Article | . 2017 Vol. 35, Issue. 2
Genomic Tools and Their Implications for Vegetable Breeding

Department of Bioresources Engineering, Sejong University1
Plant Engineering Research Institute, Sejong University2

2017.. 149:164


Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genomewide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and markertrait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

1. Acciarri N, Rotino GL, Tamietti G, Valentino D, Voltattorni S, Sabatini E (2007) Molecular markers for Ve1 and Ve2 Verticillium resistance genes from Italian tomato germplasm. Plant Breed 126:617-621. doi:10.1111/j.1439-0523.2007.01398.x  

2. Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, et al. (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136-148. doi:10.1111/tpj.12616  

3. Alpert KB, Grandillo S, Tanksley SD (1995) fw 2.2:a major QTL controlling fruit weight is common to both red- and green-fruited tomato species. Theor Appl Genet 91:994-1000. doi:10.1007/bf00223911  

4. Amano M, Mochizuki A, Kawagoe Y, Iwahori K, Niwa K, Svoboda J, et al. (2013) High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber. Theor Appl Genet 126:2983-2993. doi:10.1007/s00122-013-2187-5  

5. Anbinder I, Reuveni M, Azari R, Paran I, Nahon S, Shlomo H, et al. (2009) Molecular dissection of Tomato leaf curl virus resistance in tomato line TY172 derived from Solanum peruvianum. Theor Appl Genet 119:519-530. doi:10.1007/s00122-009-1060-z  

6. Bajgain P, Rouse MN, Tsilo TJ, Macharia GK, Bhavani S, Jin Y, Anderson JA (2016) Nested association mapping of stem rust resistance in wheat using genotyping by sequencing. PLoS One 11:e0155760. doi:10.1371/journal.pone.0155760  

7. Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, et al. ( 2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6:11. doi:10.1186/1939-8433-6-11   

8. Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, et al. (2012) Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 50:250–266. doi:10.1007/s12033-011-9443-1  

9. Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Vale G, Cattivelli L (2016) Next generation breeding. Plant Sci 242:3-13. doi:10.1016/j.plantsci.2015.07.010  

10. Behera TK, Staub JE, Behera S, Mason S (2010) Response to phenotypic and marker-assisted selection for yield and quality component traits in cucumber (Cucumis sativus L.). Euphytica 171:417-425. doi:10.1007/s10681-009-0072-8  

11. Behera TK, Staub JE, Behera S, Rao AR, Mason S (2008) One cycle of phenotypic selection combined with marker assisted selection for improving yield and quality in cucumber. Cucurbitaceae 2008:115-122.  

12. Blanca J, Esteras C, Ziarsolo P, Perez D, Fernandez-Pedrosa V, Collado C, et al. (2012) Transcriptome sequence for SNP discovery across Cucumis melo. BMC Genomics 13:280. doi:10.1186/1471-2164-13-280   

13. Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, et al. (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46:1034-1038. doi:10.1038/ng.3046   

14. Brotman Y, Kovalski I, Dogimont C, Pitrat M, Portnoy V, Katzir N, Perl-Treves R (2005) Molecular markers linked to papaya ring spot virus resistance and Fusarium race 2 resistance in melon. Theor Appl Genet 110:337-345. doi:10.1007/s00122-004-1845-z  

15. Budak H, Shearman RC, Parmaksiz I, Gaussoin RE, Riordan TP, Dweikat I (2004) Molecular characterization of Buffalograss germplasm using sequence-related amplified polymorphism markers. Theor Appl Genet 108:328-334. doi:10.1007/s00122-003-1428-4   

16. Cabezuelo JMG-, Capel J, Abad J, Tomá s DM, Ferná ndez-Muñ oz R, Moriones E, Lozano R (2012) Genotyping selection for resistance against Tomato Yellow Leaf Curl Virus (TYLCV) conferred by Ty-1 and Ty-3 genes in tomato. Mol Breed 30:1131-1142. doi:10.1007/s11032-012-9701-3   

17. Castro AMP, Vilanova S, Cañ izares J, Pascual L, Blanca JM, Dí ez MJ, et al. (2012) Application of genomic tools in plant breeding. Curr Genomics 13:179 - 195. doi:10.2174/138920212800543084   

