Key points

• An international library of blackleg isolates has been re-established as a research resource
• A set of near-isogenic canola lines that contain major blackleg resistance genes has also been made available as a research resource
• Three new major genes for blackleg resistance have been identified
• A method is being developed to phenotype canola for quantitative blackleg resistance

To address the plant resistance component of blackleg management, GRDC is partnering with CSIRO, the University of Western Australia (UWA) and the University of Melbourne to take a methodical approach to understanding the disease, as the causal fungus, Leptosphaeria maculans, constantly mutates.

This entails strengthening the armoury of resources that can be used across current and future blackleg investments, working with international experts to compile a library of blackleg variants, accessing new sources of genetic resistance and developing a disease phenotyping method to evaluate new sources of resistance.

The severity of blackleg disease has increased as the area and intensity of canola production has grown across Australia. Yield losses to blackleg infections of 50 per cent or more have been recorded in some seasons.

The fungus reproduces sexually, which makes it highly variable and enables it to overcome plant resistance and fungicides. This makes it an ongoing challenge to manage.

For these reasons, an armoury of management resources is required that incorporates knowledge of the blackleg fungus, sources of plant resistance, cultural practices and fungicides.

Resource armoury

Historically, a library of international blackleg isolates had been curated but this work had lapsed. In 2019, at the International Rapeseed Congress in Berlin, Germany, a group of international blackleg researchers agreed to re-establish this resource. Since then, researchers from the University of Melbourne have received isolates from 12 contributors, representing nine countries, and isolates from a further four countries are expected. This will be the first time isolates have been collected and analysed from countries such as Iran, South Africa, Argentina and Tunisia.

Added to this international collection are 17 isolates from the original collection and 25 Australian isolates collected between 2000 and 2021 representing all growing regions of Australia. All isolates have been characterised phenotypically and genotypically and this information is curated together with ‘passport’ information that includes collection location, who collected it and other general information.

This worldwide collection will be used to identify isolates for targeting and characterising novel sources of resistance and to establish common benchmarks across international research groups to prevent duplication and misinterpretation of data.

In addition to the international isolate collection, access has been gained to a set of near-isogenic canola lines that contain major blackleg resistance genes. These lines represent all major resistance genes that are currently available in Australian commercial varieties, as well as three major resistance genes not at present in Australian varieties. These will be a key research resource for Australia.

These resources have been provided to other GRDC-supported blackleg research programs at CSIRO and UWA and are being used for identifying novel sources of resistance, understanding quantitative resistance and characterisation of resistance genes in commercial cultivars.

New resistance sources

The genetic pool for blackleg resistance is being expanded through an interlinked research effort at UWA, University of Melbourne and CSIRO, examining both major and minor genes for blackleg resistance.

Major gene resistance relies on a single gene to confer resistance while minor gene or ‘quantitative’ resistance relies on a number of minor genes that work together.

The two forms of resistance work to control blackleg infections in different ways and are important members of the resistance armoury, as blackleg is able to rapidly overcome major gene resistance in as few as three years after commercial release.

Major gene resistance limits pathogen entry into plants while quantitative resistance restricts pathogen growth after it has entered the plant.

Researchers at the University of Melbourne and UWA have discovered three new major genes (Rlm3, Rlm4, Rlm7) for resistance and are actively screening wild varieties, introgression lines, synthetic lines and wild species for novel sources of resistance.

In addition to the discovery of novel sources of resistance, the researchers are identifying and developing molecular markers that pinpoint a part of the DNA in or near the resistance gene, which allows us to identity if the gene is present in the canola plant for all the known resistance genes for use in breeding programs.

Using state-of-the-art genome sequencing technologies, the team has already cloned resistance genes Rlm4 and Rlm7, in collaboration with researchers from Canada, and have candidate genes for Rlm1, Rlm3 and Rlm6.

Molecular markers have been established for Rlm4, Rlm7 and the previously cloned resistance genes Rlm2, Rlm9 and LepR3. These molecular markers have been provided to all Australian breeding companies and are being used routinely for screening for resistance genes in all Australian cultivars in another GRDC-supported project.

Phenotyping quantitative resistance

Traditionally, breeders have relied on field assessments to screen for quantitative resistance based on the severity of blackleg crown canker in mature plants.

However, this approach has limitations when the aim is to understand the genetics of quantitative resistance and develop molecular markers for breeding, as it does not account for environmental variation, diversity of blackleg populations and presence of major resistance genes, which prevent invasion of the plant and therefore mask the effect of quantitative resistance.

CSIRO researchers have been focusing on the development of a method to quantify blackleg disease (phenotype) to identify quantitative resistance. To develop biologically relevant phenotyping approaches, it is crucial to gain fundamental knowledge of the mechanisms, growth stages and tissues in which quantitative resistance acts, as well as interactions with the pathogen and environment.

Quantitative resistance is complex as it involves multiple genes that act together to reduce blackleg. In addition, it is masked in varieties that have major resistance genes, which prevent blackleg from entering the plant.

As each gene involved can have a small effect on disease severity, a highly sensitive molecular technique has been developed to quantify the blackleg fungus. This method has been used to generate new knowledge on how quantitative resistance functions, crucial to the development of a biologically relevant phenotyping assay.

Novel findings are that quantitative resistance does not provide partial resistance to all isolates nor does it act only in the adult plant as previously thought. Instead, it reacts with individual blackleg isolates differently, and functions in both leaves and stems from the seedling stage through to maturity.

CSIRO researchers are now applying this new knowledge and techniques to gain further understanding of the impact of environmental conditions and blackleg populations to blackleg disease and exploring novel techniques to quantify blackleg severity using machine learning.

More information: Angela Van de Wouw, 0439 900 919, apvdw2@unimelb.edu.au; Susan Sprague, 0466 643 227, susan.sprague@csiro.au; Jacqueline Batley, 0423 841669, jacqueline.batley@uwa.edu.au