Patent Publication Number: US-2021163981-A1

Title: Tospovirus Resistant Plants and Methods Thereof

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This Application is a continuation-in-part of U.S. patent application Ser. No. 15/555,937, filed on Sep. 5, 2017, which application is a 371 application of PCT/IB2017/055151 filed on Aug. 28, 2017; the disclosures of which applications are herein incorporated by reference. 
    
    
     INTRODUCTION 
     Field of the Invention 
     The present invention relates to the field of agricultural biotechnology more specifically to the development of disease resistant tomato lines. 
     Background 
     Viruses of the genus TOSPO cause significant worldwide crop losses.  Tospoviruses  have a tripartite RNA genome of ambisense polarity. The  Tospovirus  genus includes plant viruses that infect a wide range of plant species including vegetable, fruit, and ornamental crops. The viruses belonging to this genus are popularly described as  Tospovirus  and the tomato spotted wilt virus is a type of species belonging to this genus.  Tospoviruses  are distributed in tropical, subtropical and temperate regions throughout the Northern Hemisphere, Western Europe and Asia. Groundnut bud necrosis virus (GBNV) is currently recognized as the most economically important  Tospovirus  in South Asia &amp; South East Asia. Losses due to GBNV alone have been estimated at more than US$89 million per annum in Asia. 
     The transmission of the disease is by the vector  Thrips palmi.  The disease is affecting tomato crop cultivation to the tune of 350,000 hectares per year in India, especially in Kharif season. Control of  Tospoviruses  remains problematic. Cultural practices and varietal selection have proven effective in minimizing losses due to tomato spotted wilt virus (TSWV) in some field crops. A series of risk factors including prior history, planting date, cultivar selection and plant and row spacing have been identified as critical factors in peanuts. In other high-risk areas, such as Hawaii, highly susceptible crops cannot be grown profitably. In greenhouse grown crops, such as floral crops, extreme measures including screening of production areas with fine-meshed cloth, preventative  Thrips  management strategies and use of propagation material shown to be free of TSWV and impatiens necrosis spot virus (INSV) are necessary for control of these viruses. 
     While forms of resistance have been introduced into various crops, they have nearly always been overcome by the rapid occurrence of resistance-breaking strains of the virus. TSWV is thought to exist in nature as a complex heterogeneous mixture of distinct isolates that can exchange genetic information through re-assortment of genome segments. This provides a readily available reservoir of genetic information to facilitate adaptation. For the reasons stated above control of the disease is a challenge so far. Various resistant genes were identified and designated as Swa1, Swb1, Sw2, Sw3, and Sw4, Sw-5, Sw6, Sw7 from wild source of tomato ( S. peruvianum ) against TOSPO virus. 
     However, these resistance genes are not effective to control the GBNV disease in India. Chemical control measures have not been able to contain the disease and farmers are suffering yield loss on account of the disease outbreak. The estimated loss (Kunkalikar, S. R. et al (2011) is around 80% per season of the crop. The calculated loss to the farmer in India is approximate US$25 million if approximately 50% of acreage gets affected by the disease i.e. 175,000 hectares. 
     As known genetic resistance and chemical measures are not effective in the control of the disease, there is a need to develop an edible and cultivable tomato line resistant to GNB V. 
     SUMMARY 
     Aspects of the invention include an edible and cultivable tomato line resistant to GNBV, and related method for developing such a line. 
     The invention also relates to a cultivable &amp; edible F1 hybrid variety resistant to GBNV, and related method for developing such a hybrid line. 
     The invention relates to the identification of DNA markers linked to GBNV resistance trait and use of marker-assisted breeding for selection of resistant edible and cultivable tomato line or F1 hybrid variety 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS AND FIGURES 
         FIG. 1  shows the flow chart of breeding interspecific cross up to BC2F2. 
         FIG. 2  shows the flow chart of breeding BC2F3 to current status. 
         FIG. 3  depicts the frequency distribution of TOSPO (GBNV) disease over generations. 
         FIG. 4  shows photomicrographs of the disease scoring chart. 
         FIG. 5  depicts the distribution of BC2F3 lines with different recipient allele frequency based on 2455 SNP. 
         FIG. 6  shows BC2F6 &amp; BC2F7 families (RP×SP1)×SP2 indicating trait linked markers in resistant progenies. 
     
    
    
