, 215:157 | Cite as

High-throughput identification of SNPs reveals extensive heterosis with intra-group hybridization and genetic characteristics in a large rapeseed (Brassica napus L.) panel

  • Xiang Luo
  • Yongqiang Tan
  • Chaozhi MaEmail author
  • Jinxing Tu
  • Jinxiong Shen
  • Bin Yi
  • Tingdong Fu


Genetically diverse germplasm sets are necessary for the identification of heterotic groups in hybrid breeding programs. Assigning parental lines to identified heterotic groups may increase the efficiency of hybrid rapeseed breeding programs. In this study, the genetic diversity, population structure, relationship, and linkage disequilibrium (LD) of 995 rapeseed accessions, including improved breeding lines and parental lines of elite hybrids, were analyzed using a 60K single nucleotide polymorphism array. The whole population was divided into four subgroups according to the parameters of principal component analysis and STRUCTURE. The overall LD decay was fast, and the LD of the A genome decayed faster than that of the C genome. A core set containing 35 accessions was selected using the POWER-CORE program. The heterotic groups were first assessed based on SNPs in the enlarged core set containing core set accessions and parental lines of three elite hybrid. The parental lines were assigned to certain subpopulation (Pop2 in the enlarged core set), in which the accessions are almost the semi-winter or winter OSR lines. The results revealed that the likelihood of developing heterotic hybrids is much higher with intra-group parents. The studies about information regarding the levels of population structure of core sets combined with their ecological adaptability and genetic distance may be useful for the efficient selection of ideal parental lines during rapeseed hybrid breeding program.


Single nucleotide polymorphism Genetic characterization B. napus Heterosis Intra-group hybridization 



We thank Professor Wallace Cowling at the University of Western Australia very much for critical reading of the manuscript. This work was supported by a grant from the National Key Research and Development Program of China (Nos. 2016YFD0100803, 2016YFD0101300).

Author’s contribution

CM designed the experiments and revised the manuscript. YT collected the experimental data. XL and ZX analyzed the data. XL interpreted the results and wrote the manuscript. All authors have read, edited, and approved the current version of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary file4 (XLS 3143 kb)


