Genome-based breeding approaches in major vegetable crops

  • Ning Hao
  • Deguo Han
  • Ke Huang
  • Yalin Du
  • Jingjing Yang
  • Jian Zhang
  • Changlong WenEmail author
  • Tao WuEmail author


Vegetable crops are major nutrient sources for humanity and have been well-cultivated since thousands of years of domestication. With the rapid development of next-generation sequencing and high-throughput genotyping technologies, the reference genome of more than 20 vegetables have been well-assembled and published. Resequencing approaches on large-scale germplasm resources have clarified the domestication and improvement of vegetable crops by human selection; its application on genetic mapping and quantitative trait locus analysis has led to the discovery of key genes and molecular markers linked to important traits in vegetables. Moreover, genome-based breeding has been utilized in many vegetable crops, including Solanaceae, Cucurbitaceae, Cruciferae, and other families, thereby promoting molecular breeding at a single-nucleotide level. Thus, genome-wide SNP markers have been widely used, and high-throughput genotyping techniques have become one of the most essential methods in vegetable breeding. With the popularization of gene editing technology research on vegetable crops, breeding efficiency can be rapidly increased, especially by combining the genomic and variomic information of vegetable crops. This review outlines the present genome-based breeding approaches used for major vegetable crops to provide insights into next-generation molecular breeding for the increasing global population.


Author contribution statement

NH, CLW, and TW drafted the manuscript. NH, DGH, KH, YLD, JJY, JZ, CLW, and TW performed the text sections and edited the content.


This study was supported by The National Key Research and Development Program of China (2018YFD1000800), National Natural Science Foundation of China (31972429, 31972407, 31701934, 31801887), and Beijing Municipal National Science Foundation (6172014).

Compliance with ethical standards

Conflict of interest

All authors jointly state that there is no conflict of interest.


  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178PubMedCrossRefPubMedCentralGoogle Scholar
  2. Aversano R, Contaldi F, Ercolano MR, Grosso V, Iorizzo M, Tatino F et al (2015) The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. Plant Cell 27:954–968PubMedPubMedCentralCrossRefGoogle Scholar
  3. Ballester AR, Molthoff J, de Vos R, Hekkert B, Orzaez D, Fernandez-Moreno JP et al (2010) Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Physiol 152:71–84PubMedPubMedCentralCrossRefGoogle Scholar
  4. Bannoud F, Ellison S, Paolinelli M, Horejsi T, Senalik D, Fanzone M et al (2019) Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). Theor Appl Genet 132:2485–2507PubMedCrossRefPubMedCentralGoogle Scholar
  5. Barrera-Redondo J, Ibarra-Laclette E, Vazquez-Lobo A, Gutierrez-Guerrero YT, Sanchez de la Vega G, Pinero D et al (2019) The genome of Cucurbita argyrosperma (Silver-Seed Gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita. Mol Plant 12:506–520PubMedCrossRefPubMedCentralGoogle Scholar
  6. 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 46:1034–1038PubMedCrossRefPubMedCentralGoogle Scholar
  7. Borovsky Y, Monsonego N, Mohan V, Shabtai S, Kamara I, Faigenboim A et al (2019) The zinc-finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato. Plant J 99:41–45PubMedCrossRefGoogle Scholar
  8. Branham SE, Patrick Wechter W, Lambel S, Massey L, Ma M, Fauve J et al (2018) QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon. Mol Breed 38:139CrossRefGoogle Scholar
  9. Cai C, Wang X, Liu B, Wu J, Liang J, Cui Y et al (2017) Brassica rapa Genome 2.0: a reference upgrade through sequence re-assembly and gene re-annotation. Mol Plant 10:649–651PubMedCrossRefGoogle Scholar
