Rapeseed contains glucosinolates, a toxic group of sulfur-containing glucosides, which play critical roles in defense against herbivores and microbes. However, the presence of glucosinolates in rapeseed reduces the value of the meal as feed for livestock. We performed association mapping of seed glucosinolate (GS) content using the 60K Brassica Infinium single nucleotide polymorphism (SNP) array in 520 oilseed rape accessions. A total of 11 peak SNPs significantly associated with GS content were detected in growing seasons of 2013 and 2014 and were located on B. napus chromosomes A08, A09, C03, and C09, respectively. Two associated regions of GS content covered by these markers were further verified, and three B. napus homologous genes involved in the biosynthesis and accumulation of GS were identified. These genes were multigene family members and were distributed on different chromosomes. Moreover, two genes (BnGRT2 and BnMYB28) associated with GS content were validated by the qRT-PCR analysis of their expression profiles. The further identification and functionalization of these genes will provide useful insight into the mechanism underlying GS biosynthesis and allocation in B. napus, and the associated SNPs markers could be helpful for molecular maker-assisted breeding for low seed GS in B. napus.

Candidate genes associated with lignin and lodging traits were identified by combining phenotypic, genotypic, and gene expression data in B. napus. Brassica napus is one of the world's most important oilseed crops, but its yield can be dramatically reduced by lodging, bending, and falling of its vertical stems. Lignin has been shown to contribute to stem mechanical strength. In this study, we found that the syringyl/guaiacyl (S/G) monolignol ratio exhibits a significant negative correlation with disease and lodging resistance. A total of 92 and 50 SNP and SSR loci, respectively, were found to be significantly associated with five traits, breaking force, breaking strength, lodging coefficient, acid detergent lignin content, and the S/G monolignol ratio using GWAS. To identify novel genes involved in lignin biosynthesis, transcriptome sequencing of high- (H) and low (L)-ADL content accessions was performed. The up-regulated genes were mainly involved in glycoside catabolic processes (especially glucosinolate catabolism) and cell wall biogenesis, while down-regulated genes were involved in glucosinolate biosynthesis, indicating that crosstalk exists between glucosinolate metabolic processes and lignin biosynthesis. Integrating this differential expression with the GWAS analysis, we identified four candidate genes regulating lignin, including glycosyl hydrolase (BnaA01g00480D), CYT1 (BnaA04g22820D), and two encoding transcription factors, SHINE1 (ERF family) and DAR6 (LIM family). This study provides insight into the genetic control of lodging and lignin in B. napus.