, 215:69 | Cite as

Genetic diversity of 324 cultivated tomato germplasm resources using agronomic traits and InDel markers

  • Lan Jin
  • Liping Zhao
  • Yinlei Wang
  • Rong Zhou
  • Liuxia Song
  • Liping Xu
  • Xia Cui
  • Ren Li
  • Wengui YuEmail author
  • Tongmin ZhaoEmail author


The study of morphological and molecular diversity and grouping analysis for cultivated inbred tomato lines is very important to help breeders in selecting parental lines for hybrid breeding and developing heterotic groups. In this study, a total of 324 cultivated inbred tomato lines collected from various sources were investigated for the presence of 17 agronomic traits and subsequently genotyped with a 56- (insertion–deletion) InDel assay. The phenotypic coefficient of variation ranged from 5 to 108% with an average of 36%, and the range of phenotypic diversity index was 0.41– 2.06, with an average of 1.59. The outstanding traits in terms of causing phenotypic diversity of the inbred tomato lines are resistance to gray leaf spot, hypocotyl colour, growth habit, fruit shape, plant height, days to 30% first flower, weight per fruit, hardness, brix, acid, number of locules and transverse diameter of fruit by principal component analyses (PCA). The values of Shannon’s information index, polymorphic information content and heterozygosity are 0.61, 0.33 and 0.06 respectively. The PCA and Ward’s method for cluster multivariate analysis based on 17 agronomic traits revealed that there are four major groups with rich genetic diversity within groups. Model-based population structure analysis indicated that the 324 cultivated inbred tomato lines were separated into two main groups that were different from the results of the three main groups and five subgroups by Nei’s (Am Nat 106:283–292, 1973) cluster analysis based on InDel markers. The Mantel test correlation coefficient of the matrices of morphological and InDel distances was 0.229. Overall, this study reveals that 324 cultivated inbred tomato lines are diverse with high homozygosity and a rich genetic background. Nei’s (1973) cluster analysis can serve as an effective approach for assigning germplasm into groups and for providing guidelines for parental selection in hybrid tomato breeding.


Genetic variation Heterotic groups Agronomic traits InDel marker Multivariate methods 



The authors acknowledge the National Key Research and Development Program of China (2016YFD0101703), the fifth “333” High-level Personnel Training Project of Jiangsu, the Modern Agricultural Industry Technology System Project of Jiangsu (JATS[2018]264), the State Scholarship Fund of China (201808320074), and science and technology planning project of Qinghai (2017-HZ-808).