18. Causse M, Desplat N, Pascual L, Paslier M-CL, Sauvage C, Bauchet G, et al. (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14:791. doi:10.1186/1471-2164-14-791  

19. Cheng Y, Luan F, Wang X, Gao P, Zhu Z, Liu S, et al. (2016) Construction of a genetic linkage map of watermelon (Citrullus lanatus ) using CAPS and SSR markers and QTL analysis for fruit quality traits. Sci Hort 202:25-31. doi:10.1016/j.scienta.2016.01.004  

20. Coaker GL, Francis DM (2004) Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum. Theor Appl Genet 108:1047-1055. doi:10.1007/s00122-003-1531-6  

21. Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc London 363:557-572. doi:10.1098/rstb.2007.2170  

22. Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800-804. doi:10.1038/ng.144   

23. Dekkers JCM, Hospital F (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22-32. doi:10.1038/nrg701  

24. Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, et al. (2011) A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol 11:111. doi:10.1186/1471-2229-11-111  

25. Duangjit J, Causse M, Sauvage C (2016) Efficiency of genomic selection for tomato fruit quality. Mol Breed 36:29. doi:10.1007/s11032-016-0453-3  

26. Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47:S154-S163. doi:10.2135/cropsci2007.04.0015ipbs  

27. Evenson RE, Gollin D (2003 ) Assessing the impact of the Green Revolution, 1960 to 2000. Science 300:758-762. doi:10.1126/ science.1078710  

28. Faino L, Azizinia S, Hassanzadeh BH, Verzaux E, Ercolano MR, Visser RGF, Bai Y (2011) Fine mapping of two major QTLs conferring resistance to powdery mildew in tomato. Euphytica 184:223-234. doi:10.1007/s10681-011-0551-6   

29. FAO (2016)  

30. Fazio G, Chung SM, Staub JE (2003) Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.). Theor Appl Genet 107:875-883. doi:10.1007/s00122-003-1313-1  

31. Filho HPM, Stevens MA (1980) Tomato breeding for nematode resistance: Survey of resistant varieties for horticultural characteristics and genotype of acid phosphates. Acta Hortic 100:383-394. doi:10.17660/ActaHortic.1980.100.41  

32. Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358. doi:10.1155/2007/64358  

33. Foolad MR, Panthee DR (2012) Marker-assisted selection in tomato breeding. Crit Rev Plant Sci 31:93-123. doi:10.1080/07352689.2 011.616057  

34. Fukino N, Ohara T, Monforte AJ, Sugiyama M, Sakata Y, Kunihisa M, Matsumoto S (2008) Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.). Theor Appl Genet 118:165-175. doi:10.1007/s00122-008-0885-1   

35. Gabriel J, Sanabria D, Veramendi S, Plata G, Angulo A, Crespo M (2013) Genetic resistance of tomato hybrids (Solanum lycopersicum L. (Mill.) to Tomato spotted wilt virus (TSWV). Agron Costarricense 37:61-69  

36. Gama RNCS, Santos CAF, Dias RCS, Alves JCSF, Nogueira TO (2015) Microsatellite markers linked to the locus of the watermelon fruit stripe pattern. Genet Mol Res 14:269-276. doi:10.4238/2015.January.16.11  

37. Gao P, Liu S, Zhu QL, Luan FS (2015) Marker-assisted selection of Fusarium wilt-resistant and gynoecious melon (Cucumis melo L.). Genet Mol Res 14:16255-16264. doi:10.4238/2015.December.8.16  

38. Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, et al. (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA 109:11872-11877. doi:10.1073/pnas.1205415109  

39. Geethanjali S, Chen K-Y, Pastrana DV, Wang J-F (2010) Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6. Euphytica 173:85-97. doi:10.1007/s10681-010-0125-z   

40. Geethanjali S, Kadirvel P, de la Peñ a R, Rao ES, Wang J-F (2011) Development of tomato SSR markers from anchored BAC clones of chromosome 12 and their application for genetic diversity analysis and linkage mapping. Euphytica 178:283-295. doi:10.1007/s10681-010-0331-8   

41. Gorjanc G, Jenko J, Hearne SJ, Hickey JM (2016) Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations. BMC Genomics 17:30. doi:10.1186/s12864-015-2345-z   

42. Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, et al. (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51-58. doi:10.1038/ng.2470   

