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 3.6–12.1%. 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 0.43–0.63 prediction accuracy. However, the prediction efficiency was further improved 0.55–0.88 when we integrated the GWAS information in the GP model. 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.

Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Brassica napus L.)

“…These kinds of variations in population for intricate root behavior may be critical for the genetic dissection of valuable loci (Danakumara et al, 2021;Sandhu et al, 2021). Significant genetic variation among genotypes allowed researchers to investigate genetic loci linked with the observed traits (Kang et al, 2021;Roy et al, 2021). In the current study, the RIL population was phenotyped, QTL analysis was performed under LN/LP/LK treatments, and 57, 27, and 36 loci under LN, LP, and LK, respectively, that controlled nutrient deficiency were identified (Supplementary Tables 3-5).…”

A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

“…For biotrophic pathogens, wherein the resistance is mostly governed by NLR genes, selective introgressions of NLR clusters of the BcaB genome in the BjuB background can be identified and the progenies tested for resistance. For necrotrophic pathogens like S. sclerotiorum and A. brassicae , the resistance is usually quantitative, wherein multiple genes contribute to resistance (Rajarammohan et al ., 2018; Roy et al ., 2021; Wu et al ., 2013; Wu et al ., 2019). In this scenario, the near-complete replacement of BjuB with BcaB could be achieved by intercrossing BC 1 F 1 plants with different BcaB introgressions to create new genetic diversity in the B. juncea gene pool that may confer resistance to the necrotrophic pathogens.…”