Dissection of the genetic architecture of three seed‐quality traits and consequences for breeding in Brassica napus

Abstract

SummaryGenome‐wide association studies (GWASs) 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 SNPs and 628 666 INDELs. 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 FAE1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB28 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.

An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed

“…Another hybrid was obtained from the cross between ZS11 and ZS11( sca ). All rapeseed cultivars or inbred lines were from a collection published previously (Wang et al ., 2018b). Field experiment and trait measurement, auxin treatment of seedling, measurement of hypocotyl and root elongation and gravitropism analysis of hypocotyl and inflorescence stem were described in Supporting Information Methods S1.…”

“…Genetic distance was expressed in cM using the Kosambi mapping function. Additional SSR markers were developed from B. rapa A3 chromosome sequences (http://brassicadb.org/brad/) and the Insertion/Deletion (INDEL) markers were developed from resequencing data of 018A and HS5 (Wang et al ., 2018b). All molecular markers used in SCA mapping are listed in Table S1.…”

Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

“…Highly divergent genomic selection signatures were also detected between the Asian double‐low and double‐high rapeseeds, covering 30.2 Mb genomic regions (A subgenome: 8.0 Mb; C subgenome: 22.2 Mb). Five Mb‐scale peaks found in chromosomes A08, A09, C02, C03 and C09 perfectly matched results from a previous GWAS (Wang et al ., ). These regions contain genes associated with seed‐quality traits, including erucic acid content (EAC), glucosinolate content (GSC) and seed oil content (SOC).…”

“…To analyse the genetic differentiation of Asian B. napus cultivars from European cultivars, in addition to the genomic data generated in this study, we collected publicly available genomic data of 68 Asian (30 double-low and 38 double-high) ( (Chalhoub et al, 2014;Schmutzer et al, 2015;Wang et al, 2018) (Table S6). We calculated whole-genome genetic diversity (p) for each of the three groups, that is European (EU; including both double-low and double-high accessions), Asian double-low (AS_DL) and Asian double-high (AS_DH).…”

“…Dissecting the genome of NY7 provides the opportunity to understand the evolutionary footprints associated with local adaptation and early artificial selection of Asian rapeseed. Furthermore, the genomes of the parental lines of NY7 were also de novo assembled, and a comprehensive genomic comparison was undertaken among NY7 and its parental lines as well as other publicly available genome sequences of a diverse group of European and Asian rapeseed cultivars (Huang et al, 2013;Schmutzer et al, 2015;Shen et al, 2017;Wang et al, 2018). The comparison of B. napus genomes helped us trace the origins of valuable adaptive alleles, genomic structural variations and deleterious variations during the recent breeding history of Asian rapeseed and provided novel insights into the significant impacts of interand intraspecific introgressions arising from local selective breeding on a young allopolyploid species.…”