Associative Transcriptomics Study Dissects the Genetic Architecture of Seed Glucosinolate Content in Brassica napus

Abstract

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed ‘associative transcriptomics’ (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction–based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.

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

“…For instance, the major QTL located in A08 and C03 (Table 2) totally explained 76.66% of the phenotypic variance for erucic acid, which has been widely identified previously in TN DH population and other mapping populations of B . napus [21, 22, 24, 73]. 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].…”

A genome-wide association study of plant height and primary branch number in rapeseed ( Brassica napus )

“…To test whether this method was effective, we compared the physical positions of the GWAS peaks for erucic acid content and glucosinolate content with those of their strong candidate genes, i.e., BnaA.fae1 and BnaC.fae1 [35,48] and orthologs of A. thaliana HAG1 [35,36,49] in the B. napus draft genome sequences [37]. The GWAS peaks for erucic acid content on A08 and C03 were 326 and 135 kb away from BnaA.fae1 and BnaC.fae1, respectively (Table S3).…”

Genome‐wide identification of loci affecting seed glucosinolate contents in Brassica napus L.

“…Previous studies have shown that the major genetic loci that affect SGC are located on chromosomes A09, C02, C07 and C09 of B. napus (Howell et al ; Zhao and Meng ; Harper et al ; Li et al ; Lu et al ; Qu et al ); however, ecotype‐specific loci that affect SGC have not been reported. With the rapid development and decreasing cost of next‐generation sequencing, genome‐wide association studies (GWAS) have become a promising approach for the genetic dissection of complex traits.…”