     SEQUENCE LISTING 
     A computer-readable text file, entitled “FP07311 SequenceListing.txt,” created on or about Jan. 27, 2021 with a file size of about 6 kb contains the sequence listing for this application and is hereby incorporated by reference in its entirety. The Tomato Genotype Data, including assembled tomato genome version 2.40 contained in websites and publications by Solanaceae Coordinated Agricultural Project (SolCAP) is incorporated by reference in its entirety. The tomato genome was published on May 30, 2021 at The Tomato Genome Consortium., Kazusa DNA Research Institute., Sato, S. et al. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641 (2012). https://doi.org/10.1038/nature11119; the disclosure of which is herein incorporated by reference. 
     DETAILED DESCRIPTION 
     The inventors have identified  Solanum peruvianum  line which displays tolerance or resistance to Ground nut bud necrosis virus (GBNV). The inventors have identified the Single Nucleotide Polymorphisms (SNPs) which confers the GBNV-resistance trait. Further, the inventors have successfully been able to introgress the trait from the donor  Solanum peruvianum  in  Solanum lycopersicum  lines through marker assisted breeding. This has led to the development of cultivable and edible variety of  Solanum lycopersicum  which are resistant to GBNV. 
     Accordingly, the present invention provides an edible and cultivable tomato line resistant to Ground nut bud necrosis virus (GBNV), and related method for developing such line. 
     The invention also relates to development of cultivable and edible F1 hybrid variety resistant to GBNV, and related method thereof. 
     The invention relates to the identification of markers and use of marker assisted breeding for selection of GBNV resistant edible and cultivable tomato line. 
     The donor is a  Solanum peruvianum  line obtained from World Vegetable Centre—Asian Vegetable Research and Development Center (AVRDC), Taiwan. The donor line is commercially available, and it is also available from the Asian Vegetable Research and Development Center (AVRDC), Taiwan under Accession No. L00671. 
     Cultivated lines used for development of progeny were SP-1 (Susceptible parent 1—Sel 22, obtained from Indian Institute of Horticultural Research Bengaluru (IIHR), a commercial variety since 1985) and SP-2 (Susceptible line)—collected from AVRDC carrying Ty 2 gene that gives partial resistance against TyLCV (Tomato Yellow Leaf Curl Virus) but susceptible to TOSPO (GBNV). 
     In an embodiment, any suitable susceptible line of  Solanum lycopersicum  can be used for development of the progeny having resistance to GBNV. Preferably, a  S. lycopersicum  recipient plant according to the invention is a commercial plant or line. 
     The term “Resistance” as used herein is as defined by the ISF (International Seed Federation) Vegetable and Ornamental Crops Section for describing the reaction of plants to pests or pathogens, and abiotic stresses for the Vegetable Seed Industry. 
     The term “single nucleotide polymorphism” or “SNP” means substitution of a deoxynucleotide in a single stranded DNA sequence by a different deoxynucleotide. Such substitution is commonly referred to as single base substitution, where the bases are adenine, guanine, cytosine, and thymine. The respective deoxynucleotides are deoxyadenylate, deoxyguanylate, deoxycytidylate, and deoxythymidylate. The bases and the deoxynucleotides are represented as A, G, C, and T respectively. When a SNP is linked to a specific trait (such as resistance to GBNV), the deoxynucleotide that is substituted is considered the SNP. 
     The term “variant” refers to a single nucleotide polymorphism that is different than its wild type counterpart, and which can confer the GBNV-resistance trait. 
     The term “The term “quantitative trait locus” or “QTL” refers to a polymorphic genetic locus with at least two alleles that differentially affect the expression of a phenotypic trait in at least one genetic background, e.g., in at least one breeding population or progeny. 
     In one embodiment, the present invention discloses molecular genetic markers, especially SNPs, linked to the GBNV resistance loci. 
     In one embodiment, the invention provides a method of producing a tomato plant, wherein the tomato plant exhibits resistance to Groundnut bud necrosis virus infection, comprising:
         i) providing a donor  Solanum peruvianum  tomato plant exhibiting resistance to Groundnut bud necrosis virus infection, wherein the donor plant comprises at least one SNP corresponding to a quantitative trait locus (QTL) indicative of Groundnut bud necrosis virus resistance on chromosome 1 or chromosome 2, and wherein the SNP is selected from a group consisting of:
           (a) variant A or T of SNP solcap_snp_sl_1815 at position 74315042 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 1);   (b) variant C or G of SNP solcap_snp_sl_1819 at position 74329911 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 2);   (c) variant A or T of SNP solcap_snp_sl_1824 at position 74464953 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 3);   (d) variant A or G of SNP solcap_snp_sl_17075 at position 74483269 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 4);   (e) variant A or T of SNP solcap_snp_sl_1827 at position 74602284 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 5);   (f) variant A or G of SNP solcap_snp_sl_21280 at position 76783695 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 6);   (g) variant A or C of SNP solcap_snp_sl_34568 at position 76905658 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 7);   (h) variant T or C of SNP solcap_snp_sl_36202 at position 47651366 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 8);   (i) variant A or G of SNP solcap_snp_sl_21866 at position 47950096 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 9);   (j) variant A or G of SNP solcap_snp_sl_21862 at position 47981517 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 10);   (k) variant T or C of SNP solcap_snp_sl_31689 at position 47996412 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 11);   (l) variant T or G of SNP solcap_snp_sl_20063 at position 48455087 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 12);   (m) variant T or C of SNP solcap_snp_sl_21966 at position 48370810 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 13);   (n) variant A or G of SNP solcap_snp_sl_58447 at position 48602171 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 14);   (o) variant T or C of SNP solcap_snp_sl_20049 at position 48697164 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 15); and   (p) variant A or G of SNP solcap_snp_sl_21867 at position 47948927 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 16);   
           ii) crossing the donor tomato plant with a recipient  Solanum lycopersicum  plant to produce F1  Solanum lycopersicum  progeny tomato plants, wherein the recipient tomato plants does not exhibit resistance to Groundnut bud necrosis virus and the crossing results in introgression of one or more quantitative trait locus (QTL) on chromosome 1 or chromosome 2 indicative of Groundnut bud necrosis virus resistance in the progeny tomato plants;   iii) generating further offspring progeny tomato plants from said F1 progeny plant by backcrossing or selfing; and   iv) identifying and selecting a Groundnut bud necrosis virus resistant progeny tomato plant obtained through step (b) and step (c), wherein the progeny tomato plant comprises at least one SNP corresponding to a quantitative trait locus (QTL) indicative of Groundnut bud necrosis virus resistance on chromosome 1 or chromosome 2, and wherein the SNP is selected from a group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16.   In one embodiment, the introgressed sequences are preferably found at one or more of the loci defined by the following SNP markers:
           (a) variant A of SNP solcap_snp_sl_1815 at position 74315042 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 1);   (b) variant T of SNP solcap_snp_sl_1815 at position 74315042 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 1);   (c) variant C of SNP solcap_snp_sl_1819 at position 74329911 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 2);   (d) variant G of SNP solcap_snp_sl_1819 at position 74329911 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 2);   (e) variant A of SNP solcap_snp_sl_1824 at position 74464953 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 3);   (f) variant T of SNP solcap_snp_sl_1824 at position 74464953 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 3);   (g) variant A of SNP solcap_snp_sl_17075 at position 74483269 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 4);   (h) variant G of SNP solcap_snp_sl_17075 at position 74483269 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 4);   (i) variant A of SNP solcap_snp_sl_1827 at position 74602284 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 5);   (j) variant T of SNP solcap_snp_sl_1827 at position 74602284 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 5);   (k) variant A of SNP solcap_snp_sl_21280 at position 76783695 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 6);   (l) variant G of SNP solcap_snp_sl_21280 at position 76783695 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 6);   (m) variant A of SNP solcap_snp_sl_34568 at position 76905658 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 7);   (n) variant C of SNP solcap_snp_sl_34568 at position 76905658 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 7);   (o) variant T of SNP solcap_snp_sl_36202 at position 47651366 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 8);   (p) variant C of SNP solcap_snp_sl_36202 at position 47651366 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 8);   (q) variant A of SNP solcap_snp_sl_21866 at position 47950096 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 9);   (r) variant G of SNP solcap_snp_sl_21866 at position 47950096 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 9);   (s) variant A of SNP solcap_snp_sl_21862 at position 47981517 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 10);   (t) variant G of SNP solcap_snp_sl_21862 at position 47981517 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 10);   (u) variant T of SNP solcap_snp_sl_31689 at position 47996412 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 11);   (v) variant C of SNP solcap_snp_sl_31689 at position 47996412 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 11);   (w) variant T of SNP solcap_snp_sl_20063 at position 48455087 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 12);   (x) variant G of SNP solcap_snp_sl_20063 at position 48455087 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 12);   (y) variant T of SNP solcap_snp_sl_21966 at position 48370810 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 13);   (z) variant C of SNP solcap_snp_sl_21966 at position 48370810 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 13);   (aa) variant A of SNP solcap_snp_sl_58447 at position 48602171 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 14);   (bb) variant G of SNP solcap_snp_sl_58447 at position 48602171 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 14);   (cc) variant T of SNP solcap_snp_sl_20049 at position 48697164 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 15); and   (dd) variant C of SNP solcap_snp_sl_20049 at position 48697164 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 15); and   (ee) variant A of SNP solcap_snp_sl_21867 at position 47948927 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 16);   (ff) variant G of SNP solcap_snp_sl_21867 at position 47948927 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 16).   
               