  10. Cambiaso V, Pratta GR, Pereira da Costa JH, Zorzoli R, Francis DM, Rodríguez GR (2019) Whole genome re-sequencing analysis of two tomato genotypes for polymorphism insight in cloned genes and a genetic map construction. Sci Hortic 247:58–66CrossRefGoogle Scholar
  11. Cao W, Du Y, Wang C, Xu L, Wu T (2018) Cscs encoding chorismate synthase is a candidate gene for leaf variegation mutation in cucumber. Breed Sci 68:571–581PubMedPubMedCentralCrossRefGoogle Scholar
  12. Chaudhary J, Alisha A, Bhatt V, Chandanshive S, Kumar N, Mir Z et al (2019) Mutation breeding in tomato: advances, applicability and challenges. Plants 8:128PubMedCentralCrossRefGoogle Scholar
  13. Chen C, Liu M, Jiang L, Liu X, Zhao J, Yan S et al (2014) Transcriptome profiling reveals roles of meristem regulators and polarity genes during fruit trichome development in cucumber (Cucumis sativus L.). J Exp Bot 65:4943–4958PubMedPubMedCentralCrossRefGoogle Scholar
  14. Chen F, Fu B, Pan Y, Zhang C, Wen H, Weng Y et al (2017) Fine mapping identifies CsGCN5 encoding a histone acetyltransferase as putative candidate gene for tendril-less1 mutation (td-1) in cucumber. Theor Appl Genet 130:1549–1558PubMedCrossRefPubMedCentralGoogle Scholar
  15. Chen K, Wang Y, Zhang R, Zhang H, Gao C (2019) CRISPR/Cas Genome editing and precision plant breeding in agriculture. Annu Rev Plant Biol 70:667–697PubMedCrossRefGoogle Scholar
  16. Cheng Q, Wang P, Liu J, Wu L, Zhang Z, Li T et al (2018) Identification of candidate genes underlying genic male-sterile msc-1 locus via genome resequencing in Capsicum annuum L. Theor Appl Genet 131:1861–1872PubMedCrossRefGoogle Scholar
  17. Corem S, Doron-Faigenboim A, Jouffroy O, Maumus F, Arazi T, Bouche N (2018) Redistribution of CHH methylation and small interfering RNAs across the genome of tomato ddm1 mutants. Plant Cell 30:1628–1644PubMedPubMedCentralCrossRefGoogle Scholar
  18. Dou J, Lu X, Ali A, Zhao S, Zhang L, He N, Liu W (2018a) Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.). PLoS ONE 13:e0200617PubMedPubMedCentralCrossRefGoogle Scholar
  19. Dou J, Zhao S, Lu X, He N, Zhang L, Ali A et al (2018b) Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.). Theor Appl Genet 131:947–958PubMedPubMedCentralCrossRefGoogle Scholar
  20. FAO (1990) FAOSTAT.
  21. FAO (2017) FAOSTAT.
  22. Fernandez-Moreno JP, Tzfadia O, Forment J, Presa S, Rogachev I, Meir S et al (2016) Characterization of a new pink-fruited tomato mutant results in the identification of a null allele of the SlMYB12 transcription factor. Plant Physiol 171:1821–1836PubMedPubMedCentralCrossRefGoogle Scholar
  23. Fu W, Ye X, Ren J, Li Q, Du JT, Hou AL et al (2019) Fine mapping of lcm1, a gene conferring chlorophyll-deficient golden leaf in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Breed 39:52CrossRefGoogle Scholar
  24. Gao M, Hu L, Li Y, Weng Y (2016) The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit. Theor Appl Genet 129:1961–1973PubMedCrossRefGoogle Scholar
  25. Gao L, Gonda I, Sun H, Ma Q, Bao K, Tieman DM et al (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51:1044–1051PubMedCrossRefGoogle Scholar
  26. Garcia V, Bres C, Just D, Fernandez L, Tai FW, Mauxion JP et al (2016) Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing. Nat Protoc 11:2401–2418PubMedCrossRefPubMedCentralGoogle Scholar
  27. 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 109:11872–11877PubMedCrossRefGoogle Scholar
  28. Golicz A, Bayeret P, Barker G, Edger P, Kim H, Martinez P et al (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390PubMedPubMedCentralCrossRefGoogle Scholar
  29. 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 45:51–58PubMedCrossRefPubMedCentralGoogle Scholar
  30. Guo G, Wang S, Liu J, Pan B, Diao W, Ge W, Gao C, Snyder JC (2017) Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens). Theor Appl Genet 130:41–52PubMedCrossRefPubMedCentralGoogle Scholar
