From field to the genome. Application of third generation sequencing to direct genotyping of canola pathogens
Term: 3 years, beginning in 2019
Status: Ongoing
Researcher(s): Hossein Borhan, Agriculture and Agri-Food Canada
SaskCanola Investment: $155,250
Total Project Cost: $310,500
Funding Partners: Alberta Canola Producers Commission
Project Description
Control of clubroot disease, which is best achieved by the use of resistant canola cultivars and crop rotation, requires continuous monitoring of pathogen presence and pathogen load. In addition, not all P. brassicae pathotypes (isolates) are the same in terms of their virulence. Therefore, it is important to know what are the most prevalent clubroot pathotypes in a canola field. To help canola growers with management of clubroot disease, here we propose to develop a sensitive and rapid diagnostic tool that not only could detect the presence of pathogen but it will also determine the clubroot pathotypes that make up the clubroot population in a field, as well as the relative abundance/pathogen load. Plant pathogens contain effector (virulence) genes that are highly variable and function in overcoming plant defense, and are hence named virulence genes. Sequence variation of P. brassicae effector genes could be used as molecular markers to distinguish various pathotypes.
Objectives
To expend the existing genome sequence database of P. brassicae by sequencing recently discovered Canadian clubroot pathotypes.
To apply and compare direct sequencing and targeted sequencing as diagnostic and genotyping methods.
To compare laboratory detection methods with direct in-field detection methods.