43. Guo X, Wang H, Pandey M, Ji X, Holbrook C, Culbreath A, et al. (2015) Phenotypic assessments of peanut nested association mapping (NAM) populations. University of Georgia Plant Center Retreat Meeting (Abstract)   

44. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461-485. doi:10.1007/s11103-005-0257-z   

45. He S, Schulthess AW, Mirdita V, Zhao B, Korzun V, Bothe R, et al. (2016) Genomic selection in a commercial winter wheat population. Theor Appl Genet 129:641–651. doi:10.1007/s00122-015-2655-1   

46. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1-12. doi:10.2135/ cropsci2008.08.0512   

47. Hemming MN, Basuki S, McGrath DJ, Carroll BJ, Jones DA (2004) Fine mapping of the tomato I-3 gene for fusarium wilt resistance Genomic Tools and Their Implications for Vegetable Breeding   

48. Horticultural Science and Technology 161 and elimination of a co-segregating resistance gene analogue as a candidate for I-3. Theor Appl Genet 109:409-418. doi:10.1007/s00122-004-1646-4  

49. Heusden AWv, Koornneef M, Voorrips RE, Brü ggemann W, Pet G, Vrielink-van Ginkel R, et al. (1999) Three QTLs from Lycopersicon peruvianum confer a high level of resistance to Clavibactermichiganensis ssp. michiganensis. Theor Appl Genet 99:1068–1074. doi:10.1007/s001220051416   

50. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156-161. doi:10.1016/j.pbi.2007.01.003   

51. Huang B, Paulob M-J, Boerb M, Effgena S, Keizerb P, Koornneef M, Eeuwijk FAv (2011) Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc Natl Acad Sci USA 108:4488–4493. doi:10.1073/ pnas.1100465108  

52. Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation intercross population for genetic analysis in wheat. Plant Biotechnol J 10:826-839. doi:10.1111/j.1467-7652.2012.00702.x   

53. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, et al. (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275-1281. doi:10.1038/ng.475   

54. Hutton SF, Scott JW, Yang W, Sim S, Francis DM, Jones JB (2010) Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet 121:1275-1287. doi:10.1007/s00122-010-1387-5   

55. Iwata H, Jannink J-L (2011) Accuracy of genomic selection prediction in barley breeding programs: A simulation study based on the real single nucleotide polymorphism data of barley breeding lines. Crop Sci 51:1915-1927. doi:10.2135/cropsci2010.12.0732   

56. Jablonska B, Ammiraju JS, Bhattarai KK, Mantelin S, Martinez de Ilarduya O, Roberts PA, Kaloshian I (2007) The Mi-9 gene from Solanum arcanum conferring heat-stable resistance to root-knot nematodes is a homolog of Mi-1. Plant Physiol 143:1044-1054. doi:10.1104/pp.106.089615   

57. Joobeur T, King JJ, Nolin SJ, Thomas CE, Dean RA (2004) The Fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features. Plant J 39:283-297. doi:10.1111/j.1365-313X.2004.02134.x   

58. Jung YJ, Nou IS, Cho YG, Kim MK, Kim H-T, Kang KK (2016) Identification of an SNP variation of elite tomato (Solanum lycopersicum L.) lines using genome resequencing analysis. Hortic Environ Biotechnol 57:173-181. doi:10.1007/s13580-016-0132-7   

59. Kadirvel P, de la Peñ a R, Schafleitner R, Huang S, Geethanjali S, Kenyon L, et al. (2012) Mapping of QTLs in tomato line FLA456 associated with resistance to a virus causing Tomato Yellow Leaf Curl disease. Euphytica 190:297-308. doi:10.1007/s10681-012-0848-0   

60.  Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270-278. doi:10.1038/ng.2877   

61. Kang WH, Hoang NH, Yang HB, Kwon JK, Jo SH, Seo JK, et al. (2010) Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.). Theor Appl Genet 120:1587-1596. doi:10.1007/s00122-010-1278-9  

62. Kim KH, Hwang JH, Han DY, Park M, Kim S, Choi D, et al. (2015) Major quantitative trait loci and putative candidate genes for powdery mildew resistance and fruit-related traits revealed by an Intraspecific genetic map for watermelon (Citrullus lanatus var. lanatus). PLoS One 10:e0145665. doi:10.1371/journal.pone.0145665   

63. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, et al. (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551. doi:10.1371/journal.pgen.1000551   

64. Lee H-Y, Go H-C, Heo O-S, Kwon J-K, Kang BC (2015) Genome-wide association study (GWAS) in pepper using a core collection. Symp Korean Soc Breeding Sci (Abstract)   

65. Li C, Wang F, Yang Y, Fu F, Xu C, Shi L, et al. (2011) Significant association of SNP rs2106261 in the ZFHX3 gene with atrial fibrillation in a Chinese Han GeneID population. Hum Genet 129:239-246. doi:10.1007/s00439-010-0912-6   

66. Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, et al. (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220-1226. doi:10.1038/ng.3117   

67. Lin Y-H, Chen K-S, Liou T-D, Huang J-W, Chang P-FL (2009) Development of a molecular method for rapid differentiation of watermelon lines resistant to Fusarium oxysporum f. sp. niveum. Bot Stud 50:273-280   

68. Liu S, Gao P, Zhu Q, Luan F, Davis AR, Wang X (2016) Development of cleaved amplified polymorphic sequence markers and a CAPSbased genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome resequencing data. Breed Sci 66:244-259. doi:10.1270/jsbbs.66.244   

69. Mace ES, Hunt CH, Jordan DR (2013) Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time. Theor Appl Genet 126:1377-1395. doi:10.1007/s00122-013-2059-z   

70. Maharijaya A, Vosman B, Steenhuis-Broers G, Pelgrom K, Purwito A, Visser RG, Voorrips RE (2015) QTL mapping of thrips resistance in pepper. Theor Appl Genet 128:1945-1956. doi:10.1007/s00122-015-2558-1   

71. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. (2009) Finding the missing heritability of complex diseases. Nature 461:747-753   

72. Maurer A, Draba V, Pillen K (2016) Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping. J Exp Bot 67:2507-2518. doi:10.1093/jxb/erw070   

73. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, et al. (2009) Genetic properties of the maize nested association mapping population. Science 325 737-740. doi:10.1126/science.1174320   

74. Merk HL, Yarnes SC, Van Deynze A, Tong N, Menda N, Mueller LA, et al. (2012) Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. J Am Soc Hortic Sci 6:427-437  

75. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829   

76. Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6:1-7. doi:10.3835/plantgenome2013.03.0001in Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969- 977. doi:10.1104/pp.108.118232   

77. Moury B, Pflieger S, Blattes A, Lefebvre V, Palloix A (2000) A CAPS marker to assist selection of Tomato spotted wilt virus (TSWV) resistance in pepper. Genome 43:137–142. doi:10.1139/g99-098   

78. Munos S, Ranc N, Botton E, Berard A, Rolland S, Duffe P, et al. (2011) Increase in tomato locule number is controlled by two singlenucleotide polymorphisms located near WUSCHEL. Plant Physiol 156:2244-2254. doi:10.1104/pp.111.173997   

79. Natarajan S, Kim HT, Thamilarasan SK, Veerappan K, Park JI, Nou IS (2016) Whole genome re-sequencing and characterization of powdery mildew disease-associated allelic variation in melon. PLoS One 11:e0157524. doi:10.1371/journal.pone.0157524   

80. Nice LM, Steffenson BJ, Guedira GLB, Akhunov ED, Liu D, Kono TJY, et al. (2016) Development and genetic characterization of an advanced backcross-nested association mapping (AB-NAM) population of wild × cultivated barley. Genetics 203:1453-1467. doi:10.1534/genetics.116.190736   

81. Nicolai M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A (2012) Discovery of a large set of SNP and SSR genetic markers by highthroughput sequencing of pepper (Capsicum annuum). Genet Mol Res 11:2295-2300. doi:10.4238/2012.August.13.3   

82. Nimmakayala P, Abburi VL, Abburi L, Alaparthi SB, Cantrell R, Park M, et al. (2014a) Linkage disequilibrium and populationstructure analysis among Capsicum annuum L. cultivars for use in association mapping. Mol Genet Genomics 289:513-521. doi:10.1007/s00438-014-0827-3   

83. Nimmakayala P, Levi A, Abburi L, Abburi L, Tomason YR, Saminathan T, et al. (2014b) Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics 15:767. doi:10.1186/1471-2164-15-767  