  31. Han K, Lee HY, Ro NY, Hur OS, Lee JH, Kwon JK et al (2018) QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum. Plant Biotechnol J 16:1546–1558PubMedCentralCrossRefGoogle Scholar
  32. Hao N, Du Y, Li H, Wang C, Wang C, Gong S et al (2018) CsMYB36 is involved in the formation of yellow green peel in cucumber (Cucumis sativus L.). Theor Appl Genet 131:1659–1669PubMedCrossRefGoogle Scholar
  33. Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A et al (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative Solanum species indigenous to the old world. DNA Res 21:649–660PubMedPubMedCentralCrossRefGoogle Scholar
  34. Hu B, Li D, Liu X, Qi J, Gao D, Zhao S et al (2017) Engineering non-transgenic gynoecious cucumber using an improved transformation protocol and optimized CRISPR/Cas9 system. Mol Plant 10:1575–1578PubMedCrossRefGoogle Scholar
  35. 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 41:1275–1281PubMedCrossRefGoogle Scholar
  36. Huang Y, Cao H, Yang L, Chen C, Shabala L, Xiong M et al (2019) Tissue-specific respiratory burst oxidase homologue-dependent H2O2 signaling to the plasma membrane H+-ATPase confers potassium uptake and salinity tolerance in Cucurbitaceae. J Exp Bot. CrossRefPubMedPubMedCentralGoogle Scholar
  37. Hwang I, Kim Y, Han J, Nou IS (2016) Orange color is associated with CYC-B expression in tomato fleshy fruit. Mol Breed 36:42CrossRefGoogle Scholar
  38. Illa-Berenguer E, Van Houten J, Huang Z, van der Knaap E (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128:1329–1342PubMedCrossRefPubMedCentralGoogle Scholar
  39. Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J et al (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 48:657–666PubMedCrossRefPubMedCentralGoogle Scholar
  40. Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S (2015) CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem Biophys Res Commun 467:76–82PubMedCrossRefPubMedCentralGoogle Scholar
  41. Jian W, Cao H, Yuan S, Liu Y, Lu J, Lu W et al (2019) SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits. Hortic Res 6:22PubMedPubMedCentralCrossRefGoogle Scholar
  42. Jiang H, Tian H, Yan C, Jia L, Wang Y, Wang M et al (2019) RNA-seq analysis of watermelon (Citrullus lanatus) to identify genes involved in fruit cracking. Sci Hortic 248:248–255CrossRefGoogle Scholar
  43. Khan MZ, Zaidi SS, Amin I, Mansoor S (2019) A CRISPR way for fast-forward crop domestication. Trends Plant Sci 24:293–296PubMedCrossRefGoogle Scholar
  44. 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 46:270–278PubMedCrossRefGoogle Scholar
  45. Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT et al (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18:210PubMedPubMedCentralCrossRefGoogle Scholar
  46. Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y et al (2014) Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 21:481–490PubMedPubMedCentralCrossRefGoogle Scholar
  47. Kreplak J, Madoui MA, Capal P, Novak P, Labadie K, Aubert G et al (2019) A reference genome for pea provides insight into legume genome evolution. Nat Genet 51:1411–1422PubMedCrossRefGoogle Scholar
  48. Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N et al (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biol 16:258PubMedPubMedCentralCrossRefGoogle Scholar
  49. Lee J (2019) Development and evolution of molecular markers and genetic maps in Capsicum species. In: Ramchiary N, Kole C (eds) The Capsicum genome. Springer, Cham, pp 85–103CrossRefGoogle Scholar
  50. Lee YP, Cho Y, Kim S (2014) A high-resolution linkage map of the Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility in radish (Raphanus sativus L.) produced by a combination of bulked segregant analysis and RNA-Seq. Theor Appl Genet 127:2243–2252PubMedCrossRefGoogle Scholar
  51. Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L et al (2018) Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. Plant J 94:562–570PubMedCrossRefGoogle Scholar