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  1. Acosta-Quezada PG, Vilanova S, Martínez-Laborde JB, Prohens J (2012) Genetic diversity and relationships in accessions from different cultivar groups and origins in the tree toamto (Solanum betaceum Cav.). Euphytica 187:87–97CrossRefGoogle Scholar
  2. Alvarez AE, van de Wiel CCM, Smulders MJM, Vosman B (2001) Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theor Appl Genet 103:1283–1292CrossRefGoogle Scholar
  3. Andrea M, Roberto P, Elena B et al (2007) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 11:657–669Google Scholar
  4. Badu-Apraku B, Lum AF (2007) Agronomic performance of Striga resistant early maturing maize varieties and inbred lines in the savannas of West and Central Africa. Crop Sci 47:2–15CrossRefGoogle Scholar
  5. Bauchet G, Causse M (2012) Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Caliskan M (ed) Genetic diversity in plants. InTech, Rijeka, pp 133–162Google Scholar
  6. Benor S, Zhang M, Wang Z, Zhang H (2008) Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. J Genet Genomics 35:373–379CrossRefGoogle Scholar
  7. Berhanu TE, Kassa S, Biswanath D et al (2017) Genetic variation and population structure of maize inbred lines adapted to the midaltitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers. BMC Genomics 18:777CrossRefGoogle Scholar
  8. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefGoogle Scholar
  9. Causse M, Desplat N, Pascual L et al (2013) Whole genomeresequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14:791CrossRefGoogle Scholar
  10. Chen C, Li B, Huang CQ et al (2010) Comparison analysis of Phytophthora infestans population genetic structure from different hosts based on SSR markers. Chinese Agricultural Science, Bulletin, BeijingGoogle Scholar
  11. Corrado G, Caramante M, Piffanelli P, Rao R (2014) Genetic diversity in Italian tomato landraces: implications for the development of a core collection. Sci Hortic 168:138–144CrossRefGoogle Scholar
  12. da Silveira LCI, Brasilleiro BP (2015) Genetic diversity and coefficient of kinship among potential genitors for obtaining cultivars of energy cane1. Revista Ciência Agronômica 46(2):358–368CrossRefGoogle Scholar
  13. Das S, Upadhyaya HD, Srivastava R et al (2015) Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA Res 22:377–386CrossRefGoogle Scholar
  14. Doyle JJ, Doyle JL (1987) A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  15. Feng JJ (2017) Genetic diversity and genome-wide association study on the key agronomic traits of wild tomato Solanum pimpinellifolium Google Scholar
  16. Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS ONE 4(10):e7433CrossRefGoogle Scholar
  17. Frankel R (1983) Heterosis in the tomato. Theor Appl Genet 6:189Google Scholar
  18. Geleta LF, Labuschagne MT, Viljoen CD (2005) Genetic variability in pepper (Capsicum annuum L.) estimated by morphological data and amplified fragment length polymorphismmarkers. Biodivers Conserv 14:2361–2375CrossRefGoogle Scholar
  19. Giandomenico C, Martina C, Piffanelli P et al (2014) Genetic diversity in Italian tomato landraces: implications for the development of a core collection. Sci Hortic 168:138–144CrossRefGoogle Scholar
  20. Hardy OJ, Vekemans X (2002) SPAGeDI: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  21. Khalil MR (2004) Breeding studies on tomato. M.Sc. Thesis. Fac. Agric. Minufiya Univ., Egypt, pp 1–99Google Scholar
  22. Li XX, Du YC (2006) Description and data standard for tomato. China Agriculture Press, BeijingGoogle Scholar
  23. Liu XX (2017) Associaton and genetic identification of loci for four fruit traits in tomato using InDel markers. Front Plant Sci 8:1269CrossRefGoogle Scholar
  24. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefGoogle Scholar
  25. Liu K, Goodman MM, Muse S, Smith JSC, Buckler ES, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2121PubMedPubMedCentralGoogle Scholar
  26. Lu ZM, Xu B (2010) On significance of heterotic group theory in hybrid rice breeding. Rice Sci 17:94–98CrossRefGoogle Scholar
  27. Luckwill LC (1943) The genus Lycopersicon: an historical, biological, and taxonomical survey of the wild and cultivated tomatoes. Aberdeen Univ Stud 120:1–44Google Scholar
  28. Lund B (2002) Repatriation of Nordic barley germplasm. Ph.D. dissertation, The Royal Veterinary and Agricultural University, Section of Plant Breeding and Crop Science, Copenhagen, DenmarkGoogle Scholar
  29. Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  30. Melchinger AE, Gumber RK (1998) Overview of heterosis and heterotic groups in agronomic crops. In: Lamkey KR, Staub JE (eds) Concepts and breeding of heterosis in crop plants. CSSA, Madison, pp 29–44Google Scholar
  31. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci 43:1235–1248CrossRefGoogle Scholar
  32. Moll RH, Longquist LH, Fortuna JY, Johnson EC (1965) The relation of heterosis and genetic divergence in maize. Genetics 52:139–144PubMedPubMedCentralGoogle Scholar
  33. Nei M (1973) Genetic distance between populations. Am Nat 106:283–292CrossRefGoogle Scholar
  34. Pritchard JK, Stephens P, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  35. Reif JC, Hallauer AR, Melchinger AE (2005) Heterosis and heterotic patterns in maize. Maydica 50:215Google Scholar
  36. Reif JC, Zhao Y, Wurschum T, Gowda M (2013) Genomic prediction of sunflower hybrid performance. Plant Breed 132:107–114CrossRefGoogle Scholar
  37. Rui WJ, Wang XM (2018) Genetic diversity analysis of 353 tomato germplasm resources by phenotypic traits. Acta Hortic Sin 45(3):561–570Google Scholar
  38. Sherry AF, Edward SB, Peter T et al (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. Plos one 4(10):e7433CrossRefGoogle Scholar
  39. Soller M, Beckmann J (1983) Genetic polymorphism in varietal identification and genetic improvement. Theor Appl Genet 67:25–33CrossRefGoogle Scholar
  40. Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  41. Tarek AS (2013) Mode of gene action, heterosis and inbreeding depression for yield and its components in tomato(Solanum lycopersicumL.). Sci Hortic 164:540–543CrossRefGoogle Scholar
  42. Thiphan N, Kim MK, Sung-Chur S (2016) Genetic variations of F1 tomato cultivars revealed by a core set of SSR and Indel markers. Sci Hortic 212:155–161CrossRefGoogle Scholar
  43. Thompson JA, Nelson RL, Vodkin LO (1998) Identification of diverse soybean germplasm using RAPD markers. Crop Sci 38:1348–1355CrossRefGoogle Scholar
  44. Tong VG, Du YC (2016) Development of In Del Markers and Fine-mapping of locule number 2.2 in TomatoGoogle Scholar
  45. Wang K, Qiu FL, Paz MAD, Zhuang JY (2014) Genetic diversity and structure of improved indica rice germplasm. Plant Genet Resour 12(2):248–254CrossRefGoogle Scholar
  46. Wang K, Qiu FL, Larazo W et al (2015) Heterotic groups of tropical indica rice germplasm. Theor Appl Genet 128:421–430CrossRefGoogle Scholar
  47. Ward Joe H (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58:236–244CrossRefGoogle Scholar
  48. Yang J, Wang Y, Shen H, Yang W (2014) In silico identification and experimentalvalidation of insertion–deletion polymorphisms in tomato genome. DNA Res 21:429–438CrossRefGoogle Scholar
  49. Yeh FC, Boyle TJB (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belgian J Bot 129:157Google Scholar
  50. Zhao LP, Zhao TM, Wang YL et al (2014). Research progress in gray leaf spot of tomato. Jiangsu J Agric Sci 1000-4440 06-1524-07Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Lan Jin
    • 1
    • 2
    • 3
  • Liping Zhao
    • 1
    • 2
  • Yinlei Wang
    • 1
    • 2
  • Rong Zhou
    • 4
  • Liuxia Song
    • 1
    • 2
  • Liping Xu
    • 5
  • Xia Cui
    • 6
  • Ren Li
    • 6
  • Wengui Yu
    • 1
    • 2
    • 3
    Email author
  • Tongmin Zhao
    • 1
    • 2
    Email author
  1. 1.Vegetable Research InstituteJiangsu Academy of Agricultural ScienceNanjingChina
  2. 2.Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu ProvinceNanjingChina
  3. 3.College of HorticultureNanjing Agricultural UniversityNanjingChina
  4. 4.Department of Food ScienceAarhus UniversityÅrslevDenmark
  5. 5.Xining Vegetable Research Institute in Qinghai ProvinceXiningChina
  6. 6.The Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina

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