84. Ning X, Wang X, Gao X, Zhang Z, Zhang L, Yan W, Li G (2014) Inheritances and location of powdery mildew resistance gene in melon Edisto47. Euphytica 195:345-353. doi:10.1007/s10681-013-1000-5  

85. Palomares-Rius FJ, Viruel MA, Yuste-Lisbona FJ, Lopez-Sese AI, Gomez-Guillamon ML (2011) Simple sequence repeat markers linked to QTL for resistance to Watermelon Mosaic Virus in melon. Theor Appl Genet 123:1207-1214. doi:10.1007/s00122-011-1660-2   

86. Panthee DR, Brown AF, Yousef GG, Ibrahem R, Anderson C, Havey M (2013) Novel molecular marker associated with Tm2a gene conferring resistance to tomato mosaic virus in tomato. Plant Breeding 132:413-416. doi:10.1111/pbr.12076   

87. Pascual L, Albert E, Sauvage C, Duangjit J, Bouchet JP, Bitton F, et al. (2016) Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Sci 242:120-130. doi:10.1016/ j.plantsci.2015.06.017   

88. Pascual L, Desplat N, Huang BE, Desgroux A, Bruguier L, Bouchet JP, et al. (2015) Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotech J 13:565-577. doi:10.1111/pbi.12282   

89. Pavan S, Zheng Z, Borisova M, van den Berg P, Lotti C, De Giovanni C, et al. (2008) Map- vs. homology-based cloning for the recessive gene ol-2 conferring resistance to tomato powdery mildew. Euphytica 162:91-98. doi:10.1007/s10681-007-9570-8   

90. Pei CC, Wang H, Zhang JY, Wang YY, Francis DM, Yang WC (2012) Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3. Theor Appl Genet 124:533-542. doi:10.1007/s00122-011-1726-1   

91. Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, et al. (2012) Genomic selection in wheat breeding using genotyping-bysequencing. Plant Genome 5:103-113. doi:10.3835/plantgenome2012.06.0006   

92. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909. doi:10.1038/ng1847   

93. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959   

94. Qi J, Liu X, Shen D, Miao H, Xie B, Li X, et al. (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510-1515. doi:10.1038/ng.2801   

95. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, et al. (2014a) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA. 111:5135-5140. doi:10.1073/pnas.1400975111  

96. Ranc N, Muñ os S, Xu J, Paslier ML, Chauveau A, Bounon R, et al. (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3-Genes Genom Genet 2:853- 864. doi:10.1534/g3.112.002667  

97. Reddy UK, Almeida A, Abburi VL, Alaparthi SB, Unselt D, Hankins G, et al. (2014a) Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections. PLoS One 9:e86393. doi:10.1371/ journal.pone.0086393  

98. Reddy UK, Nimmakayala P, Levi A, Abburi VL, Saminathan T, Tomason YR, et al. (2014b) High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon. G3-Genes Genom Genet 4:2219-2230  

99. Ren R, Ray R, Li P, Xu J, Zhang M, Liu G, et al. (2015a) Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon. Mol Genet Genomics 290:1457–1470. doi:10.1007/s00438-015-0997-7  

100. Ren Y, Di J, Gong G, Zhang H, Guo S, Zhang J, Xu Y (2015b) Genetic analysis and chromosome mapping of resistance to Fusarium oxysporum f. sp. niveum (FON) race 1 and race 2 in watermelon (Citrullus lanatus L.). Mol Breed 35:183. doi:10.1007/s11032-015-0375-5  

101. Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, et al. (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4:e5795. doi:10.1371/journal.pone.0005795  

102. Robbins MD, Casler MD, Staub JE (2008) Pyramiding QTL for multiple lateral branching in cucumber using inbred backcross lines. Mol Breed 22:131-139. doi:10.1007/s11032-008-9162-x  

103. Robbins MD, Masud MAT, Panthee DR, Gardner RG, Francis DM, Stevens MR (2010) Marker-assisted selection for coupling phase resistance to Tomato Spotted Wilt Virus and Phytophthora infestans (late blight) in tomato. HortScience 45:1424-1428  

104. Robert VJM, West MAL, Inai S, Caines A, Arntzen L, Smith JK, Clair DAS (2001) Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Mol Breed 8:217–233. doi:10.1023/A:1013734024200  