  52. Li Y, Wen C, Weng Y (2013) Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor. Theor Appl Genet 126:2187–2196PubMedCrossRefPubMedCentralGoogle Scholar
  53. Li S, Pan Y, Wen C, Li Y, Liu X, Zhang X et al (2016) Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber. Theor Appl Genet 129:1007–1022PubMedCrossRefGoogle Scholar
  54. Li B, Zhao Y, Zhu Q, Zhang Z, Fan C, Amanullah S, Gao P, Luan F (2017) Mapping of powdery mildew resistance genes in melon (Cucumis melo L.) by bulked segregant analysis. Sci Hortic 220:160–167CrossRefGoogle Scholar
  55. Li R, Fu D, Zhu B, Luo Y, Zhu H (2018) CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. Plant J 94:513–524PubMedCrossRefGoogle Scholar
  56. Liang D, Chen M, Qi X, Xu Q, Zhou F, Chen X (2016) QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber. Front Plant Sci 7:1000PubMedPubMedCentralGoogle Scholar
  57. Lin T, Wang S, Zhong Y, Gao D, Cui Q, Chen H (2016) A truncated F-box protein confers the dwarfism in cucumber. J Genet Genomics 43:223–226PubMedCrossRefGoogle Scholar
  58. Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS (2012) Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS ONE 7:e36406PubMedPubMedCentralCrossRefGoogle Scholar
  59. Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930PubMedPubMedCentralCrossRefGoogle Scholar
  60. Liu L, Sun T, Liu X, Guo Y, Huang X, Gao P, Wang X (2019a) Genetic analysis and mapping of a striped rind gene (st3) in melon (Cucumis melo L.). Euphytica 215:20CrossRefGoogle Scholar
  61. Liu G, Zhao T, You X, Jiang J, Li J, Xu X (2019b) Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum). BMC Plant Biol 19:15PubMedPubMedCentralCrossRefGoogle Scholar
  62. Lu H, Lin T, Klein J, Wang S, Qi J, Zhou Q et al (2014) QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theor Appl Genet 127:1491–1499PubMedCrossRefPubMedCentralGoogle Scholar
  63. Lun Y, Wang X, Zhang C, Yang L, Gao D, Chen H et al (2015) A CsYcf54 variant conferring light green coloration in cucumber. Euphytica 208:509–517CrossRefGoogle Scholar
  64. Ma C, Liu M, Li Q, Si J, Ren X, Song H (2019) Efficient BoPDS gene editing in cabbage by the CRISPR/Cas9 system. Hortic Plant J 5:164–169CrossRefGoogle Scholar
  65. Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444:139–158CrossRefGoogle Scholar
  66. Moghe GD, Hufnagel DE, Tang H, Xiao Y, Dworkin I, Town CD et al (2014) Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 26:1925–1937PubMedPubMedCentralCrossRefGoogle Scholar
  67. Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Marti-Gomez C et al (2018) De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol J 16:1161–1171PubMedCrossRefPubMedCentralGoogle Scholar
  68. Nimmakayala P, Abburi VL, Bhandary A, Abburi L, Vajja VG, Reddy R et al (2014) Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Mol Breed 34:537–548CrossRefGoogle Scholar
  69. Nimmakayala P, Abburi VL, Saminathan T, Alaparthi SB, Almeida A, Davenport B et al (2016) Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L. Sci Rep 6:38081PubMedPubMedCentralCrossRefGoogle Scholar
  70. Osorio S, Alba R, Damasceno CM, Lopez-Casado G, Lohse M, Zanor MI et al (2011) Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157:405–425PubMedPubMedCentralCrossRefGoogle Scholar
  71. Ou L, Li D, Lv J, Chen W, Gao H, Zeng Q et al (2018) Pan-genome of cultivated pepper (Capsicum) and its use in gene presence–absence variation analyses. New Phytol 220:360–363PubMedCrossRefPubMedCentralGoogle Scholar
  72. Pan C, Ye L, Qin L, Liu X, He Y, Wang J et al (2016) CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6:24765PubMedPubMedCentralCrossRefGoogle Scholar
  73. Paudel L, Clevenger J, McGregor C (2019) Chromosomal locations and interactions of four loci associated with seed coat color in watermelon. Front Plant Sci 10:788PubMedPubMedCentralCrossRefGoogle Scholar
  74. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  75. 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 45:1510–1515PubMedCrossRefPubMedCentralGoogle Scholar
