Abstract
BackgroundIncreasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions.ResultsHigh-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions.ConclusionsThe combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus.
Highlights
Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding
Previous studies have identified many Single nucleotide polymorphism (SNP) that were significantly associated with seed oil content (SOC) in Brassica napus, none of them have combined the analysis with transcriptome sequencing to obtain candidate genes contributing to SOC
We obtained 17 SNPs that were significantly associated with seed oil content (SOC) in Brassica napus, 12 of which were overlapped with previous studies (Table 2), supporting the high reliability of loci detected in current study
Summary
Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. Genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions. Quantitative trait locus (QTL) mapping and genomewide association study (GWAS) have been widely used to dissect the regulatory loci and genetic architecture of complex agronomical quantitative traits at the whole genome level. GWAS has recently been widely used in the study of important complex traits in B. napus, such as seed germination and vigor [16], plant height and primary branch [32, 52], harvest index [38, 42], yield traits [39, 57]. GWAS has been reported in various plants, such as Arabidopsis [1], rice [21, 22, 65], soybean [23] and maize [28, 50] and so on
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