     Insofar as the introgressed sequences from  Solanum peruvianum  conferring resistance to GBNV can be marked by the specific alleles of the SNP markers of the invention, a plant of the invention has at least one of the alleles or variants as defined by the embodiments of this invention. Preferably, the SNPs detailed for the embodiments of the present invention are used as markers for the detection of introgressed sequence from  Solanum peruvianum.    
     In another embodiment, the invention provides a method for producing the tomato plant, wherein SNPs present on chromosome 1 are indicated by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7 and SNPs present on chromosome 2 are indicated by SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16. 
     In another embodiment, the invention provides a method for producing the tomato plant of claim  1 , wherein the progeny tomato plant does not exhibit one or more trait indicative of Groundnut bud necrosis virus infection selected from a group consisting of deformed shape, uneven ripening, yellow patch formation on the fruit, wilting of the top portion of the plant, dark brown spots on the leaves and dark brown patches on stems of the plants. Some of the post infection common characteristics traits of the recipient tomato plant which is susceptible to TOSPO are deformed shape and uneven ripening of the fruit, wilting of the top portion of the plant, dark brown spots on the leaves and dark brown patches on stems of the plants. 
     In another embodiment, the progeny plant is selected at each stage on the basis of one or more of the alleles or variants of the SNP markers as defined in the embodiments of the present invention. 
     In another embodiment, the SNP markers according to the embodiment of the invention are marker loci linked to chromosomal regions or QTL that are involved in or associated with the GBNV tolerance or resistance phenotype. The allele or variants of these markers thus indicates whether the sequences surrounding the markers are introgressed from  Solanum peruvianum  or not, introgressed sequences at this locus being correlated to resistance or tolerance to Groundnut Bud Necrosis Virus (GBNV). 
     Regarding the QTL or chromosomal regions marked by the SNPs of the invention and correlated with the phenotype, a single of this SNP marker may impart the desired phenotype. 
     The transfer of one or more nucleic acids is performed by crossing the donor tomato plant with a recipient tomato plant to produce progeny tomato plants comprising at least one QTL for TOSPO virus resistance as in introgression, and wherein identification and selection is performed on one or more progeny plants. 
     The method of transfer of one or more nucleic acids is based on selecting the TOSPO (GBNV) resistant plants from progenies of an interspecific cross. The crossing was made possible using embryo rescue technique to overcome incompatibility. 
     Further, the method of the invention is performed by detecting the marker in DNA isolated from the recipient tomato plants or from one or more of progeny plants. 
     In one embodiment, the extracted or isolated DNA was used for conducting single nucleotide polymorphism analysis based on the Solanaceae Coordinated Agricultural Project (SolCAP). Solcap (Solanaceae Coordinated Agricultural Project) was supported by the Agriculture and Food Research Initiative Applied Plant Genomics CAP Program of USDA&#39;s National Institute of Food and Agriculture which led to the development of the Solcap Infinium SNP panel for tomato. This panel is an SNP array that is publicly available and contains information regarding SNPs in tomato. SolCAP is a commonly used tool in tomato genome research to identify polymorphic SNPs in wild or cultivated tomato germplasm. 
     In another embodiment, SolCAP Infinium genotyping SNP panel has been used for identifying the SNPs associated with the resistance to Groundnut Bud Necrosis virus. The SNPs indicated in the SolCAP Infinium SNP panel is on the basis of chromosome positions as indicated in the tomato genome version SL 2.40. The tomato genotype data, including genome version 2.40 is publicly available on various websites (such as http://solcap.msu.edu/). 
     The method of the invention comprises selecting a recipient tomato plant that comprises within its genome at least two QTLs selected from the group consisting of QTL1, QTL2 and virus-resistance related parts thereof. 
     The method of the invention comprises selecting a recipient tomato plant that comprises QTL1 and QTL2 within its genome. 
     The method of the invention comprises selecting a recipient tomato plant that comprises within its genome a QTL or a viral resistance related part thereof, and at least one QTL selected from the group consisting of QTL1, QTL2 and related parts thereof. 
     The method of the invention further comprises a step of crossing a recipient tomato plant with a plant of a cultivated variety of tomato to produce progeny plants. 
     The method of the invention comprises the recipient tomato plant as same as that of the plant of the cultivated variety of tomato to which the recipient tomato plant is crossed. 
     The resistance provided against by the method of the invention is for a Groundnut Bud Necrosis Virus (GBNV) which is a TOSPO virus. 
     The invention is for a tomato plant exhibiting TOSPO virus resistance, and the said tomato plant or part thereof comprises a QTL selected from the group consisting of QTL1, QTL2 and TOSPO virus-related parts thereof, wherein the QTLs or viral resistance-related parts thereof are not present in the natural genetic background of the edible tomato plants. 
     The tomato plant exhibiting TOSPO virus resistance, is produced by backcrossing the tomato plant BC 1 (back cross 1) with a tomato plant that exhibits commercially desirable characteristics, wherein the resulting hybrid plant comprises at least one QTL selected from the group consisting of QTL1, QTL2 and TOSPO virus resistance-related parts thereof, wherein at least one QTL is not present in the natural background of either the tomato plant selected in step 1 (c) or the tomato plant exhibiting commercially desirable characteristics. 
     Standard embryo rescue method was employed to overcome sexual incompatibility between  S. peruvianum  &amp;  S. lycopersicum,  and to raise the seven day old fertilized ovules on tissue culture medium. 
     In another embodiment, the invention provides a method of identifying a tomato plant resistant to Groundnut bud necrosis virus infection, comprising identifying through genotyping in a nucleic acid sample of the tomato plant at least one SNP selected from a group consisting of:
         (a) variant A or T of SNP solcap_snp_sl_1815 at position 74315042 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 1);   (b) variant C or G of SNP solcap_snp_sl_1819 at position 74329911 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 2);   (c) variant A or T of SNP solcap_snp_sl_1824 at position 74464953 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 3);   (d) variant A or G of SNP solcap_snp_sl_17075 at position 74483269 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 4);   (e) variant A or T of SNP solcap_snp_sl_1827 at position 74602284 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 5);   (f) variant A or G of SNP solcap_snp_sl_21280 at position 76783695 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 6);   (g) variant A or C of SNP solcap_snp_sl_34568 at position 76905658 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 7);   (h) variant T or C of SNP solcap_snp_sl_36202 at position 47651366 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 8);   (i) variant A or G of SNP solcap_snp_sl_21866 at position 47950096 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 9);   (j) variant A or G of SNP solcap_snp_sl_21862 at position 47981517 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 10);   (k) variant T or C of SNP solcap_snp_sl_31689 at position 47996412 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 11);   (l) variant T or G of SNP solcap_snp_sl_20063 at position 48455087 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 12);   (m) variant T or C of SNP solcap_snp_sl_21966 at position 48370810 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 13);   (n) variant A or G of SNP solcap_snp_sl_58447 at position 48602171 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 14);   (o) variant T or C of SNP solcap_snp_sl_20049 at position 48697164 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 15); and   (p) variant A or G of SNP solcap_snp_sl_21867 at position 47948927 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 16);   wherein the presence of one or more SNP is indicative of Groundnut bud necrosis virus infection resistance trait of the tomato plant.       

