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Research & Discoveries

The main research focus of the Batley lab is genetics and genomics. We work on a range of crop and pathogen species, including subterranean clover, soybean, wheat, banana and chickpea, with other fun projects on parasitic plants, pearl oyster and guppies, but our primary research focus is on the agricultural oilseed crop Brassica napus (canola), and its interactions with the disease-causing fungus Leptosphaeria maculans (blackleg). Related research projects include identification of blackleg disease resistance genes in canola and investigation of the blackleg genome through next-generation sequencing and high-throughput molecular marker approaches. New projects are investigating the role of structural variation in the Brassica genomes, specifically in relation to disease resistance and understanding the evolution of disease resistance genes. In conjunction with this our lab continues to work on development of genomes and pan genomes.

More information on our exciting research can be seen in these videos:

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Current Projects

Understanding disease resistance gene evolution across the Brassicaceae

In this ARC funded project, we recognise build on our findings that Pan genomes represent the diversity of a species, including structural and sequence variation, which cannot be provided by a reference genome alone. Here we will develop pan genomes for a range of Brassicaceae species and characterise resistance gene diversity across these pan genomes. Through comparison with resistance gene diversity in cultivated Brassica species we will understand selection underlying resistance gene evolution in wild species and subsequent domestication and breeding. We are then building on this knowledge of how variation affects disease susceptibility, especially to the devastating fungal pathogen blackleg, and contributes to phenotypic variation, which will lead to improved plant protection strategies and increased crop resilience. In future we would love to take this further and look at resistance genes in all plant genomes, given how many reference genomes and pan genomes are available:

List of Genomes.pdf (

RG Augury Results.pdf (

Who’s who in the plant gene world

In this ARC funded project led by Dave Edwards we are harnessing information from the many plant genome sequences available. As many more plant genomes are sequenced, the bottleneck is being able to interrogate and translate this data explosion into applications for crop improvement. In this project we are developing and applying a population graph database, hosting genome data for diverse crops and their wild relatives, allowing us to characterise gene diversity on an unparalleled scale, with a focus on genes for important agronomic traits including disease resistance, flowering time and legume nitrogen fixation.

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Current Projects

Towards effective control of blackleg of canola: Identification of novel sources of blackleg resistance genes

In these GRDC funded projects we are collaborating with researchers at the University of Melbourne to further our understanding of the canola-blackleg interaction for improved crop production.  The success of the Australian canola industry since its development in the 1970s has been driven by protecting the crop against blackleg disease, the main disease of canola globally. Protection against blackleg can be achieved using plant resistance (R) genes, that recognize specific proteins made by the fungus to mount a highly effective defence response. As the first Brassica resistance genes and the Leptosphaeria maculans Avr genes have been cloned and analysed, it has been discovered that the genetics is considerably more complex than first thought.  For example, cloned plant resistance genes have been shown to be different alleles of the same gene and from the pathogen side, the presence of one avirulence product can ