in Table 11, and the correlation between SNPs and tolerance or resistance is shown in Table 11. One-way ANOVA for each SNP allele for each QTL is disclosed in Table 12-Table 14. The marker associated with QTL1.2 (i.e., CU6-0005119) explained 42% of the observed resistance or tolerance phenotype (Rsquare 0.423506).

[0270] DRCE1301 (CPVO application number A202000408) is a cucumber variety (Cucumis sativus L.) known to express resistance to CGMMV. Comparative testing was performed using SNPs associated with QTL1.1 (Table 6) and QTL1.2 (Table 8). Alleles represented by QTL1.1 and QTL1.2 are present in Cuc58.4 but not in DRCE1301. Therefore, QTL1.1 and QTL1.2 are not present in DRCE1301 (see Table 15).

[0271] Patent application US2021 / 285008 also describes cucumber plants resistant to CGMMV. The resistance QTL disclosed in this patent application is located on chromosome 1. Based on the published cucumber genome v2 map, the QTL is at the beginning of chromosome 1, starting at 1723554bp and ending at 3791533bp (Table 2, US2021 / 285008).

[0272] According to the same genetic map, QTL1.1 is located between 930046bp (CU-0000760) and 2695663bp (CU-0006247) at the start of chromosome 1, and QTL1.2 is located between 23286654bp (CU-0006143) and 24850252bp (CU-0000987) at the end of chromosome 1. Therefore, the QTL disclosed in US2021 / 285008 and QTL1.2 disclosed in the present application are located at each end of chromosome 1, respectively, and are therefore two different QTLs at least 19000000bp apart.

[0273] Table 5: SNPs present at the boundaries of QTL1.1 on chromosome 1 (QTL1.1 is contained between any combination of one SNP from group X and one SNP from group Y). Polymorphisms are indicated in brackets. Both alleles of each SNP represent one boundary of QTL1.1. Location on cucumber genome published by Li et al., 2019 (9930v3).

[0274]

[0275] Table 6: SNPs present in QTL1.1 on chromosome 1. Polymorphisms are indicated in brackets. The allele representing the presence of the QTL is shown in "bold" in brackets and reported in the last column (tolerant T allele). Location in cucumber genome was published by Li et al., 2019 (9930v3).

[0276]

[0277]

[0278]

[0279] Table 7: SNPs present at the boundaries of QTL1.2 on chromosome 1 (QTL1.2 is contained between any combination of one SNP from group X and one SNP from group Y). Polymorphisms are indicated in brackets. Both alleles of each SNP represent one boundary of QTL1.2. Location in cucumber genome was published by Li et al., 2019 (9930v3).

[0280]

[0281] Table 8: SNPs present in QTL1.2 on chromosome 1. Polymorphisms are indicated in brackets. The allele representing the presence of the QTL is shown in "bold" in brackets and reported in the last column (tolerant T allele). Location on the cucumber genome was published by Li et al., 2019 (9930v3).

[0282]

[0283]

[0284]

[0285] Table 9: SNPs present at the boundaries of QTL5 on chromosome 5 (QTL5 is contained between any combination of one SNP from group X and one SNP from group Y). Polymorphisms are indicated in brackets. Both alleles of each SNP represent one boundary of QTL5. Location on cucumber genome published by Li et al., 2019 (9930v3).

[0286]

[0287] Table 10: SNPs present in QTL5 on chromosome 5. Polymorphisms are indicated in brackets. The allele representing the presence of the QTL is shown in "bold" in brackets and reported in the last column (tolerant T allele). Location on the cucumber genome was published by Li et al., 2019 (9930v3).

[0288]

[0289]

[0290] Table 11: QTL analysis of F2 population. Correlation between SNPs and tolerance or resistance. Location on cucumber genome was published by Li et al., 2019 (9930v3). The Lod parameter does indicate correlation with the tolerance phenotype (highest value indicates highest correlation), and the heritability value (% var) indicates the effect of the marker on the disease tolerance phenotype (highest value indicates highest effect on the tolerance phenotype).

