Development and validation of three KASP markers for highly virulent pathotypes of Plasmodiophora brassicae.
McDonald, M.R., Sedaghatkish, A., and Gossen, B.D. 2023. Development and validation of three KASP markers for highly virulent pathotypes of Plasmodiophora brassicae. Poster 307, 16th Intern Rapeseed Congress, September 24-27, 2023. Sydney, Australia.
Résumé en langage clair
Clubroot, caused by the obligate Chromist Plasmodiophora brassicae (Wor.), is an important disease of brassica crops worldwide. Clubroot management in canola (Brassica napus L.) in Canada is almost entirely based on single resistance genes. The single-gene resistance initially deployed in canola in Canada was not durable and a new cohort of highly-virulent pathotypes emerged quickly.
The reaction of differential lines has been used to identify pathotypes, but this approach is slow, resource-intensive and often variable. Only a few molecular markers have been developed for identification of a few specific pathotypes world-wide.
To compare the genome of the new cohort of highly virulent pathotypes with the initial cohort of pathotypes present in Canada and identify virulence factors that can be used for pathogen identification.
Whole-genome sequences of 43 collections of P. brassicae from locations around the world were assessed for the presence of the target DNA sequences of existing molecular markers. These sequences were developed in an earlier study and uploaded to GenBank. The pathotype of each sequence was known, and several sequences represented the new cohort of highly virulent pathotypes from Canada that were able to overcome single-gene resistance in canola. Also, virulence-specific single nucleotide polymorphisms associated with these highly virulent pathotypes were searched for in these collections. Three KASP markers were designed to detect the new, highly virulent pathotypes and these markers assessed by two research teams. The putative structure, domains, and gene ontogeny of the protein product of the gene associated with this virulence factor were predicted using NovaFold AI and I-TASSER software.
The few molecular markers currently in the literature could not be used to separate the initial cohort of pathotypes in Canada from the cohort of highly virulent pathotypes. However, a gene that contains around 20 single nucleotide polymorphisms was present in the highly virulent pathotypes, and was not present in the initial cohort of pathotypes present in Canada. The three KASP markers detected the virulent pathotypes and the results were consistent between the two labs. The prediction models could not identify the gene or product but suggested that the protein product of the gene was likely localized intracellularly, with involvement in cellular processes and catalytic activity.
The KASP markers can be used for the rapid detection of highly virulent pathotypes of P. brassicae in Canada, and potentially around the world. This represents a step toward the molecular identification of pathotypes in P. brassicae. Molecular markers for pathotype identification are urgently needed to ensure that cultivars carrying specific resistance genes are only deployed where they will be effective.