Brassica crops include cabbage, cauliflower, broccoli, kale and canola. Canola is a high return crop and a major oilseed industry for Australia, exporting 308,417 tonnes of canola in January 2020.

The challenge for canola breeders is that production can be limited by blackleg disease. Blackleg is caused by the fungal pathogen Lepstosphaeria maculans and forms cankers on the stem, as well as leaf lesions and in some cases infected pods. If the plant becomes infected, it can cause lodging, leading to yield loss. Resistance is through a gene for gene interaction, where a resistance gene in the plant recognises an effector protein in the pathogen.

Blackleg is a real problem in Australia, but also globally, realising an average of 10% yield loss per year. One of the most damaging incidences was documented in South Australia following the breakdown of resistance in 2003. This outbreak resulted in 90% production loss, equating to approximately 7.3 million USD.

The Batley Lab

Professor Jacqueline Batley came to the University of Western Australia (UWA) in 2014, with an Australian Research Council (ARC) Future Fellowship. She leads the Batley Lab, a research team in crop genetics and genomics in the School of Biological Sciences, with a focus on disease resistance in Brassicas.

Professor Batley is recognised internationally as a prominent canola genomics researcher and her Batley Lab are leaders in this research area. In 2019 she was awarded the prestigious Nancy Mills Medal from the Australian Academy of Science. She currently Chairs the Multinational Brassica Genome Project, an international collaboration with sequencing, database development and management tasks shared among a global consortium.

The Batley Lab team work closely with other researchers and international breeding companies based in Australia and their research benefits the Australian and global farming community.

It’s through working together, that we can make new discoveries.

Prof. Jacqueline Batley, UWA

Research goals

The team’s goals focus primarily on the oilseed crop Brassica napus (canola) and its interactions with the disease-causing fungus Leptosphaeria maculans (blackleg).

• identify the genes that underlie the resistance in canola and the pressure exerted by the pathogen
• understand the evolution of these genes

The team uses genome sequencing and molecular marker technology to find novel and sustainable sources of resistance against blackleg for breeders and farmers.

We need to make sure that we have sources of resistance so that we have enough food on our table in the future as the population grows.

Prof. Jacqueline Batley, UWA

Screening to improve crops

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. They are used by breeders to understand what traits are present in their plant material.

With funding from the Australian Research Council (ARC), in 2018 the Batley Lab team worked with the UWA Applied Bioinformatics group to develop the Crop SNP database (CropSNPdb). The online data repository allows researchers and breeding companies to query the genotypes, download results, and submit data generated using the Illumina Infinium™ Brassica 60K array.

The Crop SNP database provides researchers and breeding companies with an accurate source of data for future crop selection as well as associated economic benefits. Farmers and growers can use the information to associate with traits, including resistance, which helps to increase their yield and provide food security for consumers.

In 2019, a further project funded by the Grains Research and Development Corporation (GRDC), including collaborators from the University of Melbourne School of Biosciences, the team have developed molecular markers for the known (and newly identified) blackleg R genes. These markers have been made available to the breeding companies for use in routine screening of plants. In house, the team also use the markers to screen all Australian cultivars.

This molecular method of assessing complex plant traits including tolerance and resistance is faster and 100% accurate compared to the existing plant phenotyping technology, which has limitations due to masking of resistance genes.

The research I do is important because we need to be able to have sustainable food production in the future, and we want to reduce the use of chemicals on the land with less economic loss.

Prof. Jacqueline Batley, UWA

The team have also used their next generation sequencing technique to characterise the diversity and evolution of resistance genes in wild and cultivated Brassica species, undertake phenotypic analysis of the disease and identify novel sources of resistance.

Assembling the pan-genome

A pan-genome is the entire gene set of all strains of a species. Characterising and mapping the pan genome allows detection of its variants.

In 2019, the Batley Lab team were the first to publish the genome-wide repertoire across all the different brassica species, facilitating reference-based mapping for disease resistance phenotypes. The team looked at the diversity of resistance genes across multiple different genome sequences of Brassica lines. Their research showed that 40% of resistance genes are present in some cultivars and absent in other cultivars. This demonstrated that it is not just single mutations of a sequence that can exist, it can also be that the gene is present in one and absent in another.

We find something new and it throws up a whole new challenge. We love to keep working on it and there is still so much left to solve. We can’t stop now.

Prof. Jacqueline Batley, UWA

The power of resistance

The team’s research is part of a multi-faceted approach required to control blackleg and ensure sustainable resistance.