     In another embodiment, the invention provides a method of selecting a tomato plant, wherein SNPs present on chromosome 1 are indicated by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7 and SNPs present on chromosome 2 are indicated by SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16. 
     In another embodiment, the invention provides a tomato plant exhibiting resistance to Groundnut bud necrosis virus infection produced, wherein the tomato plant comprises at least one SNP corresponding to a quantitative trait locus on chromosome 1 or chromosome 2, and wherein the SNP is selected from a group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16. 
     In another embodiment, the invention provides a tomato plant, wherein SNPs present on chromosome 1 are indicated by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7 and SNPs present on chromosome 2 are indicated by SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16. 
     In another embodiment, the invention provides a seed of the tomato plant produced by the process as described herein. 
     Scoring of the disease symptoms (phenotyping) was performed in a hot spot location for TOSPO (GBNV) disease and were categorized into 5 types (1) whole plant diseased (score 1); (2) diseased with few green stem and leaves (score 2); (3) 50% plant covered-may have 1 or 2 fruit (score 3); (4) Except for the top leaves, stem and other plant parts are healthy (score 4); (5) Healthy plants (score 5) using the phenotypic symptoms observed in the field at young and adult plant stages, e.g., 40, 60, 80 days after transplantation in the field. 
     EXAMPLES 
     The following examples are for the purpose of illustration of the invention and are not intended in any way to limit the scope of the invention. 
     Materials: 
       Solanum peruvianum  line was obtained from World Vegetable Centre—Asian Vegetable Research and Development Center (AVRDC), Taiwan. The donor line is commercially available, and it is also available from the Asian Vegetable Research and Development Center (AVRDC), Taiwan under Accession No. L00671. 
     The cultivated lines used were SP-1 (Susceptible parent 1—Sel 22, purchased from Indian Institute of Horticultural Research Bengaluru (IIHR), a commercial line since 1985). SP-2 (Susceptible line)—A Ty 2 line collected from AVRDC but susceptible to TOSPO. 
     Example 1 
     Development and Determination of Disease Resistant Phenotype 
     The  Solanum peruvianum  accession L00671 was used as donor. The  S. peruvianum  accession L00671 from AVRDC is resistant to Ground nut bud necrosis virus. The donor was crossed with a GBNV susceptible  S. lycopersicum  line (SP1—that responds well to tissue culture). 
     To overcome sexual incompatibility between  S. peruvianum  &amp;  S. lycopersicum,  standard embryo rescue method was employed to raise the seven day old fertilized ovules on ( FIG. 1  detailing the crossing and backcrossing) tissue culture medium. 
     More than 5000 ovules were subjected to embryo rescue method and only two embryos were able to develop into true hybrid plants (F1) (seen phenotypically). 
     These F1s were crossed with another GBNV susceptible line of  S. lycopersicum  as it was agronomically better &amp; had more firm fruits (SP2—Susceptible parent 2 (Square Round)) and obtained BC1 seeds. The crossed ovules from these BC1 pollinations, using the inter-specific F1 as pollen source, were subjected to embryo rescue to get BC1 plants that were grown to fruiting. 
     BC1F1 progeny was grown in the field in rainy season under high  Thrips  pressure. 
     Pollen from plants, that showed no GBNV symptoms were used to pollinate the SP1 recipient parent to obtain BC2F1 seeds. 
     BC2F1 plants were grown and selfed to obtained BC2F2 seeds. Selected BC2F2 plants were grown to obtain BC2F3 ( FIG. 2 ). 
     Selected BC2F3 families were planted in hot spot location along with the parents (donor as well as recipient) in an augmented design where a susceptible check variety was planted repeatedly after every 10 rows in each bed. 
     Frequency distribution of the disease in various generations and resistant (RP) and susceptible (SP) parent shown in  FIG. 3 . 
     Example 2 
     Development of Field Screening for Disease and Disease Rating Scores 
     Using the phenotypic symptoms observed in the field at young and adult plant stages, e.g., 40, 60, 80 days after transplantation in the field, the disease symptoms were categorized into 5 types as in  FIG. 4  as (1) whole plant diseased (score 1); (2) diseased with few green stem and leaves (score 2); (3) 50% plant covered-may have one or two fruit (score 3); (4) Except for the top leaves, stem and other parts healthy (score 4); (5) Healthy plants (score 5). 
     Based on data on GBNV scores at 40, 60 &amp; 80 days after transplanting (DAT) the families were grouped into three categories of: 1) Resistant (scores 4, 5); 2) intermediates (score 3) and 3) susceptible (scores 1 and 2). Three individual plants per category were harvested for obtaining BC2F4 seeds. BC2F4 families were again raised and BC2F5 progenies harvested from same groups of families. 
     The frequency distribution for disease score 1 to 5 for GBNV incidence on resistant parent, susceptible recipient, BC2F3 &amp; BC2F4 progenies are provided in  FIG. 3 . Disease pressure during the screening has been very high as can be seen by the over 65 percent of susceptible parent shows susceptibility rating of 1 and 2 and another 15 percent having score of 3. 
     The resistant parent on the other hand showed 90 percent plants scoring rating 5 and another 10 percent scoring a rating of 4, confirming high resistance in this parent ( S. peruvianum ). BC2F3 distribution for the disease rating shows a normal distribution ( FIG. 3 : bottom left) indicative of an incomplete dominance for resistance and involvement of more than one gene for its inheritance. 
     BC2 F4 progenies derived from the susceptible and resistant families of BC2F3 showed the population moving towards resistant &amp; susceptible groups ( FIG. 3 : bottom right). This indicates that it was possible to select high resistant genotypes with a disease rating scale of 4 &amp; 5. 
     The mean disease ratings and their standard deviation in case of the BC2F3, BC2F4 &amp; BC2F5 families versus resistant &amp; susceptible parents as well as intermediates are presented in  FIG. 3  below. 
     These data represents three seasons of screening. BC2F5 progenies show an overall stable resistance which is closer to the donor parent while as the susceptible (recipient parent) and a super susceptible line as well as the progenies of intermediate resistance show clear susceptibility over all three seasons of testing. The BC2F5 progenies have further planted and the top stable lines for resistance to GBNV has been selected. 
     Example 3 
     Genotyping, Linkage and OTL Analysis—Identification of Trait Linked Molecular Markers 
     To understand precisely the location of resistance genes, 181 leaf samples consisting of 174 BC2F3 families (bulks of 4-20 plants) and 3 parental lines were used. DNA was extracted from each sample using standard extraction method. 
     For Marker Identification SNP Panel was Used 
     
