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.

土壤盐分对油菜（甘蓝型油菜）的产量产生负面影响。特别是，高土壤盐分会阻碍幼苗的生长和生长。鉴定甘蓝型油菜幼苗具有高耐盐性的自然遗传变异是在盐胁迫下进行繁殖以提高生产力的有效方法。为了确定与盐胁迫的差异反应有关的遗传变异，我们评估了228个甘蓝型油菜的多样性关联。盐胁迫下四个苗期性状的登录，以建立胁迫敏感性指数（SSI）和胁迫耐受指数（STI）值，并使用201,817个高质量单核苷酸多态性（SNP）标记进行了全基因组关联研究（GWAS）。我们的GWAS鉴定了142个与所有油菜染色体上的耐盐性密切相关的重要SNP标记，C基因组中有78个SNP，A基因组中有64个SNP，我们的分析随后确定了有利的等位基因和优良品种。我们鉴定了117个与这些SNP相关的候选基因：95/117与拟南芥是直系同源的编码转录因子，水通道蛋白和结合蛋白的基因。通过定量实时PCR（qRT-PCR）验证了十个候选基因的表达水平，并且发现这些基因在盐胁迫条件下在耐盐和易盐系之间差异表达。我们的结果为通过基因组或标记辅助选择提高种子发芽和幼苗期油菜基因型的耐盐性提供了新的遗传资源和信息，并为推定基因候选物的未来功能表征提供了新的遗传资源和信息。