  76. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135–5140PubMedCrossRefPubMedCentralGoogle Scholar
  77. Ren J, Liu ZY, Du JT, Fu W, Hou AL, Feng H (2019) Fine-mapping of a gene for the lobed leaf, BoLl, in ornamental kale (Brassica oleracea L. var. acephala). Mol Breed 39:40CrossRefGoogle Scholar
  78. Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C et al (2017) Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 8:14953PubMedPubMedCentralCrossRefGoogle Scholar
  79. Rodriguez GR, Kim HJ, van der Knaap E (2013) Mapping of two suppressors of OVATE (sov) loci in tomato. Heredity (Edinb) 111:256–264CrossRefGoogle Scholar
  80. Rong F, Chen F, Huang L, Zhang J, Zhang C, Hou D et al (2019) A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cul) in cucumber (Cucumis sativus L.). Theor Appl Genet 132:113–123PubMedCrossRefPubMedCentralGoogle Scholar
  81. Ruangrak E, Su X, Huang Z, Wang X, Guo Y, Du Y et al (2018) Fine mapping of a major QTL controlling early flowering in tomato using QTL-seq. Can J Plant Sci 98:672–682CrossRefGoogle Scholar
  82. Saidou AA, Thuillet AC, Couderc M, Mariac C, Vigouroux Y (2014) Association studies including genotype by environment interactions: prospects and limits. BMC Genet 15:3PubMedPubMedCentralCrossRefGoogle Scholar
  83. Schrager-Lavelle A, Gath NN, Devisetty UK, Carrera E, Lopez-Diaz I, Blazquez MA et al (2019) The role of a class III gibberellin 2-oxidase in tomato internode elongation. Plant J 97:603–615PubMedCrossRefGoogle Scholar
  84. Semagn K, Babu R, Hearne S, Olsen M (2013) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14CrossRefGoogle Scholar
  85. Shang Y, Ma Y, Zhou Y, Zhang H, Duan L, Chen H et al (2014) Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346:1084–1088PubMedCrossRefGoogle Scholar
  86. 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 Hortic 203:38–46CrossRefGoogle Scholar
  87. Shu J, Liu Y, Zhang L, Li Z, Fang Z, Yang L et al (2018) QTL-seq for rapid identification of candidate genes for flowering time in broccoli x cabbage. Theor Appl Genet 131:917–928PubMedCrossRefGoogle Scholar
  88. Soyk S, Lemmon ZH, Oved M, Fisher J, Liberatore KL, Park SJ et al (2017) Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169:1142–1155PubMedCrossRefGoogle Scholar
  89. Sun H, Wu S, Zhang G, Jiao C, Guo S, Ren Y et al (2017) Karyotype stability and unbiased fractionation in the Paleo-Allotetraploid Cucurbita genomes. Mol Plant 10:1293–1306PubMedCrossRefGoogle Scholar
  90. Sun D, Wang C, Zhang X, Zhang W, Jiang H, Yao X et al (2019a) Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species. Hortic Res 6:82PubMedPubMedCentralCrossRefGoogle Scholar
  91. Sun X, Shu J, Ali Mohamed AM, Deng X, Zhi X, Bai J et al (2019b) Identification and characterization of EI (Elongated Internode) gene in tomato (Solanum lycopersicum). Int J Mol Sci 20:2204PubMedCentralCrossRefPubMedGoogle Scholar
  92. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183PubMedCrossRefGoogle Scholar
  93. Tan C, Liu Z, Huang S, Li C, Ren J, Tang X et al (2018) Pectin methylesterase inhibitor (PMEI) family can be related to male sterility in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 293:343–357PubMedCrossRefPubMedCentralGoogle Scholar
  94. Tanksley S, Ganal M, Prince JP, de Vicente MC, Bonierbale MW, Broun P et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedPubMedCentralGoogle Scholar
  95. Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32:e5PubMedPubMedCentralCrossRefGoogle Scholar
  96. Tian S, Jiang L, Gao Q, Zhang J, Zong M, Zhang H et al (2017) Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Rep 36:399–406PubMedCrossRefPubMedCentralGoogle Scholar
  97. Tian S, Jiang L, Cui X, Zhang J, Guo S, Li M et al (2018) Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing. Plant Cell Rep 37:1353–1356PubMedCrossRefPubMedCentralGoogle Scholar