[0291]

[0292]

[0293]

[0294]

[0295] Table 12: One-way ANOVA analysis of QTL1.1 by CU0002804

[0296]

[0297] Table 13: One-way ANOVA analysis of QTL1.2 by CU0005159

[0298]

[0299] Table 14: One-way ANOVA analysis of QTL5 by CU0007750

[0300]

[0301] Table 15: Comparative test: Presence of SNPs associated with QTL1.1 and QTL1.2 in Cuc58.4 and DRCE1301. Alleles representing the presence of QTL1.1 and QTL1.2 are shown in "bold" and reported in the last column (tolerant T allele).

[0302]

Claims

1. A cucumber plant resistant to cucumber green mottle mosaic virus (CGMMV), comprising a quantitative trait locus (QTL) on chromosome 1 in its genome, wherein: The QTL confers tolerance to CGMMV on the plant.

2. The plant according to claim 1, wherein The QTL on chromosome 1 is QTL1.2 located within the chromosomal region delineated by CU-0006144 (SEQ ID NO: 36) and CU-0001483 (SEQ ID NO: 39).

3. The plant according to claim 1 or 2, wherein: QTL1.2 includes at least one of the following alleles: Allele A of CU-0006143 consisting of SEQ ID NO:40, wherein the nucleotide at position 36 is A, Allele A of CU-0003007 consisting of SEQ ID NO:41, wherein the nucleotide at position 36 is A, Allele A of CU-0001935 consisting of SEQ ID NO:42, wherein the nucleotide at position 36 is A, Allele A of CU-0003410 consisting of SEQ ID NO:43, wherein the nucleotide at position 36 is A, Allele G of CU-0002841 consisting of SEQ ID NO:44, wherein the nucleotide at position 36 is G, Allele G of CU-0005159 consisting of SEQ ID NO:45, wherein the nucleotide at position 36 is G, Allele A of CU-0003498 consisting of SEQ ID NO:46, wherein the nucleotide at position 36 is A, Allele G of CU-0004638 consisting of SEQ ID NO:47, wherein the nucleotide at position 36 is G, Allele A of CU-0000697 consisting of SEQ ID NO:48, wherein the nucleotide at position 36 is A, Allele G of CU-0000649 consisting of SEQ ID NO:49, wherein the nucleotide at position 36 is G, Allele A of CU-0003579 consisting of SEQ ID NO:50, wherein the nucleotide at position 36 is A, Allele G of CU-0003759 consisting of SEQ ID NO:51, wherein the nucleotide at position 36 is G, Allele G of CU-0001719 consisting of SEQ ID NO:52, wherein the nucleotide at position 36 is G, Allele A of CU-0000987 consisting of SEQ ID NO:53, wherein the nucleotide at position 36 is A.

4. The plant of any one of claims 1 to 3, further comprising at least one additional QTL conferring tolerance to CGMMV, wherein The at least one additional QTL is: QTL1.1, located on chromosome 1, within the chromosomal region delineated by CU-0001918 (SEQ ID NO: 1) and CU-0006297 (SEQ ID NO: 8); and / or QTL5, located on chromosome 5, is within the chromosomal region delineated by CU-00005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57).

