Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches

Abstract

Single nucleotide polymorphisms (SNPs) have rapidly become the molecular marker of choice in plant and animal association mapping (AM) studies. In this work, a genome-wide association study (GWAS) and candidate quantitative trait loci (cQTL) approaches were used to identify SNP markers associated with seed quality traits, in a Brassica napus L. association panel composed of 89 adapted winter oilseed rape accessions. Six seed quality traits (oil and protein content, linolenic acid, total glucosinolates, hemicellulose and cellulose content) were evaluated in two different locations for two seasons. For GWAS, 4025 SNP markers evenly distributed along the B. napus genome were genotyped using a 6K Illumina array platform. For cQTL, 100 SNP markers previously discovered in genomic regions underlying seed quality QTL were genotyped using a competitive allele-specific PCR (KASPar). Analysis of the population structure revealed the presence of two weakly differentiated subpopulations (F ST = 0.037), with 82 % of the pairwise kinship comparisons ranging from 0 to 0.1. The GWAS approach resulted in the identification of 17 and 5 significant associations for seed glucosinolate content and seed hemicellulose content, respectively. The cQTL approach identified 4 significant associations for seed glucosinolate content and 6 significant associations for seed hemicellulose content. The associated SNPs were consistently identified across environments and were mapped to previously reported QTL. These results illustrate the suitability of AM to identify SNP markers associated with seed quality traits in B. napus.

Seed Quality Traits Can Be Predicted with High Accuracy in Brassica napus Using Genomic Data

“…The major QTL located on C03 and explaining 16.44% of the phenotypic variance for oil content was identified in both of TN DH population and KN DH population [74]. The QTL with large genetic effects for total seed glucosinolates located in A08, C01 and C03, were also identified previously in this and other mapping populations [9, 19, 75]. These QTLs are interesting targets for marker-assisted selection, which can be applied in rapeseed breeding in combination with the enrichment of target alleles for F 2 populations prior to producing DH populations.…”

Genome‐wide association study for frost tolerance in rapeseed/canola (Brassica napus) under simulating freezing conditions

“…There is no clear consensus on the number of genotypes to be used for GWAS. However, GWAS studies have been conducted in B. napus using 49 genetically diverse winter‐type germplasm for seed phenolic compounds (Rezaeizad et al, ), 89 winter‐type accessions were used for six seed quality traits (Gajardo et al, ), 139 spring‐, semi‐winter‐ and winter‐type germplasm were used for blackleg disease (Rahman et al, ), 143 spring‐, semi‐winter‐ and winter‐type accessions were used for branch angle (Liu et al, ), 172 B. napus germplasm was used for seed oil content (Zou et al, ), 248 winter‐type germplasm was used for seed germination and early vigour (Hatzig et al, ), 405 accessions of winter oilseed, winter fodder, swede, semi‐winter, spring, spring fodder and vegetable types were used for agronomic and seed quality traits (Körber et al, ), and 540 accessions of winter, semi‐winter, spring and vegetable types were used for fatty acid profiles (Qu et al, ).…”

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

“…The incorporation of both K and PK matrices into a MLM has been successfully used in other species that exhibited significant population structure and relatedness (Gajardo et al, 2015;Zhou et al, 2016). Furthermore, the K model computational time is faster, and no additional steps like identifying population structure and PCs in the germplasm are required (Pasam et al, 2012).…”