Open AccessHigh‐throughput multiplex cp DNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus , Brassica rapa and Brassica oleracea
Author(s) -
Qiao Jiangwei,
Cai Mengxian,
Yan Guixin,
Wang Nian,
Li Feng,
Chen Binyun,
Gao Guizhen,
Xu Kun,
Li Jun,
Wu Xiaoming
Publication year - 2016
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12395
Subject(s) - brassica rapa , biology , chloroplast dna , brassica oleracea , genetics , genetic diversity , ploidy , haplotype , genome , population , botany , gene , allele , demography , sociology
Summary 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 (cp DNA ) 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 cp DNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cp DNA of the current global B. napus population comprises more than 400 variants ( SNP s and short InDels) and maintains one predominant haplotype (Bncp1). Whole‐genome resequencing of the cp DNA 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 cp DNA diversity than B. rapa ; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cp DNA haplotype, in contrast to its wild C‐genome relatives. This finding suggests that the cp DNA of the three Brassica species is well differentiated. The predominant B. napus cp DNA haplotype may have originated from uninvestigated relatives or from interactions between cp DNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cp DNA would provide fundamental data for research on cp DNA and chloroplasts.