Dissecting the genetic mechanisms of waterlogging tolerance in Brassica napus through linkage mapping and a genome-wide association study

Brassica napus provides not only edible vegetable oil for human consumption, but also triglyceride source for biofuel and lubricant production. Waterlogging is a major abiotic stress that significantly reduces seed yields of B. napus. However, the genetic architecture underlying waterlogging tolerance is still not clear. In the present study, waterlogging tolerance was investigated using seedling death rate (SDR) as the index after complete plant submergence. A recombinant inbred line (RIL) population containing 189 lines and a germplasm set comprising 520 accessions were performed using linkage mapping and a genome-wide association study (GWAS) associated with SDR. Both the populations were genotyped using the Brassica 60 K SNP BeadChip. Quantitative trait locus (QTL) mapping revealed 17 consensus QTLs for SDR in RIL population in five experiments. Among them, three QTLs cqSDR.C3-2, cqSDRC8-1 and cqSDRC8-2 were stably expressed in two experiments, and the major QTL cqSDR.C3-2 accounted for 10.30 % and 23.32 % of the phenotypic variance. In addition, 26 significant associations for SDR were identified by GWAS in one experiment, including 13 single nucleotide polymorphisms were repeatedly detected using general and the mixed linear models. Interestingly, no locus was simultaneously identified by QTL mapping and GWAS. These results provide valuable information for better understanding the genetic control of waterlogging tolerance, and the stable QTLs and waterlogging-tolerant lines in RIL population can be used as elite genetic resources in B. napus breeding.