Theoretical and Applied Genetics

, Volume 126, Issue 1, pp 231–239 | Cite as

Development of InDel markers for Brassica rapa based on whole-genome re-sequencing

  • Bo Liu
  • Yan Wang
  • Wen Zhai
  • Jie Deng
  • Hui Wang
  • Yang Cui
  • Feng Cheng
  • Xiaowu Wang
  • Jian Wu
Original Paper

Abstract

Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3–5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77 %) yielded single PCR fragments and showed polymorphisms, 7 (1 %) did not amplify a product, and 141 (22 %) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77 %) were polymorphic, 111 (22 %) were not polymorphic and 5 (1 %) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90 % amplified a PCR product; 132 (25 %) showed polymorphism between the two B. napus accessions and 41 (8 %) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa.

Supplementary material

122_2012_1976_MOESM1_ESM.xlsx (83 kb)
Supplementary Document (XLSX 83 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Bo Liu
    • 1
  • Yan Wang
    • 1
  • Wen Zhai
    • 1
  • Jie Deng
    • 1
  • Hui Wang
    • 1
  • Yang Cui
    • 1
  • Feng Cheng
    • 1
  • Xiaowu Wang
    • 1
  • Jian Wu
    • 1
  1. 1.Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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