Canadian Canola Clubroot Cluster Pillar 2: Developing novel resistance resources and strategies to address the new threat of clubroot canola production on the Prairies

Project Summary

Background

Variety resistance is a key part of clubroot management in canola, but the rapidly changing pathogen population observed in Alberta presents a big challenge to effective use of the strategy because the single-gene resistance can quickly be overcome. Current canola cultivars likely have a low diversity in clubroot resistance (CR), and many of the newly-identified pathotypes/variants cause severe infection on these resistant cultivars. New CR genes, especially those with broad-based resistance (since it’s unlikely that a single CR gene can resist all pathotypes), may help enhance the efficacy and durability of resistance. Therefore it is important to look at strategies when CR gene are being deployed.

This study focusses on identifying novel CR genes from existing CR germplasm pools, as well as tapping into new brassica sources for resistance against ‘new’ pathotypes/variants (identified recently in Alberta), and on developing unique CR canola germplasm and SNP markers to broaden the CR arsenal. Next-generation sequencing will be used to conduct mapping by sequencing analysis to locate CR genes and develop SNP markers tightly linked to these CR genes efficiently. Multi-gene strategies will be explored to increase the resistance spectrum and durability.

This study complements the efforts of identifying quantitative resistance in Canadian Canola Clubroot Cluster Pillar 3 and Canadian Canola Clubroot Cluster Pillar 1: Integrated disease management.

Objectives

The proposed study builds on recent identification and development of CR genes against common pathotypes of P. brassicae found previously in Canada, including pathotypes 2, 3, 5, 6, 8 and several populations of 5x. These CR genes will be assessed further, singly and in combinations, against the new pathotypes identified recently in Alberta (Strelkov et al. 2018). The deployment of these CR genes in canola germplasm will be guided by their modes of action against different pathotypes for maximum efficacy and durability.

The specific objectives include:

1. Characterize CR genes in the donor lines of Rcr3, Rcr4, Rcr5, Rcr7, Rcr8, and a rutabaga CR line (A8) for resistance against new pathotypes found recently in Alberta (Strelkov et al. 2018).
2. Identify QTL with both major and minor effects on clubroot resistance to new pathotypes in several Canadian Clubroot Differential (CCD) lines (Strelkov et al. 2018) with broad and unique  CR functions.
3. Develop SNP markers tightly linked to each of the QTLs for marker assisted selection and transfer QTL into spring-type canola.
4. Screen up to 1500 B. napus (AC genome), B. oleracea (C genome) and B. rapa (A genome) accessions for novel CR genes against the newly evolved pathotypes,  map genomic regions contributing to the resistance, identify molecular markers associated with these CR genes for use in marker-assisted breeding, and incorporated selected new CR genes into canola.
5. Assess and identify unique and broad-spectrum resistance during screening and based on multiple CR gene interactions.
6. Understand the resistance spectrum of CR-gene combinations  to guide the deployment of novel CR genes in a multiple-gene strategy for durable resistance
7. Conduct ‘tub testing’ of selected B. napus lines with multiple CR genes (singly or stacked) to determine the durability of resistance against single and mixed pathotype populations.

The longer-term objective of study is to increase the diversity of CR genes in canola cultivars and the durability of cultivar resistance by judicious deployment of multiple CR genes. This strategy will address the threat from not only the current predominant pathotypes/variants, but also new pathotypes that emerge in the future.

Research activities

This research project is made up of multiple studies or research activities, which are led by different researchers, as provided below.

• Assessment of new Brassica accessions for resistance to newly identified pathotypes of P. brassicae (Fredua-Agyeman, Rahman)
• Genetic mapping of resistance genes (Rahman, Fredua-Agyeman)
• Broaden resistance spectrum with the deployment of multiple CR genes against the new pathotypes (Peng, Yu)
• Identification of QTL for resistance to new pathotypes of P. brassicae (Yu, Peng)
• Introgressing new CR genes into canola germplasm (Rahman, Fredua-Agyeman)

Key outcomes

1. Completed genetic mapping and development of molecular markers for four CR sources representing different Brassica species against the Canadian Clubroot Differential set. These CR sources will be of value to canola breeding for novel clubroot resistance.

2. Identified a CR gene originating from Mendel that is different from the first generation of resistant canola cultivars and two genes in B. rapa and B. napus, respectively, which were resistant to multiple major races of P. brassicae.
3. Identified race non-specific resistance genes in B. oleracea, which could be of the potential for more durable resistance to clubroot.
4. The genetic resources, information and molecular markers linked to the CR genes described above have been distributed to breeding companies via the AAFC Clubroot Consortium II.
5. Identified B. oleracea accessions carrying resistance to the newly evolved pathotypes 3H, 3A, 2B, L-G1 and L-G2 populations of X.
6. Identified chromosome regions of the C genome of B. oleracea carrying resistance to pathotypes 3A and L-G1.
7. Developed clubroot resistant B. napus lines from B. napus × B. oleracea (clubroot resistant) interspecific crosses.
8. Mapped the rutabaga clubroot resistances introgressed into canola, and developed markers for use in breeding.
9. Developed clubroot resistant elite canola lines and converted them to cytoplasmic male-sterile (CMS) lines and provided industry the CMS lines to develop clubroot resistant hybrid cultivars.
10. Developed one clubroot resistant commercial canola cultivar.
11. Contributed to our knowledge of retention/loss of resistance during the development of clubroot resistant canola through analysis of clubroot-resistant lines developed from 1st and 2nd cycles of breeding against 10 different pathotypes.
12. Contributed to the knowledge of effect resulting from clubroot resistance on agronomic and seed quality traits.
13. Contributed to the knowledge of the molecular basis of clubroot resistance in canola through transcriptome and metabolome analysis.