5. The plant according to claim 4, wherein: The QTL1.1 includes at least one of the following alleles: Allele G of CU-000760 consisting of SEQ ID NO:9, wherein the nucleotide at position 36 is G, Allele G of CU-0005918 consisting of SEQ ID NO: 10, wherein the nucleotide at position 36 is G, Allele G of CU-0001201 consisting of SEQ ID NO: 11, wherein the nucleotide at position 36 is G, Allele C of CU-0004609 consisting of SEQ ID NO: 12, wherein the nucleotide at position 36 is C, Allele G of CU-0000028 consisting of SEQ ID NO: 13, wherein the nucleotide at position 36 is G, Allele A of CU-0003841 consisting of SEQ ID NO: 14, wherein the nucleotide at position 36 is A, Allele A of CU-0005952 consisting of SEQ ID NO: 15, wherein the nucleotide at position 36 is A, Allele G of CU-0000131 consisting of SEQ ID NO: 16, wherein the nucleotide at position 36 is G, Allele G of CU-0004274 consisting of SEQ ID NO: 17, wherein the nucleotide at position 36 is G, Allele G of CU-0002804 consisting of SEQ ID NO: 18, wherein the nucleotide at position 36 is G, Allele A of CU-0008736 consisting of SEQ ID NO: 19, wherein the nucleotide at position 36 is A, Allele G of CU-0000648 consisting of SEQ ID NO: 20, wherein the nucleotide at position 36 is G, Allele A of CU-0002063 consisting of SEQ ID NO: 21, wherein the nucleotide at position 36 is A, Allele G of CU-0008746 consisting of SEQ ID NO: 22, wherein the nucleotide at position 36 is G, Allele A of CU-0002751 consisting of SEQ ID NO:23, wherein the nucleotide at position 36 is A; Allele A of CU-0002122 consisting of SEQ ID NO: 24, wherein the nucleotide at position 36 is A, Allele C of CU-0006155 consisting of SEQ ID NO:25, wherein the nucleotide at position 36 is C, Allele G of CU-0001458 consisting of SEQ ID NO: 26, wherein the nucleotide at position 36 is G, Allele G of CU-0006165 consisting of SEQ ID NO: 27, wherein the nucleotide at position 36 is G, Allele G of CU-0006164 consisting of SEQ ID NO: 28, wherein the nucleotide at position 36 is G, Allele A of CU-0006180 consisting of SEQ ID NO: 29, wherein the nucleotide at position 36 is A, Allele A of CU-0000058 consisting of SEQ ID NO:30, wherein the nucleotide at position 36 is A, Allele C of CU-0000848 consisting of SEQ ID NO:31, wherein the nucleotide at position 36 is C, Allele G of CU-0001233 consisting of SEQ ID NO:32, wherein the nucleotide at position 36 is G, Allele C of CU-0005032 consisting of SEQ ID NO:33, wherein the nucleotide at position 36 is C, Allele A of CU-0004710 consisting of SEQ ID NO:34, wherein the nucleotide at position 36 is A, and Allele A of CU-0006247 consisting of SEQ ID NO:35, wherein the nucleotide at position 36 is A; and / or The QTL5 comprises at least one of the following alleles: Allele G of CU-0000533 consisting of SEQ ID NO:58, wherein the nucleotide at position 36 is G, Allele G of CU-0001575 consisting of SEQ ID NO:59, wherein the nucleotide at position 36 is G, Allele A of CU-0009561 consisting of SEQ ID NO:60, wherein the nucleotide at position 36 is A, Allele G of CU-0007750 consisting of SEQ ID NO:61, wherein the nucleotide at position 36 is G, Allele A of CU-0002973 consisting of SEQ ID NO:62, wherein the nucleotide at position 36 is A, Allele G of CU-0001079 consisting of SEQ ID NO:63, wherein the nucleotide at position 36 is G, Allele A of CU-0005413 consisting of SEQ ID NO:64, wherein the nucleotide at position 36 is A.

6. The plant according to any one of claims 1 to 5, wherein Said QTL1.2, QTL1.1 and QTL5 conferring tolerance to CGMMV can be obtained from a donor plant deposited with NCIMB under accession number 43844, having the genetic background of the seed genome of plant CUC58.4, or from its progeny comprising said QTL.

7. The plant according to any one of claims 1 to 5, wherein The plant is a descendant of, or is derived from, plant CUC58.4, seeds of which have been deposited at NCIMB under accession number 43844.

8. A cell of a cucumber plant according to any one of claims 1 to 7, comprising QTL1.2, and optionally QTL1.1 and / or QTL5 in its genome, wherein: The QTL confers tolerance to CGMMV.

9. A plant part of the cucumber plant according to any one of claims 1 to 8, comprising QTL1.2, and optionally QTL1.1 and / or QTL5 in its genome, in particular a seed, an explant, a propagation material, a scion, a cutting, a fruit, a root, a rootstock, a pollen, an ovule, an embryo, a protoplast, a leaf, an anther, a stem, a petiole or a flower.

10. A seed of a cucumber plant, said seed being capable of developing into a plant according to any one of claims 1 to 7.