105. Sakata Y, Kubo N, Morishita M, Kitadani E, Sugiyama M, Hirai M (2006) QTL analysis of powdery mildew resistance in cucumber (Cucumis sativus L.). Theor Appl Genet 112:243-250. doi:10.1007/s00122-005-0121-1  

106. Shang J, Li N, Li N, Xu Y, Ma S, Wang J (2016) Construction of a high-density genetic map for watermelon (Citrullus lanatus L.) based on large-scale SNP discovery by specific length amplified fragment sequencing (SLAF-seq). Sci Hort 203:38-46. doi:10.1016/ j.scienta.2016.03.007  

107. Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, et al. (2013) Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res 20:593-603. doi:10.1093/dnares/dst033   

108. Sim S, Durstewitz G, Plieske J, Wieseke R, Ganal M, Van Deynze A, et al. (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7:e40563. doi:10.1371/journal.pone.0040563   

109. Sim SC, Robbins MD, Wijeratne S, Wang H, Yang WC, Francis DM (2015) Association analysis for Bacterial Spot resistance in a directionally selected complex breeding population of tomato. Phytopathology 105:1437-1445. doi:10.1094/PHYTO-02-15- 0051-R  

110. Staniaszek M, Sczechura W, Marczewski W (2014) Identification of a new molecular marker C2-25 linked to the Fusarium oxysporum f.sp. radicis-lycopersici resistance Frl gene in tomato. Czech J Genet Plant Breed 50:285–287   

111. Steinmetz KA, Potter JD (1996) Vegetables, fruit, and cancer prevention. J Am Diet Assoc 96:1027-1039. doi:10.1016/S0002-8223(96)00273-8   

112. Stich B (2009) Comparison of mating designs for establishing nested association mapping populations in maize and Arabidopsis thaliana. Genetics 183:1525-1534. doi:10.1534/genetics.109.108449   

113. Sun C, Mao SL, Zhang ZH, Palloix A, Wang LH, Zhang BX (2015) Resistances to anthracnose (Colletotrichum acutatum) of Capsicum mature green and ripe fruit are controlled by a major dominant cluster of QTLs on chromosome P5. Sci Hort 181:81-88. doi:10.1016/j.scienta.2014.10.033   

114. Takken FLW, Schipper D, Nijkamp HJJ, Hille J (1998) Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. Plant J 14:401–411. doi:10.1046/j.1365-313X.1998.00135.x   

115. Tanaka Y, Yoneda H, Hosokawa M, Miwa T, Yazawa S (2014) Application of marker-assisted selection in breeding of a new fresh pepper cultivar (Capsicum annuum) containing capsinoids, low-pungent capsaicinoid analogs. Sci Hort 165:242-245. doi:10.1016/j.scienta.2013.10.025   

116. Tezuka T, Waki K, Kuzuya M, Ishikawa T, Takatsu Y, Miyagi M (2011) Development of new DNA markers linked to the Fusarium wilt resistance locus Fom-1 in melon. Plant Breeding 130:261-267. doi:10.1111/j.1439-0523.2010.01800.x   

117. Thabuis A, Palloix A, Servin B, Daubè ze AM, Signoret P, Hospital F, Lefebvre V (2004) Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects. Mol Breed 14:9–20. doi:10.1023/B:MOLB.0000037991.38278.82   

118. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641. doi:10.1038/nature11119  

119. Tomason Y, Nimmakayala P, Levi A, Reddy UK (2013) Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon. Mol Breed 31:829-841. doi:10.1007/s11032-013-9837-9   

120. Truong HTH, Kim JH, Cho MC, Chae SY, Lee HE (2013) Identification and development of molecular markers linked to Phytophthora root rot resistance in pepper (Capsicum annuum L.). Eur J Plant Pathol 135:289-297. doi:10.1007/s10658-012-0085-3   

121. Truong HTH, Kim K-T, Kim S, Cho M-C, Kim H-R, Woo J-G (2011) Development of gene-based markers for the Bs2 bacterial spot resistance gene for marker-assisted selection in pepper (Capsicum spp.). Hortic Environ Biotechnol 52:65-73. doi:10.1007/s13580- 011-0142-4  

