Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

Abstract Seed oil content (SOC) is a highly important and complex trait in oil crops. Here we report deciphering of the genetic basis of natural variation of SOC in Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) controlling SOC in eight environments, evaluated the effect of each QTL on SOC, and analyzed the selection in QTL regions during breeding. Six hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing the population transcriptomes from seeds. A gene prioritization framework, POCKET (PriOritizing the Candidate genes by incorporating information of Knowledge-based gene sets, Effects of variants, GWAS (genome-wide association studies) and TWAS (transcriptome-wide association studies), was implemented to determine the causal genes in QTL regions based on multi-omic datasets. A pair of homologous genes, BnPMT6s, in two QTLs were identified and experimentally validated to negatively regulate SOC. This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery directing oil accumulation in the seeds of B. napus and other oil crops.