Blackleg pathogen genes interact directly with the host’s genes. If plant populations with a particular resistance gene are replanted over three years, the pathogen adapts and is able to reinfect the population. As such, the Grains Research and Development Corporation (GRDC) in Australia recommends that growers plant crops with different resistance genes, in different years.

The team have undertaken research into the identification of resistance genes since 2009. Their research has led to the development of new commercial canola cultivars with enhanced productivity, profit, and stable yields for breeding companies.

In 2020, in collaboration with University of Melbourne School of Biosciences and funding from the ARC and GRDC (UOM1905-003RTX) the team characterised all the resistance genes across different species that have had their genome sequenced. Their project established a resource for the identification and characterization of resistance genes in Brassica. This is used by researchers and breeders to see which resistance genes are present and to ensure a sustainable level of new resistance genes is introduced into the Australian cropping system.

By knowing whether their cultivar has an appropriate resistance gene, farmers are also able to improve yield and lower the use of fungicide on their crops.

We need to be able to understand the interaction and through identifying the genes that underlie this, you can improve the crop, improve yield and improve economic outcomes.

Prof. Jacqueline Batley, UWA

Same gene, but different

Breeders do not want to have all the different resistance genes in one cultivar, because the pathogen will eventually wipe it out. Professor Batley attends regular meetings with breeding companies and industry where updates are provided on new resistance genes identified.

RLM genes are blackleg resistance genes, some of which were suspected as being identical or allelic variants, due to the markers used in their mapping. In the past, phenotyping was the method used, however phenotyping can mask the presence of different RLM genes.

The Batley Lab team discovered a number of RLM black leg resistance genes, alongside a Canadian research team. They went on to develop markers using the genes they had co-identified, and the teams continue to collaborate on their research.

Professor Batley’s genomic sequencing method finds differences in the DNA of a host compared to resistance to the pathogen. Their research showed that in some cases, different alleles of the same gene were some of the different RLM genes. Whilst these have the same underlying gene, the sequence of them are slightly different.

The team used their method to identify disease resistance genes, a key strategy for breeders to improve cultivars. This knowledge is a valuable resource in the identification of resistance genes to maintain blackleg resistance.

A wild idea

As pathogen populations change and adapt, new sources of resistance need to be found.

In 2019, with funding from the GRDC (UWA1905-006RTX), the Batley Lab team and colleagues from the University of Melbourne used wild, closely related species to identify novel resistance genes to bring diverse resistance genes into the canola germplasm.

By combining genomics and bioinformatics techniques, the genetic variation in wild species are identified and can be used by breeders for the introgression of desired traits. These wild species play an important role in food security and for sustainable plant production in the future.

Although genomics is taking the centre stage, in 2021 the team concluded that a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction backed by big data capabilities will ultimately ensure the selection of future-proof Brassica crops.

I’m inspired to know that what we are doing has real benefit.

Prof. Jacqueline Batley, UWA

An evolving theory

Plants have evolved defence mechanisms to protect themselves against microbial pathogens and understanding their genetic basis for disease resistance is crucial to managing blackleg disease. In Blackleg disease, the fungal pathogen Leptosphaeria maculans has evolved to interact and adapt a ‘gene to gene’ interaction with the host plant, making it difficult for the host to maintain resistance.

In 2018, the team used Brassica napus (rapeseed, canola) as a model for studies of genetic and genomic evolution. Their study proposed that inbreeding and low levels of genetic diversity were major driving forces behind genome evolution in this agricultural crop species.

Building on their previous work, in November 2020, the team looked at the evolution of disease resistance genes in Brassicas as well as other agriculturally important plants, to gain insight into their function and inform the identification of resistance genes for the breeding of resistant lines.

The most abundant resistance gene family is NLR (Nucleotide Binding Site Leucine Rich Repeat). Funded by the ARC in 2021, their research showed that the evolution of NLR genes is influenced by genomic processes and pathogen selection, with pathogen populations exerting different selection pressures on crops throughout their evolutionary history.

Further afield

Through her work on genomics and disease resistance, Professor Batley has been approached by collaborators to apply her knowledge on projects outside her usual scope of work. For example:

• Pearl oysters: using next-generation sequencing to understand traits of interest in oysters.
• Subterranean clover: providing genomics insight for the identification of desired traits, marker-assisted breeding, mapping and identification of genes for the improvement of legume crops.

I love expanding out to different species. Once you can understand the DNA, identify the genes and look at what’s causing certain traits, you can get to work on anything.

Prof. Jacqueline Batley, UWA