  98. Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  99. Tomlinson L, Yang Y, Emenecker R, Smoker M, Taylor J, Perkins S et al (2019) Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele. Plant Biotechnol J 17:132–140PubMedCrossRefPubMedCentralGoogle Scholar
  100. Ueta R, Abe C, Watanabe T, Sugano SS, Ishihara R, Ezura H et al (2017) Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9. Sci Rep 7:507PubMedPubMedCentralCrossRefGoogle Scholar
  101. Urasaki N, Takagi H, Natsume S, Uemura A, Taniai N, Miyagi N et al (2017) Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Res 24:51–58PubMedPubMedCentralGoogle Scholar
  102. Vlasova A, Capella-Gutierrez S, Rendon-Anaya M, Hernandez-Onate M, Minoche AE, Erb I et al (2016) Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 17:32PubMedPubMedCentralCrossRefGoogle Scholar
  103. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039PubMedCrossRefGoogle Scholar
  104. Wang HS, Yu C, Tang XF, Zhu ZJ, Ma NN, Meng QW (2014) A tomato endoplasmic reticulum (ER)-type omega-3 fatty acid desaturase (LeFAD3) functions in early seedling tolerance to salinity stress. Plant Cell Rep 33:131–142PubMedCrossRefGoogle Scholar
  105. Wang L, Chen L, Li R, Zhao R, Yang M, Sheng J et al (2017) Reduced drought tolerance by CRISPR/Cas9-mediated SlMAPK3 mutagenesis in tomato plants. J Agric Food Chem 65:8674–8682PubMedCrossRefGoogle Scholar
  106. Wang C, Li H, Li Y, Meng Q, Fei X, Xu YJ et al (2019) Genetic characterization and fine mapping BrCER4 in involved cuticular wax formation in purple cai-tai (Brassica rapa L. var. purpurea). Mol Breeding 39:12CrossRefGoogle Scholar
  107. Win KT, Zhang C, Silva RR, Lee JH, Kim YC, Lee S (2019) Identification of quantitative trait loci governing subgynoecy in cucumber. Theor Appl Genet 132:1505–1521PubMedCrossRefGoogle Scholar
  108. Wu T, Qin Z, Zhou X, Feng Z, Du Y (2010) Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167:905–913PubMedCrossRefGoogle Scholar
  109. Wu S, Shamimuzzaman M, Sun H, Salse J, Sui X, Wilder A et al (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus. Plant J 92:963–975PubMedCrossRefGoogle Scholar
  110. Wu S, Wang X, Reddy U, Sun H, Bao K, Gao L et al (2019) Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. Plant Biotechnol J 17(12):2246–2258. CrossRefPubMedPubMedCentralGoogle Scholar
  111. Wurschum T (2012) Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet 125:201–210PubMedCrossRefGoogle Scholar
  112. Xin T, Zhang Z, Li S, Zhang S, Li Q, Zhang Z et al (2019) Genetic regulation of ethylene dosage for cucumber fruit elongation. Plant Cell 31:1063–1076PubMedPubMedCentralCrossRefGoogle Scholar
  113. Xu X, Xu R, Zhu B, Yu T, Qu W, Lu L et al (2014) A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq). Front Plant Sci 5:768PubMedCrossRefGoogle Scholar
  114. Xu X, Lu L, Zhu B, Xu Q, Qi X, Chen X (2015) QTL mapping of cucumber fruit flesh thickness by SLAF-seq. Sci Rep 5:15829PubMedPubMedCentralCrossRefGoogle Scholar
  115. Xu X, Chao J, Cheng X, Wang R, Sun B, Wang H et al (2016) Mapping of a novel race specific resistance gene to phytophthora root rot of pepper (Capsicum annuum) using bulked segregant analysis combined with specific length amplified fragment sequencing strategy. PLoS ONE 11:e0151401PubMedPubMedCentralCrossRefGoogle Scholar
  116. Xu C, Jiao C, Sun H, Cai X, Wang X, Ge C et al (2017) Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun 8:15275PubMedPubMedCentralCrossRefGoogle Scholar
  117. Xu L, Wang C, Cao W, Zhou S, Wu T (2018) CLAVATA1-type receptor-like kinase CsCLAVATA1 is a putative candidate gene for dwarf mutation in cucumber. Mol Genet Genom 293:1393–1405CrossRefGoogle Scholar
  118. Xu ZS, Yang QQ, Feng K, Xiong AS (2019) Changing carrot color: insertions in DcMYB7 alter the regulation of anthocyanin biosynthesis and modification. Plant Physiol. CrossRefPubMedPubMedCentralGoogle Scholar