         
         
           
             Solcap Infinium SNP panel 
             6,007 SNPs resulted in genotypes with &lt;10% missing datapoints 
             1,767 showed segregation in the population 
             556 SNPs selected for linkage construction and QTL analysis based on: Missing datapoints &lt;20% 
             SNPs were observed to be polymorphic between SP2 and RP1 (original parents) 
           
         
       
    
     Trait linked molecular markers by way of multiple QTLs in specified chromosomes is identified. 7000 SNPs were generated and used to screen and identify the SNPs that were closely linked with the resistant trait. Out of 7000 SNPs that were used for the screening on the segregating materials, 16 SNPs were found to be associated with the resistance to GBNV trait. 
     The screening was done by using Illumina SolCAP Tomato genotyping panel (developed by Illumina, USA). The SolCAP Tomato genotyping panel uses tomato genome sequence version 2.40. The details and the location of the SNPs as indicated in the SolCAP Tomato genotyping panel is indicated in Table 1 along with their sequences. 
                     TABLE 1                  Details of SNPs as indicated on SolCAP Infinium SNP panel based on       tomato genome version SL 2.40                                         Chromosome               SEQ ID       SNP   No   Sequence   SNP   Position   NO               QTL 1                           SNP527   1   CATGTAAATGTGGGTCGCTTGAT   [A/T]   74315042   SEQ ID       (solcap_       CAAATTTTTAGTTTCTTGGAGAT           NO: 1       snp_sl_       CTGA[A/T]AAACAAGGGCTGTAT                   1815)       GAGAAAATCTTAGAATTGAGCC                           ATACAATGGCACT                           SNP001   1   TAATCTGTTTCTGGATAAATGCC   [C/G]   74329911   SEQ ID       (solcap_       TCTCCAATTTCGATAAATAAGGG           NO: 2       snp_sl_       ATCG[C/G[AAGGAGATAGGAGA                   1819)       AAAGTACAACACCATCGAGAGT                           CACCACTAACAGTG                           SNP224   1   GATGGTTTTGGTTTCGCTAGCCA   [A/T]   74464953   SEQ ID       (solcap_       AATTTTTAACATCAATCAAGCAA           NO: 3       snp_sl_       GAGT[A/T]AAAGCAGGCATATTT                   1824)       ATATCTGAGGATCCAACAGTGTT                           CACCTCTTCTTC                           SNP540   1   CCATCAGCTGATCTCAACTACCC   [A/G]   74483269   SEQ ID       (solcap_       GTCATTCATTGCCTTGTACAGCA           NO: 4       snp_sl_       TTGA[A/G[GGAAACTTCACTTTG                   17075)       TTGGAGCAGAAATTCAAGAGGA                           CAGTTACAAATGT                           SNP066   1   CACTACAAGCCTAGATAACAAA   [A/T]   74602284   SEQ ID       (solcap_       AGTATATCCTTCAGTAAGCATAC           NO: 5       snp_sl_       ATGGT[A/T]TCAGCCAACTTCAA                   1827)       ACCCCGAGACTTGAAGAATCAA                           TCCTTCCCGAGGCT                           SNP521   1   AAGTATGGCTGGTATCATCGTCG   [A/G]   76783695   SEQ ID       (solcap_       TCGTCGTCCCGGAAGAATCCAAT           NO: 6       snp_sl_       ATCA[A/G]AAAAAAAGGGTTCTT                   21280)       CTTCCTCCTCCTGTAAAATTGTC                           GGCTGAGATTGA                           SNP434   1   GATTATGGGGACGAGGATGCAA   [A/C]   76905658   SEQ ID       (solcap_       ACAAAACACTAGCCAAGCTGTA           NO: 7       snp_sl_       AGTAGT[A/C]TCTCATGGATTAT                   34568)       ATTATACGAACTTTTAAAAAATA                           TTATCGCAGAGCGT                           QTL2                           SNP044   2   TTAGGCATGTACTCGTAAACCAA   [T/C]   47651366   SEQ ID       (solcap_       AAGATTTGTCTCATGATTCGAGC           NO: 8       snp_sl_       AAAA[T/C]CCTAATAATCTAACA                   36202)       ATGTGCCTGTGTCGGATCCTCCC                           AAGAGTCTGTAT                           SNP017   2   CACTTCACCGACACCCATCTCCT   [A/G]   47950096   SEQ ID       (solcap_       TATCTACTTTTCTATCGTCACAT           NO: 9       snp_sl_       ACTC[A/G]ACGGAATTTGTATGC                   21866)       TTTCTTAGTTACTGCCAAAATTG                           CTCTTCGAACTA                           SNP304   2   CGTCGATCAAAATACTCTTCCAA   [A/G]   47981517   SEQ ID       (solcap_       ACCTACCGCAAAAGATAATAGC           NO: 10       snp_sl_       AGGCA[A/G]TAACAACAAAGATT                   21862)       AATCTCCCCCCTATATATGACTT                           GAGTTGTCAGGAA                           SNP131   2   AATAGAAATGGAAATTGTACTC   [T/C]   47996412   SEQ ID       (solcap_       CATTTTGACGAATTTTGGTTGCA           NO: 11       snp_sl_       CATTG[T/C]TAGGGACTTCACAA                   36189)       CATTGATTTGCTACTCATTTTTAT                           GTGCCCGTTACT                           SNP155   2   ATCCTCTAATCGTTCGGCCGATT   [T/G]   48455087   SEQ ID       (solcap_       CGACTCAGTCGAAAAATCCTTTT           NO: 12       snp_sl_       CAGT[T/G]GCTGCTTCCACCGAT                   20063)       GCAGATTCCTCCACCGCCACCAC                           CACCGCCGCCTC                           SNP151   2   AAGGCGAAAATTGGGAAGGAAT   [T/C]   48370810   SEQ ID       (solcap_       CATTACTAGAATTTGGCCAAACA           NO: 13       snp_sl_       CAAAG[T/C]ACCTTGATGTGATA                   21966)       GTCACAGGTGCAATGGCTCAAT                           ATATACCTACTTTG                           SNP193   2   ATTTTGTTTCTTTTGATTCAATTT   [A/G]   48602171   SEQ ID       (solcap_       CAGTTTCTTCTTTTCTCCTTTTCA           NO: 14       snp_sl_       CA[A/G]AAGCAAAAAGACAGAG                   58447)       AACAGCTGCAATCAAGATCAAT                           GTTCCAACTACA                           SNP097   2   TTCTTCAATTGTTGGTCTGAAAT   [T/C]   48697164   SEQ ID       (solcap_       AGCGCGCAGTGGAGATTCCAAT           NO: 15       snp_sl_       CTTAT[T/C]GTTAATAAACCGCCG                   20049)       GTTCTGGACCGTTGGTTTCCTGA                           ATTTGTTGCTAG                           SNP034   2   GGTAACAAAATATACGTAGAAG   [A/G]   47948927   SEQ ID       (solcap_       GGGGATATTACTTCGAGGGGTAT           NO: 16       snp_sl_       TGGGT[A/G]GAAATCGTGGGAAC                   21867)       GTACGATAACATCACCGACAGG                           TATTTAGCAATAGA                    
The following were used for Linkage construction
         556 SNPs used for linkage construction   330 SNPs were non-redundant (not co-segregated)   Mapped to 12 linkage groups   Linkage groups ranged from 79.2 cM to 174.9 cM   Total length 1,567.2 cM   Based on physical coordinates, linkage groups covered most of the genome       

