Genome-wide mapping and genomic prediction conditioning sclerotinia stem rot resistance in different ecotypes of Brassica napus (L.) germplasm collections

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is a destructive disease in canola that significantly reduces seed yield and oil quality. This research aimed to identify the genomic regions and evaluate the potential of genomic prediction for S. sclerotiorum resistance by screening a diverse panel of 143 spring (SP), and 152 semiwinter and winter (SwW) populations through two rounds of plant inoculation during the full flowering stage. A comprehensive phenotypic evaluation involving four distinct traits identified several lines as potential sources of resistance, which showed superior resistance compared to known resistant check cultivars. A Genome-wide association (GWA) study using two different algorithms identified 29 and 19 SNPs in the SP and SwW populations, respectively, with two or more traits were regarded as significant. Ten and seven significant SNPs from SP and SwW populations, respectively, were co -localized with the previously reported SNPs/QTLs by linkage/ GWA mapping studies. Within the regions flanking the significant SNPs, we identified a total of 33 and 22 putative candidate genes related to plant defense responses in the SP and SwW populations, respectively. The genomic prediction (GP) revealed higher predictive ability for the SP population (0.46-0.57) over the SwW population (0.10-0.19), depending on trait specifications. In summary, our study revealed that favorable alleles from significant SNPs from GWA mapping could be utilized as valuable resources for introducing and pyramiding resistance alleles to enhance SSR resistance in canola. Genomic selection could also be used as a potential genomics-assisted approach to improve SSR resistance in canola.