title: Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.
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.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China. lb_bobo@yahoo.cn
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Wen
authors.initials: W
authors.lastname: Zhai
authors.forename: Jie
authors.initials: J
authors.lastname: Deng
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Yang
authors.initials: Y
authors.lastname: Cui
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
mesh_terms: D000483:Alleles; D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D054643:INDEL Mutation; D008957:Models, Genetic; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005819:Genetic Markers