11. The tissue culture of regenerable cells of a cucumber plant according to any one of claims 1 to 7, wherein The regenerable cells are derived from embryos, protoplasts, meristems, callus, pollen, leaves, anthers, stems, petioles, roots, root tips, seeds, flowers, cotyledons and / or hypocotyls, and contain QTL1.2, and optionally QTL1.1 and / or QTL5, which QTLs confer tolerance to CGMMV.

12. A CGMMV-resistant hybrid cucumber plant obtainable by hybridizing a cucumber plant with the CGMMV-resistant cucumber plant according to any one of claims 1 to 7.

13. A cucumber plant or seed, or use of its progeny, wherein the plant or seed is deposited with NCIMB under accession number 43844, and the progeny is homozygous for carrying the QTL1.1, QTL1.2 and QTL5 that are tolerant to CGMMV, for use as a breeding partner in a breeding program for conferring tolerance to CGMMV on cucumber plants, preferably cucumber plants susceptible to CGMMV.

14. A method for detecting and / or selecting cucumber plants comprising a QTL as defined in claims 1 to 7 and conferring tolerance to CGMMV, wherein: The method comprises in a sample of genetic material of the cucumber plant: The QTL1.2 is detected by the presence of at least one of the following alleles: Allele A of CU-0006143 consisting of SEQ ID NO:40, wherein the nucleotide at position 36 is A, Allele A of CU-0003007 consisting of SEQ ID NO:41, wherein the nucleotide at position 36 is A, Allele A of CU-0001935 consisting of SEQ ID NO:42, wherein the nucleotide at position 36 is A, Allele A of CU-0003410 consisting of SEQ ID NO:43, wherein the nucleotide at position 36 is A, Allele G of CU-0002841 consisting of SEQ ID NO:44, wherein the nucleotide at position 36 is G, Allele G of CU-0005159 consisting of SEQ ID NO:45, wherein the nucleotide at position 36 is G, Allele A of CU-0003498 consisting of SEQ ID NO:46, wherein the nucleotide at position 36 is A, Allele G of CU-0004638 consisting of SEQ ID NO:47, wherein the nucleotide at position 36 is G, Allele A of CU-0000697 consisting of SEQ ID NO:48, wherein the nucleotide at position 36 is A, Allele G of CU-0000649 consisting of SEQ ID NO:49, wherein the nucleotide at position 36 is G, Allele A of CU-0003579 consisting of SEQ ID NO:50, wherein the nucleotide at position 36 is A (SEQ ID NO:50), Allele G of CU-0003759 consisting of SEQ ID NO:51, wherein the nucleotide at position 36 is G, Allele G of CU-0001719 consisting of SEQ ID NO:52, wherein the nucleotide at position 36 is G, Allele A of CU-0000987 consisting of SEQ ID NO:53, wherein the nucleotide at position 36 is A; and Optionally, said QTL1.1 is detected by the presence of at least one of the following alleles: Allele G of CU-000760 consisting of SEQ ID NO:9, wherein the nucleotide at position 36 is G, Allele G of CU-0005918 consisting of SEQ ID NO: 10, wherein the nucleotide at position 36 is G, Allele G of CU-0001201 consisting of SEQ ID NO: 11, wherein the nucleotide at position 36 is G, Allele C of CU-0004609 consisting of SEQ ID NO: 12, wherein the nucleotide at position 36 is C, Allele G of CU-0000028 consisting of SEQ ID NO: 13, wherein the nucleotide at position 36 is G, Allele A of CU-0003841 consisting of SEQ ID NO: 14, wherein the nucleotide at position 36 is A, Allele A of CU-0005952 consisting of SEQ ID NO: 15, wherein the nucleotide at position 36 is A, Allele G of CU-0000131 consisting of SEQ ID NO: 16, wherein the nucleotide at position 36 is G, Allele G of CU-0004274 consisting of SEQ ID NO: 17, wherein the nucleotide at position 36 is G, Allele G of CU-0002804 consisting of SEQ ID NO: 18, wherein the nucleotide at position 36 is G, Allele A of CU-0008736 consisting of SEQ ID NO: 19, wherein the nucleotide at position 36 is A, Allele G of CU-0000648 consisting of SEQ ID NO: 20, wherein the nucleotide at position 36 is G, Allele A of CU-0002063 consisting of SEQ ID NO: 21, wherein the nucleotide at position 36 is A, Allele G of CU-0008746 consisting of SEQ ID NO: 22, wherein the nucleotide at position 36 is G, Allele A of CU-0002751 consisting of SEQ ID NO: 23, wherein the nucleotide at position 36 is A, Allele A of CU-0002122 consisting of SEQ ID NO: 24, wherein the nucleotide at position 36 is A, Allele C of CU-0006155 consisting of SEQ ID NO:25, wherein the nucleotide at position 36 is C, Allele G of CU-0001458 consisting of SEQ ID NO: 26, wherein the nucleotide at position 36 is G, Allele G of CU-0006165 consisting of SEQ ID NO: 27, wherein the nucleotide at position 36 is G, Allele G of CU-0006164 consisting of SEQ ID NO: 28, wherein the nucleotide at position 36 is G, Allele A of CU-0006180 consisting of SEQ ID NO: 29, wherein the nucleotide at position 36 is A, Allele A of CU-0000058 consisting of SEQ ID NO:30, wherein the nucleotide at position 36 is A, Allele C of CU-0000848 consisting of SEQ ID NO:31, wherein the nucleotide at position 36 is C, Allele G of CU-0001233 consisting of SEQ ID NO:32, wherein the nucleotide at position 36 is G, Allele C of CU-0005032 consisting of SEQ ID NO:33, wherein the nucleotide at position 36 is C, Allele A of CU-0004710 consisting of SEQ ID NO:34, wherein the nucleotide at position 36 is A, and Allele A of CU-0006247 consisting of SEQ ID NO:35, wherein the nucleotide at position 36 is A; and Optionally, the QTL5 is detected by the presence of at least one of the following alleles: Allele G of CU-0000533 consisting of SEQ ID NO:58, wherein the nucleotide at position 36 is G, Allele G of CU-0001575 consisting of SEQ ID NO:59, wherein the nucleotide at position 36 is G, Allele A of CU-0009561 consisting of SEQ ID NO:60, wherein the nucleotide at position 36 is A, Allele G of CU-0007750 consisting of SEQ ID NO:61, wherein the nucleotide at position 36 is G, Allele A of CU-0002973 consisting of SEQ ID NO:62, wherein the nucleotide at position 36 is A, Allele G of CU-0001079 consisting of SEQ ID NO:63, wherein the nucleotide at position 36 is G, Allele A of CU-0005413 consisting of SEQ ID NO:64, wherein the nucleotide at position 36 is A.

