Genome-wide association mapping and genomic prediction for adult stage sclerotinia stem rot resistance in Brassica napus (L) under field environments

Abstract

Sclerotinia stem rot (SSR) is a fungal disease of rapeseed/canola that causes significant seed yield losses and reduces its oil content and quality. In the present study, the reaction of 187 diverse canola genotypes to SSR was characterized at full flowering stage using the agar plug to stem inoculation method in four environments. Genome-wide association study (GWAS) using three different algorithms identified 133 significant SNPs corresponding with 123 loci for disease traits like stem lesion length (LL), lesion width (LW), and plant mortality at 14 (PM_14D) and 21 (PM_21D) days. The explained phenotypic variation of these SNPs ranged from 3.6 to 12.1%. Nineteen significant SNPs were detected in two or more environments, disease traits with at least two GWAS algorithms. The strong correlations observed between LL and other three disease traits evaluated, suggest they could be used as proxies for SSR resistance phenotyping. Sixty-nine candidate genes associated with disease resistance mechanisms were identified. Genomic prediction (GP) analysis with all the four traits employing genome-wide markers resulted in 0.41–0.64 predictive ability depending on the model specifications. The highest predictive ability for PM_21D with three models was about 0.64. From our study, the identified resistant genotypes and stable significant SNP markers will serve as a valuable resource for future SSR resistance breeding. Our study also suggests that genomic selection holds promise for accelerating canola breeding progress by enabling breeders to select SSR resistance genotypes at the early stage by reducing the need to phenotype large numbers of genotypes.

Host Induced Gene Silencing of theSclerotinia sclerotiorum ABHYDROLASE-3gene reduces disease severity inBrassica napus

“…Next, we challenged BN1703 lines with S. sclerotiorum using a petal inoculation method on leaf tissues [11] and the mycelial plug method on stems [45] (Fig. 2a).…”

Genetic Mapping and Genomic Prediction of Sclerotinia Stem Rot Resistance to Rapeseed/Canola (Brassica Napus L.) at Seedling Stage

“…Throughout the study, a highly virulent single isolate WM031 of S. sclerotiorum was used for all inoculations to germplasm accessions (Roy et al 2021;Shahoveisi et al 2021). The inoculum was prepared by culturing the surface sterilized sclerotia of the isolate on autoclaved potato dextrose agar (PDA) medium (24 gL-1 potato dextrose broth and 15 gL-1 agar) at 22-24℃.…”

“…Each member of the diversity panel was genotyped as described by Roy et al (2021) and Rahman et al (2021). In brief, total genomic DNA was extracted from fresh young and lyophilized leaf tissues using Qiagen DNeasy kit (Qiagen, CA, USA).…”

“…To manage the associated risk of SSR disease, growers primarily depend on the use of conventional rotation with non-host crop species and chemical controls which are neither completely effective nor economically and environmentally feasible (Derbyshire and Denton-Giles 2016; Roy et al 2021). Therefore, breeding for durable SSR resistant varieties would be a more economically feasible, environment-friendly, and sustainable strategy to manage this disease.…”

“…The screening procedure used in these studies were based on direct inoculation of mycelium to the main intact stem of the growing plant and/or to its detached stem during the owering stage. Several investigations on SSR resistance reported a signi cant interaction and negative correlation between owering time and stem resistance (Wu et al 2019;Zhang et al 2019;Roy et al 2021). Therefore, we screened our association panel using a PIT method to evaluate the performance of the germplasm collections at the seedling stage to eliminate the con icts between early maturation and SSR resistance in rapeseed/canola breeding.…”