122. United Nations (2015) World Population Prospects, The 2015 Revision. Key Findings and Advance Tables Varshney RK, Bansal KC, Aggarwal PK, Datta SK, Craufurd PQ (2011) Agricultural biotechnology for crop improvement in a variable climate: hope or hype? Trends Plant Sci 16:363-371. doi:10.1016/j.tplants.2011.03.004  

123.  Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: Applying genome sequencing technologies to crop breeding. PLoS Biol 12:e1001883. doi:10.1371/journal.pbio.1001883  

124. Wang Y, Yang W, Zhang W, Han Q, Feng M, Shen H (2013) Mapping of a heat-stable gene for resistance to Southern root-knot nematode in Solanum lycopersicum. Plant Mol Biol Rep 31:352-362. doi:10.1007/s11105-012-0505-8  

125. Wei Q, Wang Y, Qin X, Zhang Y, Zhang Z, Wang J, et al. (2014) An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics 15:1158. doi:10.1186/1471- 2164-15-1158  

126. Weinberger K, Lumpkin TA (2007) Diversification into horticulture and poverty reduction: A research agenda. World Dev 35:1464- 1480. doi:10.1016/j.worlddev.2007.05.002  

127. Xu Y, Lu Y, Xie C, Gao S, Wan J, Prasanna BM (2012) Whole-genome strategies for marker-assisted plant breeding. Mol Breed 29:833-854. doi:10.1007/s11032-012-9699-6  

128. Yang L, Li D, Li Y, Gu X, Huang S, Garcia-Mas J, Weng Y (2013) A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC Plant Biol 13:53. doi:10.1186/1471-2229-13-53   

129. Yang S, Fresnedo-Ramirez J, Wang M, Cote L, Schweitzer P, Barba P, et al. (2016) A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. J Hort Res 3:16002. doi:10.1038/ hortres.2016.2   

130. Yang W, Francis MD (2005) Marker-assisted selection for combining resistance to bacterial spot and bacterial speck in tomato. J Amer Soc Hort Sci 130:716–721  

131. Yang W, Sacks EJ, Ivey MLL, Miller SA, Francis DM (2005) Resistance in Lycopersicon esculentum intraspeciflc crosses to race T1 strains of Xanthomonas campestris pv. vesicatoria causing bacterial spot of tomato. Phytopathology 95:519-527. doi:10.1094/ PHYTO-95-0519   

132. Yang X, Caro M, Hutton SF, Scott JW, Guo Y, Wang X, et al. (2014) Fine mapping of the tomato Yellow Leaf Curl Virus resistance gene Ty-2 on chromosome 11 of tomato. Mol Breed 34:749-760. doi:10.1007/s11032-014-0072-9   

133. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539-551. doi:10.1534/genetics.107.074245   

134. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203-208. doi:10.1038/ng1702   

135. Yu JM, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155-160. doi:10.1016/j.copbio.2006.02.003   

136. Yuste-Lisbona FJ, Capel C, Sarria E, Torreblanca R, Gó mez-Guillamó n ML, Capel J, et al. (2010) Genetic linkage map of melon (Cucumis melo L.) and localization of a major QTL for powdery mildew resistance. Mol Breed 27:181-192. doi:10.1007/s11032-010-9421-5   

137. Zhang C, Liu L, Zheng Z, Sun Y, Zhou L, Yang Y, et al. (2013) Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato. Theor Appl Genet 126:2643-2653. doi:10.1007/s00122-013-2162-1   

138. Zhang H, Yi H, Wu M, Zhang Y, Zhang X, Li M, Wang G (2016) Mapping the flavor contributing traits on "Fengwei melon" (Cucumis melo L.) chromosomes using parent resequencing and super bulked-segregant analysis. PLoS One 11:e0148150. doi:10.1371/ journal.pone.0148150   

139. Zhang XP, Rhodes BB, Baird WV (1996) Development of genic male-sterile watermelon lines with delayed-green seedling marker. HortScience 31:123–126  

140. Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, et al. (2015) Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. Plant Cell 27:1595-1604. doi:10.1105/tpc.114.135848  

141. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5-20. doi:10.3835/ plantgenome2008.02.0089  

142. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5-20. doi:10.3835/ plantgenome2008.02.0089  

143. Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, et al. (2016) A high-density genetic linkage map for cucumber (Cucumis sativus L.): Based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber. Front Plant Sci 7:437. doi:10.3389/fpls.2016.00437