Genome-wide association study (GWAS) combined with transcriptome analysis reveals the key genes underlying the production of seed oil, mono and poly-unsaturated fatty acids in Brassica napus

Understanding the genetic factors that affect oil biosynthesis and fatty acid composition (FAC) helps improve the quality of oil in Brassica napus. Here, we aimed to identify causal genes controlling seed oil content (SOC) and FAC by utilizing 52,157 single nucleotide polymorphisms (SNPs) genotyped in 119 varieties combined with weighted gene co-expression network analysis (WGCNA) of the canola transcriptome. A field experiment was conducted over two years and gas chromatography-mass spectrometry (GC–MS) was used to analyze FAC. The predominant fatty acid (FA) in the oil samples was oleic acid. In total, 782 SNPs were found to be associated with SOC and FAC, with 42 showing pleiotropic effects on grain yield and oil traits. Of the haplotypes identified, the alleles AACGAAA and AAAAGGA located between 11,286,344 – 11,473,154 bp position on chromosome C04 were associated with higher SOC. A major hotspot located in the 18,170–18,935 Kbps region on chromosome A08 contained the BnaA08g11130D and BnaA08g11440D genes contributed to oil accumulation pathways. Additionally, a total of 44,973,333 and 44,863,333 reads for low and high SOC varieties were used to identify 33 candidate genes, including acetyl-coenzyme A carboxylase, stearoyl-ACP 9-desaturase, long-chain acyl-CoA synthetase 6, 3-oxoacyl-ACP synthase II, and 3-hydroxyacyl ACP dehydratase, which were associated with higher SOC and valuable FAs. The WGCNA revealed six gene networks that regulate SOC and provided insights into the genetic factors that influence canola oil production.