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.

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.

Potential impact

Newly identified pathotypes or pathotype variants of Plasmodiophora brassicae are clearly a threat to clubroot management on canola in western Canada due to their virulence to all current resistant cultivars in the marketplace. So new CR genes, especially those with broad-based resistance, will help enhance the spectrum and potentially durability of resistance.

In the short term, the output of this study will increase the diversity of CR genes against the new pathotype variants. The information on resistance mechanisms will help “label” CR genes or gene combinations. In the longer term, multi-gene deployment strategies via stacking or gene rotation may substantially strengthen the durability of clubroot resistance and sustainability of clubroot management. The study also complements the efforts of identifying quantitative resistance in Canadian Canola Clubroot Cluster Pillar 3.

Research activities

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

1. Assessment of new Brassica accessions for resistance to newly identified pathotypes of P. brassicae (Fredua-Agyeman, Rahman)

Thirty B. napus lines and several B. oleracea lines found resistant to 5x isolates under current projects will be assessed for resistance to the new pathotypes initially. Up to 1400 Brassica accessions will be screened for qualitative and quantitative resistance against the new pathotypes as well.

2. Genetic mapping of resistance genes (Rahman, Fredua-Agyeman)

CR candidates resistant to new pathotypes will be selected for mapping population development and used in genetic crosses. The double haploid (DH) lines will also be tested in clubroot disease nurseries for resistance to pathotypes 3 and 5x, respectively.

In the case of partial resistance, QTL analysis will conducted and additional analysis will be used to determine the association of each marker with resistance against each of the P. brassicae strains.

3. Broaden resistance spectrum with the deployment of multiple CR genes against the new pathotypes (Peng, Yu)

Multi CR-gene B. napus lines will be generated initially based on the resistance against pathotype 3 and 5x, and later on further data against predominant pathotypes variants. This study may also include newly identified materials with quantitative resistance for completely different modes of action. Resistance stability of multi-gene lines will be assessed against single CR genes in “tub testing” via repeated exposure to recycled pathogen inoculum of single- and mixed-pathotype populations, respectively.

This study will involve additional efforts focused on Developing CR sources and Interactions between CR genes.

4. Identification of QTL for resistance to new pathotypes of P. brassicae (Yu, Peng)

This study involves:

• Evaluating BC1S1 or DH populations for resistance to new strains of P. brassicae.
• Identifying variants, variant filtering, construction of linkage map and QTL mapping.
• Developing SNP markers tightly linked to each resistance gene.

5. Introgressing new CR genes into canola germplasm (Rahman, Fredua-Agyeman)

The introgression of selected new CR genes into canola germplasm will be done by crossing and backcrossing with a B. napus line until BC4. Self-pollination will be performed in each generation. SNP markers tightly linked to each of the CR genes will be used for marker-assisted selection (MAS). The presence of the genes will be confirmed by MAS and phenotyping in each of the backcrossing and self-pollinating generations. Stable BC4S2 B. napus lines carrying homozygous CR genes will be obtained by the end of project. Additionally, introgression of novel CR gene(s) into quantitative resistance background will be explored to generate broad-based CR B. napus germplasm.