Identification of genetic variation for salt tolerance in Brassica napus using genome-wide association mapping

Soil salinity negatively impacts rapeseed (Brassica napus) crop production. In particular, high soil salinity is known to hinder seedling growth and establishment. Identifying natural genetic variation for high salt tolerance in Brassica napus seedlings is an effective way to breed for improved productivity under salt stress. To identify genetic variants involved in differential response to salt stress, we evaluated a diverse association panel of 228 Brasica napus accessions for four seedling traits under salt stress to establish stress susceptibility index (SSI) and stress tolerance index (STI) values, and performed genome-wide association studies (GWAS) using 201,817 high-quality single nucleotide polymorphic (SNP) markers. Our GWAS identified 142 significant SNP markers strongly associated with salt tolerance distributed across all rapeseed chromosomes, with 78 SNPs in the C genome and 64 SNPs in the A genome, and our analyses subsequently pinpointed both favorable alleles and elite cultivars. We identified 117 possible candidate genes associated with these SNPs: 95/117 were orthologous with Arabidopsis thaliana genes encoding transcription factors, aquaporins, and binding proteins. The expression level of ten candidate genes was validated by quantitative real-time PCR (qRT-PCR), and these genes were found to be differentially expressed between salt-tolerant and salt-susceptible lines under salt stress conditions. Our results provide new genetic resources and information for improving salt tolerance in rapeseed genotypes at the seed germination and seedling stages via genomic or marker-assisted selection, and for future functional characterization of putative gene candidates.