     As indicted in Table 1, based on chromosome positions as indicated in the tomato genome version SL 2.40, said  S. lycopersicum  plant is characterized by the presence of least one of the following variants:
         (a) variant A or T of SNP solcap_snp_sl_1815 at position 74315042 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 1)   (b) variant C or G of SNP solcap_snp_sl_1819 at position 74329911 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 2)   (c) variant A or T of SNP solcap_snp_sl_1824 at position 74464953 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 3)   (d) variant A or G of SNP solcap_snp_sl_17075 at position 74483269 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 4)   (e) variant A or T of SNP solcap_snp_sl_1827 at position 74602284 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 5)   (f) variant A or G of SNP solcap_snp_sl_21280 at position 76783695 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 6)   (g) variant A or C of SNP solcap_snp_sl_34568 at position 76905658 of chromosome 1 on the tomato genome version 2.40 (SEQ ID NO: 7)   (h) variant T or C of SNP solcap_snp_sl_36202 at position 47651366 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 8)   (i) variant A or G of SNP solcap_snp_sl_21866 at position 47950096 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 9)   (j) variant A or G of SNP solcap_snp_sl_21862 at position 47981517 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 10)   (k) variant T or C of SNP solcap_snp_sl_31689 at position 47996412 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 11)   (l) variant T or G of SNP solcap_snp_sl_20063 at position 48455087 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 12)   (m) variant T or C of SNP solcap_snp_sl_21966 at position 48370810 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 13)   (n) variant A or G of SNP solcap_snp_sl_58447 at position 48602171 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 14)   (o) variant T or C of SNP solcap_snp_sl_20049 at position 48697164 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 15)   (p) variant A or G of SNP solcap_snp_sl_21867 at position 47948927 of chromosome 2 on the tomato genome version 2.40 (SEQ ID NO: 16)       

     The above-identified markers were subsequently validated for their presence in the progeny plants. It was found that the markers are associated with GBNV-resistance trait. 
     Example 4 
     Production of TOSPO Virus Resistant Tomato Line by Non-Transgenic Method 
     The BC2F6 progenies, resulting from individual plant selections (pedigree selection) since when the BC2F3 families were first screened in the rainy season in Hyderabad have shown high resistance levels to TOSPO during Kharif 16 at the hot spot locations. A summary data on the TOSPO scores of these progenies in K 16 vs checks and historically in their parent families are shown in Table 2 below. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 TOSPO Resistant lines at BC2F6 vs susceptible (SP 1 &amp; 2) parents, Resistant 
               
               
                 (RP) parent and a general susceptible check along with historical TOSPO scores over seasons 
               
               
                 TOSPO scores over seasons 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 TOSPO 
                   
                 TOSPO 
                   
               
               
                   
                   
                 TOSPO 
                 K 16 
                 Scr 
                   
                 Scr K 
                   
               
               
                   
                   
                 Scr 
                 Fruit 
                 K 16 (Lost 
                 TOSPO 
                 15 
                 TOSPO 
               
               
                 Kharif(K)16 
                 Source 
                 K 16 
                 Wt 
                 due 
                 Scr 
                 Fruit  
                 Scr 
               
               
                 code  
                 # in K15 
                 MEAN ± SD 
                 (g) 
                 Flood) 
                 K15 
                 Wt (g) 
                 K14 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 GB0001 
                 H2-7-2-1 
                 4.69 ± 1.11 
                 30 
                 4.21 ± 0.97 
                    3 ± 1.87 
                 15 
                 3.71 ± 143  
               
