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

Theor Appl Genet. 2013 Jan;126(1):231-9. doi: 10.1007/s00122-012-1976-6. Epub 2012 Sep 13.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Base Sequence
  • Brassica / genetics*
  • Chromosome Mapping
  • Genetic Markers*
  • Genome, Plant*
  • Genotype
  • INDEL Mutation
  • Models, Genetic
  • Polymerase Chain Reaction / methods
  • Polymorphism, Genetic
  • Sequence Analysis, DNA
  • Software


  • Genetic Markers