15. A method for detecting and / or selecting cucumber plants comprising a QTL as defined in claims 1 to 7 and conferring tolerance to CGMMV, the method comprising: a) testing cucumber plants for the presence of at least one genetic marker genetically associated with QTL1.2 and optionally, (i) at least one genetic marker genetically associated with QTL1.1, and / or (ii) at least one genetic marker genetically associated with QTL5; b) selecting plants comprising said genetic marker and the QTL conferring tolerance to CGMMV, Wherein, the QTL1.1 is located on chromosome 1, within the chromosomal region delineated by CU-0001918 (SEQ ID NO: 1) and CU-0006297 (SEQ ID NO: 8); The QTL1.2 is located on chromosome 1, within the chromosomal region delineated by CU-0006144 (SEQ ID NO: 36) and CU-0001483 (SEQ ID NO: 39); The QTL5 is located on chromosome 5, within the chromosomal region delineated by CU-00005234 (SEQ ID NO: 54) and CU-0007979 (SEQ ID NO: 57).

16. A method for reducing yield loss in cucumbers under CGMMV infection, comprising growing cucumber plants comprising in their genome said QTL as defined in claims 1 to 6 and 14 and conferring tolerance to CGMMV on said plants, wherein, The QTL is present in the genome of the plant with seed CUC58.4, NCIMB number 43844.

17. A use of a cucumber plant resistant to CGMMV for controlling CGMMV infection in fields, arch sheds, greenhouses or glass houses, wherein: The cucumber plant comprises in its genome the QTL as defined in claims 1 to 6 and 14 and confers tolerance to CGMMV to the plant, wherein the QTL is present in the genome of the plant of seed CUC58.4, NCIMB accession number 43844.

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