Open AccessDissection of the genetic architecture of three seed‐quality traits and consequences for breeding in Brassica napus
Author(s) -
Wang Bo,
Wu Zhikun,
Li Zhaohong,
Zhang Qinghua,
Hu Jianlin,
Xiao Yingjie,
Cai Dongfang,
Wu Jiangsheng,
King Graham J.,
Li Haitao,
Liu Kede
Publication year - 2018
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.12873
Subject(s) - biology , genetic architecture , genetics , genome wide association study , indel , candidate gene , genetic variation , gene , genetic association , quantitative trait locus , allele , single nucleotide polymorphism , genotype
Summary Genome‐wide association studies ( GWAS s) combining high‐throughput genome resequencing and phenotyping can accelerate the dissection of genetic architecture and identification of genes for plant complex traits. In this study, we developed a rapeseed genomic variation map consisting of 4 542 011 SNP s and 628 666 INDEL s. GWAS was performed for three seed‐quality traits, including erucic acid content ( EAC ), glucosinolate content ( GSC ) and seed oil content ( SOC ) using 3.82 million polymorphisms in an association panel. Six, 49 and 17 loci were detected to be associated with EAC , GSC and SOC in multiple environments, respectively. The mean total contribution of these loci in each environment was 94.1% for EAC and 87.9% for GSC , notably higher than that for SOC (40.1%). A high correlation was observed between phenotypic variance and number of favourable alleles for associated loci, which will contribute to breeding improvement by pyramiding these loci. Furthermore, candidate genes were detected underlying associated loci, based on functional polymorphisms in gene regions where sequence variation was found to correlate with phenotypic variation. Our approach was validated by detection of well‐characterized FAE 1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB 28 genes at each of three major loci for GSC on chromosomes A9, C2 and C9. Four novel candidate genes were detected by correlation between GSC and SOC and observed sequence variation, respectively. This study provides insights into the genetic architecture of three seed‐quality traits, which would be useful for genetic improvement of B. napus .