               
                 GB0024 
                 H17-5-1 
                 4.83 ± 041  
                 25 
                 3.67 ± 1.12 
                  1.6 ± 1.01 
                 31 
                 2.50 ± 1.46 
               
               
                 GB0027 
                 GB0049-1-SB 
                 4.75 ± 0.45 
                 35 
                 3.75 ± 0.71 
                 5 ± 0 
                 20 
                 4.10 ± 1.16 
               
               
                 GB0038 
                 GB0720-1-2 
                 4.36 ± 0.67 
                 120 
                    4 ± 0.76 
                 5 ± 0 
                   
                   
               
               
                 GB0039 
                 GB0279-2-1 
                 4.31 ± 0.48 
                 50 
                 4.15 ± 0.69 
                 4.25 ± 1.50 
                 50 
                   
               
               
                 SP1 
                 SP1 
                  1.5 ± 0.22 
                 60 
                 1.6 ± 0.2 
                  1.2 ± 0.18 
                 55 
                 1.5 ± 0.15 
               
               
                 SP2 
                 SP2 
                  1.6 ± 0.18 
                 65 
                 1.3 ± 0.5 
                  1.4 ± 0.28 
                 60 
                 1.6 ± 0.2  
               
               
                 RP 
                 RP 
                 5 ± 0 
                 5 
                  4.9 ± 0.22 
                  4.9 ± 0.24 
                 5 
                 4.8 ± 0.15 
               
               
                 GBE002 
                 GB0134-1 
                 3.77 ± 1.17 
                 80 
                 4.27 ± 0.65 
                 4 ± 0 
                 15 
                 4 
               
               
                 GBE003 
                 GB0134-3 
                 4.73 ± 0.47 
                 60 
                    4 ± 0.77 
                 4 ± 0 
                 15 
                 4 
               
               
                 GBE004 
                 GB0135-1 
                    4 ± 1.11 
                 20 
                 4.80 ± 0.45 
                  4.5 ± 0.57 
                 20 
                 4 
               
               
                 GBE009 
                 GB0202-4 
                 3.91 ± 0.70 
                 35 
                  3.6 ± 1.12 
                 5 ± 0 
                 23 
                 4 
               
               
                 GBE034 
                 GB0074-1 
                 4.69 ± 0.48 
                 100 
                 4.07 ± 1.14 
                 1.57 ± 1.51 
                   
                 5 
               
               
                 GBE035 
                 GB0074-2 
                 4.29 ± 0.47 
                 90 
                 4.27 ± 1.19 
                 1.57 ± 1.51 
                   
                 5 
               
               
                 GBE036 
                 GB0075-1 
                 3.50 ± 1.07 
                 35 
                 5 ± 0 
                 4 ± 2 
                 15 
                 5 
               
               
                 GBE040 
                 GB0196-1 
                 4.46 ± 0.52 
                 150 
                    4 ± 1.58 
                 1 ± 0 
                   
                 4 
               
               
                 GBE062 
                 GB0703-2 
                 3.88 ± 1.81 
                 120 
                 3.79 ± 1.72 
                 5 ± 0 
                   
                 5 
               
               
                 GBE064 
                 GB0704-1 
                 4.64 ± 0.50 
                 120 
                 3.92 ± 1.31 
                   
                   
                 5 
               
               
                 GBE073 
                 GB0708-1 
                 4.86 ± 0.36 
                 100 
                 4.21 ± 0.97 
                 4 ± 0 
                   
                 5 
               
               
                 GBE074 
                 GB0709-1 
                 4.62 ± 0.51 
                 150 
                 4.43 ± 1.09 
                   
                 5 
                 5 
               
               
                 GBE075 
                 GB0710-1  
                 4.64 ± 0.50 
                 120 
                 3.50 ± 0.84 
                 5 ± 0 
                   
                 5 
               
               
                 GBE083 
                 GB0782-1 
                 4.55 ± 0.69 
                 90 
                 3.67 ± 0.50 
                 5 ± 0 
                   
                 5 
               
               
                 GBE084 
                 GB0782-BK 
                 4.83 ± 0.39 
                 30 
                 4.46 ± 0.66 
                 5 ± 0 
                   
                 5 
               
               
                 GBE085 
                 GB0783-1 
                 4.85 ± 0.38 
                 90 
                 3.93 ± 1.21 
                   
                   
                 5 
               
               
                 GBE086 
                 GB0783-BK 
                 4.90 ± 0.32 
                 30 
                 4.33 ± 0.98 
                   
                   
                 5 
               
               
                 GBE087 
                 GB0784-BK 
                 4.08 ± 1.44 
                 25 
                 4.80 ± 0.42 
                   
                   
                 5 
               
               
                 GBE088 
                 GB0785-BK 
                 4.43 ± 0.51 
                 25 
                    4 ± 0.67 
                   
                   
                 5 
               
               
                 SEL-4 (S 
                 SEL-4 
                 1.71 ± 0.49 
                 50 
                  1.8 ± 0.56 
                    2 ± 0.47 
                   
                 1.7 ± 0.56 
               
               
                 check) 
               
               
                   
               
            
           
         
       
     
     In  FIG. 4  a few TOSPO resistant lines in the field vs susceptible checks are presented. 
     Example 5 
     Production of TOSPO Virus Resistant Tomato Line by Marker Assisted Breeding 
     Following table show the results of SNP marker analysis showing linkage with the TOSPO resistance trait. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 SNP association with resistance at 40 or 60 days 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                 SNP (as 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 indicated in 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                 SoICAP Infinium 
                 Mean Resistance 
                   
                   
                   
                   
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 genotyping SNP 
                 Index 
                 F-Test 
                 T-Test 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                 panel) 
                 A 
                 B 
                 H 
                 A/B 
                 A/H 
                 B/H 
                 A/B 
                 A/H 
                 B/H 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 QT 
                 (solcap_snp_sl_1815) 
                 4.01 
                 4.44 
                 3.85 
                 0.0237 
                 0.6354 
                 0.0164 
                 1E−06 
                 0.1729 
                 3E−07 
               
               
                 L1 
                   
                 (209) 
                 (209) 
                 (117) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_1819 
                 4.01 
                 4.43 
                 3.83 
                 0.0153 
                 0.6749 
                 0.0145 
                 7E−07 
                 0.1248 
                 1E−07 
               
               
                   
                   
                 (215) 
                 (215) 
                 (116) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_1824 
                 3.91 
                 4.52 
                 3.92 
                 2E−07 
                 0.6044 
                 0.001 
                 8E−14 
                 0.9208 
                 4E−07 
               
