title: High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea.
abstract: Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts.
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Jiangwei
authors.initials: J
authors.lastname: Qiao
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Mengxian
authors.initials: M
authors.lastname: Cai
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Guixin
authors.initials: G
authors.lastname: Yan
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Nian
authors.initials: N
authors.lastname: Wang
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Binyun
authors.initials: B
authors.lastname: Chen
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Guizhen
authors.initials: G
authors.lastname: Gao
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Xu
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wu
mesh_terms: D001937:Brassica / Q000235:genetics*; D029688:Brassica napus / Q000235:genetics*; D029741:Brassica rapa / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D006239:Haplotypes / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast
keywords: Brassica napus; cpDNA variant; genetic diversity; haplotype; maternal origin; next-genetation sequencing