SNP and Haplotype Variability in the <i>BnP5CR2</i> Gene and Association with Resistance and Susceptible Cultivars for <i>Sclerotinia sclerotiorum</i> in <i>Brassica napus</i>

Sclerotinia sclerotiorum is a serious disease of oil crop. The P5CR gene is the first gene reported to be associated with resistance to Sclerotinia infection in soybeans, and its closest homologs are located on chromosomes A10 and C09 of Brassica napus. We named these BnP5CR1 and BnP5CR2, respectively. The purpose of this study was to examine the single-nucleotide polymorphism (SNP) and haplotype diversity (Hd) of BnP5CR2 among canola cultivars with different levels of resistance to S. sclerotiorum as well as the expression patterns of BnP5CR2 via an association analysis using resistant and susceptible cultivars of B. napus. The results can thus provide information for future research on the mechanisms of disease resistance to S. sclerotiorum and the breeding of resistant canola cultivars. A total of 95 and 12 polymorphic sites were detected in 1870 and 678 SNP sites in 16 BnP5CR2 and their coding DNA sequence (CDS) population, respectively. A total of six different haplotypes (H1–H6) were inferred from the 16 BnP5CR2 gene-CDS that contributed to the high level of polymorphism. Hd was equal to 0.617, and H1 shared by 10 cultivars was the dominant haplotype, suggesting that H1 is an ancient haplotype among the BnP5CR2 genes. H6 and H5 haplotpypes were present in Nan12R and ZhongYou821, respectively. The expression level in vitro of the BnP5CR2 between Nan12R and ZhongYou821 was significantly different. The upregulated expression of BnP5CR2 in resistant cultivars was higher than that of susceptible cultivars under 6 h, 12 h, 24 h, and 36 h treatments of pathogen stress, among which the expression level was significantly increased at 6 h, 12 h and 36 h in resistant cultivars, and the difference reached a highly significant level at 6 h (p BnP5CR2 gene-CDS-haplotypes, indicating that gene-CDS-haplotype diversity may have greater power than SNPs for the detection of causal genes for quantitative traits