  119. Yan C, An G, Zhu T, Zhang W, Zhang L, Peng L, Chen J, Kuang H (2019) Independent activation of the BoMYB2 gene leading to purple traits in Brassica oleracea. Theor Appl Genet 132:895–906PubMedCrossRefPubMedCentralGoogle Scholar
  120. Yang X, Li Y, Zhang W, He H, Pan J, Cai R (2013) Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.). Euphytica 196:341–348CrossRefGoogle Scholar
  121. Yang J, Liu D, Wang X, Ji C, Cheng F, Liu B et al (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48:1225–1232PubMedCrossRefPubMedCentralGoogle Scholar
  122. Yang Y, Zhu G, Li R, Yan S, Fu D, Zhu B et al (2017) The RNA editing factor SlORRM4 is required for normal fruit ripening in tomato. Plant Physiol 175:1690–1702PubMedPubMedCentralCrossRefGoogle Scholar
  123. Yang L, Liu H, Zhao J, Pan Y, Cheng S, Lietzow CD et al (2018) LITTLELEAF (LL) encodes a WD40 repeat domain-containing protein associated with organ size variation in cucumber. Plant J 95:834–847CrossRefGoogle Scholar
  124. Yang J, Zhang J, Han R, Zhang F, Mao A, Luo J et al (2019) Target SSR-Seq: a novel SSR genotyping technology associate with perfect SSRs in genetic analysis of cucumber varieties. Front Plant Sci 10:531PubMedPubMedCentralCrossRefGoogle Scholar
  125. Zhang J, Zhao J, Xu Y, Liang J, Chang P, Yan F, Li M, Liang Y, Zou Z (2015) Genome-wide association mapping for tomato volatiles positively contributing to tomato flavor. Front Plant Sci 6:1042PubMedPubMedCentralGoogle Scholar
  126. 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:e0148150PubMedPubMedCentralCrossRefGoogle Scholar
  127. Zhang L, Su W, Tao R, Zhang W, Chen J, Wu P et al (2017) RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat Commun 8:2264PubMedPubMedCentralCrossRefGoogle Scholar
  128. Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F et al (2018a) Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic Res 5:50PubMedPubMedCentralCrossRefGoogle Scholar
  129. Zhang X, Wang G, Chen B, Du H, Zhang F, Zhang H et al (2018b) Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PLoS ONE 13:e0194071PubMedPubMedCentralCrossRefGoogle Scholar
  130. Zhang Z, Wang B, Wang S, Lin T, Yang L, Zhao Z, Zhang Z, Huang S, Yang X (2019) Genome-wide target mapping shows histone deacetylase complex 1 regulates cell proliferation in cucumber fruit. Plant Physiol. CrossRefPubMedPubMedCentralGoogle Scholar
  131. Zhao J, Xu Y, Ding Q, Huang X, Zhang Y, Zou Z et al (2016) Association mapping of main tomato fruit sugars and organic acids. Front Plant Sci 7:1286PubMedPubMedCentralGoogle Scholar
  132. Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S et al (2019) Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 47:D1128–D1136PubMedCrossRefGoogle Scholar
  133. Zhou Q, Wang S, Hu B, Chen H, Zhang Z, Huang S (2015) An ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5 gene mutation confers light green peel in cucumber. J Integr Plant Biol 57:936–942PubMedCrossRefGoogle Scholar
  134. 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 7:437PubMedPubMedCentralGoogle Scholar
  135. Zhu G, Wang S, Huang Z, Zhang S, Liao Q, Zhang C et al (2018) Rewiring of the fruit metabolome in tomato breeding. Cell 172(249–261):e212Google Scholar
  136. Zhu G, Gou J, Klee H, Huang S (2019) Next-Gen approaches to flavor-related metabolism. Annu Rev Plant Biol 70:187–212PubMedCrossRefPubMedCentralGoogle Scholar
  137. Zsogon A, Cermak T, Naves ER, Notini MM, Edel KH, Weinl S et al (2018) De novo domestication of wild tomato using genome editing. Nat Biotechnol 36:1211–1216CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Horticulture and LandscapeHunan Agricultural UniversityChangshaChina
  2. 2.College of Horticulture and LandscapeNortheast Agricultural UniversityHarbinChina
  3. 3.Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry SciencesNational Engineering Research Center for VegetablesBeijingChina
  4. 4.Beijing Key Laboratory of Vegetable Germplasms ImprovementBeijingChina

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