Application of genomics and transcriptomics to accelerate development of clubroot resistant canola

Abstract

Clubroot, a soil-borne disease caused by the obligate parasite Plasmodiophora brassicae Woronin, is a threat to canola (Brassica napus L.) production in western Canada. Genetic resistance represents the most effective tool to manage this disease. However, given the rapid spread of clubroot and the emergence of new virulent pathotypes of P. brassicae, it is important to accelerate the resistance breeding effort. The advent of genome-sequencing technologies has created a new toolbox that can aid in breeding strategies. Many genomic approaches, such as genotyping-by-sequencing, high-density single nucleotide polymorphism (SNP) arrays, genome-wide association studies, and transcriptomic approaches such as bulked segregant RNA-seq analysis and microarray/RNA-seq differential expression analysis have been applied to studies of clubroot resistance or susceptibility. Here, we review the impact of traditional marker-assisted selection-based breeding for clubroot resistance, and then discuss how omics approaches have contributed to the (1) detection and genotyping of genome-wide SNP markers linked with clubroot resistance genes or quantitative trait loci, (2) understanding of host resistance mechanisms upon P. brassicae infection, and (3) acceleration of resistance breeding by identifying and characterizing candidate genes, especially those with differential efficacy against new pathotypes of P. brassicae. We suggest that the use of different omics approaches together could improve the efficiency of clubroot-resistance breeding. Finally, we propose that the CRISPR/Cas9 system for genome editing is a promising tool to facilitate the validation and use of candidate genes for clubroot-resistance breeding.