Developing allele specific molecular markers for the B.napus blackleg resistance (Rlm) genes
Term: 3 years, ending March 2025
Status: Ongoing
Researcher(s): Hossein Borhan and Nicholas Larkan, Agriculture and Agri-Food Canada; Andrew Sharpe, University of Saskatchewan (Global Institute for Food Security)
SaskCanola Investment: $128,450
Total Project Cost: $256,900
Funding Partners: Western Grains Research Foundation
Project Description
Our knowledge of pathogen virulence genes and plant race specific resistance (R) genes in the Leptosphaeria-Brassica pathosystem has tremendously advanced in the past two decades. Work conducted by our lab and other research groups have led to identification of 19 R genes from Brassica species and their corresponding effector ((Avirulence (Avr)) genes. There has been significant progress in cloning L. maculans Avr genes including our reports on cloning AvrLm2, AvrLm5-9 and AvrLms-Lep2. We have developed gene specific PCR-based makers for all the cloned L. maculans Avr genes. These Avr markers have been used by the private and public research labs to determine and monitor the L. maculans races in the field. Knowing the L. maculans race structure is important for the canola farmers in choosing the canola with R genes matching the most prevalent L. maculans Avr genotype/race present in their farm. R gene specific markers will complement the existing Avr genotyping tool and will enable canola growers and agronomist to choose the right R gene for their field. However, except for a few R genes (LepR3, Rlm2, Rlm4, Rlm7 and Rlm9) cloned by our lab, there is no information about the remaining blackleg R genes. We have designed gene specific markers for LepR3 and we are designing allele specific markers for Rlm4, Rlm7 and Rlm9. Developing gene-specific markers for the remaining R genes against blackleg will complement the pathogen genotyping tool, both tools are essential to apply research advancement in Leptosphaeria-Brassica pathosystem, to the field. This proposal aims to develop markers for Rlm2 and clone and develop markers for Rlm1 and Rlm11.
Purpose
The profitability of canola production has resulted in more intensive canola farming and shortened or even zero crop rotation practices. One of the consequences of intense farming is higher disease pressure due to the emergence of new pathogen races. An example of this is more incidence of blackleg, a disease for which extensive genetic resistance sources (19 R genes been identified) exist. Genetic resistance is the most cost effective, environmentally friendly and the best available solution to control blackleg and other plant diseases in the market driven modern agriculture. However, deployment of the appropriate R genes requires tools to determine the R gene profile of a canola cultivar as well as the race profile of blackleg isolates in the field. We have developed Avr gene markers for L. maculans that are being used by the industry. The gene specific markers for known blackleg R genes are equally important for efficient management of blackleg disease. The R /Avr markers will allow farmers to benefit from their past investment in blackleg research by bringing the research from the lab to the farm. Rotation of R genes (not the crop) based on a shift in the pathogen population will prevent the rapid breakdown of R genes and protect crops from disease outbreak. It is time for the farmers to have access to the most effective management tools and reap the benefit of research advancement. The Blackleg- Brassica pathosystem is unique in term of our understanding of pathogen-host virulence and resistance. Application of this knowledge to mitigate blackleg disease will provide an example for the management of other disease in canola and disease of other crops.
Goal
To sequence information of Rlm1 and Rlm11 genes and PCR-based markers for these as well as Rlm2 and have this information publicly available for use by all seed companies, public and private research labs and private diagnostic labs.
Objectives
Generating draft genome sequence of blackleg resistance B. napus introgression lines Topas-Rlm1 and Topas-Rlm11.
Annotation and cloning of blackleg resistance genes Rlm1 and Rlm11.
Generating B. napus transgenic lines and validation of Rlm1 and Rlm11 function.
Determining the allele sequence variation among resistance (R) and susceptible (S) alleles.
Identifying single nucleotide polymorphism (SNP) and developing Kompetitive Allele Specific PCR (KASP) markers.
Validation of KASP markers on B. napus differential lines.