               
                   
                   
                 (267) 
                 (267) 
                 (103) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_17075 
                 3.98 
                 4.47 
                 3.82 
                 0.0064 
                 0.2713 
                 0.0008 
                 2E−09 
                 0.1754 
                 7E−08 
               
               
                   
                   
                 (239) 
                 (239) 
                 (110) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_1827 
                 3.82 
                 4.51 
                 3.79 
                 1E−05 
                 0.2667 
                 3E-05 
                 3E−17 
                 0.8699 
                 2E−06 
               
               
                   
                   
                 (242) 
                 (242) 
                  (73) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_21280 
                 3.89 
                 4.53 
                 3.7 
                 2E−08 
                 0.2066 
                 2E-07 
                 8E−17 
                 0.3148 
                 4E−07 
               
               
                   
                   
                 (260) 
                 (260) 
                  (71) 
                   
                   
                   
                   
                   
                   
               
               
                 QT 
                 solcap_snp_sl_36202 
                 3.52 
                 4.56 
                 4.04 
                 2E−15 
                 0.0534 
                 6E-14 
                 3E−30 
                 0.0034 
                 0.0019 
               
               
                 L2 
                   
                 (223) 
                 (223) 
                  (47) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_21866 
                 3.5 
                 4.56 
                 4.13 
                 3E−15 
                 0.4657 
                 0.0004 
                 5E−31 
                 0.0004 
                 0.0057 
               
               
                   
                   
                 (222) 
                 (222) 
                  (48) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_21862 
                 3.5 
                 4.56 
                 4.13 
                 3E−15 
                 0.4657 
                 0.0004 
                 5E−31 
                 0.0004 
                 0.0057 
               
               
                   
                   
                 (222) 
                 (222) 
                  (48) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_36189 
                 3.51 
                 4.56 
                 4.18 
                 3E−15 
                 0.3954 
                 0.0004 
                 2E−30 
                 0.0001 
                 0.0111 
               
               
                   
                   
                 (225) 
                 (225) 
                  (51) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_20063 
                 3.71 
                 4.53 
                 4.26 
                 1E−15 
                 0.1956 
                 0.001 
                 2E−22 
                 0.0006 
                 0.0474 
               
               
                   
                   
                 (264) 
                 (264) 
                  (61) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_21966 
                 3.71 
                 4.53 
                 4.25 
                 2E−15 
                 0.2413 
                 0.0011 
                 3E−22 
                 0.0013 
                 0.0432 
               
               
                   
                   
                 (263) 
                 (263) 
                  (57) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_58447 
                 3.69 
                 4.53 
                 4.2 
                 3E−16 
                 0.1546 
                 0.0007 
                 1E−22 
                 0.0012 
                 0.0128 
               
               
                   
                   
                 (254) 
                 (254) 
                  (64) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_20049 
                 3.69 
                 4.53 
                 4.2 
                 3E−16 
                 0.1546 
                 0.0007 
                 1E−22 
                 0.0012 
                 0.0128 
               
               
                   
                   
                 (254) 
                 (254) 
                  (64) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 solcap_snp_sl_21867 
                 3.5 
                 4.56 
                 4.13 
                 2E−15 
                 0.4657 
                 0.0003 
                 4E−31 
                 0.0004 
                 0.0056 
               
               
                   
                   
                 (222) 
                 (222) 
                  (48) 
                   
                   
                   
                   
                   
                   
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Association of QTLs with index resistance 
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                 Mean 
                   
                   
                   
                   
                   
                   
               
               
                   
                   
                 Resistance 
                   
                   
                   
                   
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                 Random 
                   
                 Index 
                 F-Test 
                 T-Test 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 SNP 
                 SNP 
                 A 
                 B 
                 H 
                 A/B 
                 A/H 
                 B/H 
                 A/B 
                 A/H 
                 B/H 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                 SNP506 
                 3.62 
                 2.96 
                 3.48 
                 0.2265 
                 0.2554 
                 0.8112 
                 0.0448 
                 0.5999 
                 0.2201 
               
               
                   
                   
                 (23) 
                 (8) 
                 (14) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 SNP507 
                 3.32 
                 3.53 
                 3.6 
                 0.4254 
                 0.9966 
                 0.4276 
                 0.5264 
                 0.3218 
                 0.8441 
               
               
                   
                   
                 (16) 
                 (12) 
                 (16) 
                   
                   
                   
                   
                   
                   
               
               
                   
                 SNP508 
                 3.38 
                 3.41 
                 3.59 
                 0.9498 
                 0.3004 
                 0.2685 
                 0.9134 
                 0.4894 
                 0.5577 
               
               
                   
                   
                 (16) 
                 (18) 
                 (11) 
                   
                   
                   
                   
                   
                   
               
               
                   
               
            
           
         
       
         
         
           
             SNP flanking the QTL1 and QTL2 were significantly associated with resistance index 
             Random SNP were not associated with the resistance index 
           
         
         Table 5 provides the impact of either or both QTLs 
       
    
     
       
         
           
               
               
               
               
            
               
                   
               
               
                   
                   
                 F-test 
                 T-test 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Resistance 
                   
                   
                 QTL1/ 
                   
                   
                 QTL1/ 
               
               
                 QTL 
                 index 
                 QTL1 
                 QTL2 
                 QTL2 
                 QTL1 
                 QTL2 
                 QTL2 
               
               
                   
               
               
                 — 
                 3.59 (86)  
                 0.124189557 
                 0.356191085 
                 1.11696E−07 
                 0.029388201 
                 0.001159854 
                 6.99241E−14 
               
               
                 QTL1 
                 3.24 (129) 
                   
                 0.007012633 
                 5.22526E−18 
                   
                 1.55039E−08 
                 2.58405E−24 
               
               
                 QTL2 
                 4.06 (112) 
                   
                   
                 9.24693E−06 
                   
                   
                 5.14217E−08 
               
               
                 QTL1/QTL2 
                 4.61 (438) 
                   
                   
                   
                   
                   
                   
               
               
                   
               
            
           
         
       
         
         
           
             Lines carrying QTL2 had a significantly higher resistance index than the lines carrying QTL1 
             Lines carrying both QTL had significantly higher resistance index than either QTL 
           
         
       
    
     The results indicate that the inventors were successful in the development of  Solanum lycopersicum  progeny tomato plant which exhibits resistance to Groundnut bud necrosis virus infection.