  1. Barata C, Carena MJ (2006) Classification of North Dakota maize inbred lines into heterotic groups based on molecular and testcross data. Euphytica 151(3):339–349CrossRefGoogle Scholar
  2. Blair MW, Cortes AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet 126(2):535–548. CrossRefPubMedGoogle Scholar
  3. 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(19):2633–2635CrossRefGoogle Scholar
  4. Bus A, Körber N, Snowdon RJ, Stich B (2011) Patterns of molecular variation in a species-wide germplasm set of Brassica napus. Theor Appl Genet 123(8):1413–1423. CrossRefPubMedGoogle Scholar
  5. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953CrossRefGoogle Scholar
  6. Choudhury DR, Singh N, Singh AK, Kumar S, Srinivasan K, Tyagi R, Ahmad A, Singh N, Singh R (2014) Analysis of genetic diversity and population structure of rice germplasm from north-eastern region of India and development of a core germplasm set. PLOS One 9:e113094CrossRefGoogle Scholar
  7. Delourme R, Falentin C, Fomeju BF, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A (2013) High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genom 14(1):120CrossRefGoogle Scholar
  8. Donini P, Chen S, Nelson M, Ghamkhar K, Fu T, Cowling W (2007) Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia. Genome 51(1):1–10Google Scholar
  9. Ecke W, Clemens R, Honsdorf N, Becker HC (2009) Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L). Theor Appl Genet 120(5):921–931. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620CrossRefGoogle Scholar
  11. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567CrossRefGoogle Scholar
  12. Fu TD, Zhou YM (2013) Progress and future development of hybrid rapeseed in China. Eng Sci 5(11):13–18Google Scholar
  13. Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(2):211–217. CrossRefPubMedGoogle Scholar
  14. Gómez-Campo C, Prakash S (1999) Origin and domestication. In: Biology of Brassica coenospecies, pp 33–58Google Scholar
  15. Hao D, Zhang Z, Cheng Y, Chen G, Lu H, Mao Y, Shi M, Huang X, Zhou G, Xue L (2015) Identification of genetic differentiation between waxy and common maize by SNP genotyping. PLoS ONE 10(11):e0142585. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2(4):618–620CrossRefGoogle Scholar
  17. Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I (2012) Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30(8):798–802CrossRefGoogle Scholar
  18. Kim K-W, Chung H-K, Cho G-T, Ma K-H, Chandrabalan D, Gwag J-G, Kim T-S, Cho E-G, Park Y-J (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23(16):2155–2162CrossRefGoogle Scholar
  19. Lefortbuson M, Guillotlemoine B, Dattee Y (1987) Heterosis and genetic distance in rapeseed (Brassica napus L.). Use of different indicators of genetic divergence in a 7 × 7 diallel. Genome 29(3):413–418CrossRefGoogle Scholar
  20. Li F, Chen B, Xu K, Wu J, Song W, Bancroft I, Harper AL, Trick M, Liu S, Gao G, Wang N, Yan G, Qiao J, Li J, Li H, Xiao X, Zhang T, Wu X (2014) Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res 21(4):355–367. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Li F, Chen B, Xu K, Gao G, Yan G, Qiao J, Li J, Li H, Li L, Xiao X, Zhang T, Nishio T, Wu X (2015) A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). Plant Sci. CrossRefPubMedGoogle Scholar
  22. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129CrossRefGoogle Scholar
  23. Liu S, Fan C, Li J, Cai G, Yang Q, Wu J, Yi X, Zhang C, Zhou Y (2016) A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. Theor Appl Genet. CrossRefPubMedGoogle Scholar
  24. Luo X, Ma C, Yi B, Tu J, Shen J, Fu T (2016) Genetic distance revealed by genomic single nucleotide polymorphisms and their relationships with harvest index heterotic traits in rapeseed (Brassica napus L.). Euphytica 209(1):41–47. CrossRefGoogle Scholar
  25. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9(5):356–369. CrossRefPubMedGoogle Scholar
  26. Melchinger AE, Gumber RK (1998) Overview of heterosis and heterotic groups in agronomic crops. In: Concepts and breeding of heterosis in crop plants (concepts and bree), pp 29–44Google Scholar
  27. Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44(4):1236–1244CrossRefGoogle Scholar
  28. 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(8):904–909. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentralGoogle Scholar
  30. Qian W, Li Q, Noack J, Sass O, Meng J, Frauen M, Jung C (2009) Heterotic patterns in rapeseed (Brassica napus L.): II. Crosses between European winter and Chinese semi-winter lines. Plant Breed 128(5):466–470. CrossRefGoogle Scholar
  31. Reif JC, Melchinger AE, Xia XC, Warburton ML, Hoisington DA, Vasal SK, Beck D, Bohn M, Frisch M (2003) Use of SSRs for establishing heterotic groups in subtropical maize. Theor Appl Genet 107(5):947–957. CrossRefPubMedGoogle Scholar
  32. Tian HY, Channa SA, Hu SW (2015) Heterotic grouping and the heterotic pattern among Chinese rapeseed (L.) accessions. Agron J 107:1321CrossRefGoogle Scholar
  33. Tolera K, Mosisa W, Habtamu Z (2017) Combining ability and heterotic orientation of mid-altitude sub-humid tropical maize inbred lines for grain yield and related traits. Afr J Plant Sci 11(6):229–239. CrossRefGoogle Scholar
  34. Wang K, Qiu F, Larazo W, dela Paz MA, Xie F (2014) Heterotic groups of tropical indica rice germplasm. Theor Appl Genet 128(3):421–430. CrossRefPubMedGoogle Scholar
  35. Xiao Y, Cai D, Yang W, Ye W, Younas M, Wu J, Liu K (2012) Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites. Theor Appl Genet 125(3):437–447. CrossRefPubMedGoogle Scholar
  36. Xie F, He Z, Esguerra MQ, Qiu F, Ramanathan V (2013) Determination of heterotic groups for tropical Indica hybrid rice germplasm. Theor Appl Genet. CrossRefPubMedGoogle Scholar
  37. Yan J, Yang X, Shah T, Sánchez-Villeda H, Li J, Warburton M, Zhou Y, Crouch JH, Xu Y (2009) High-throughput SNP genotyping with the GoldenGate assay in maize. Mol Breed 25(3):441–451. CrossRefGoogle Scholar
  38. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17(2):155–160CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in WuhanHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  2. 2.Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouPeople’s Republic of China
  3. 3.Xiangyang Academy of Agricultural SciencesXiangyangPeople’s Republic of China

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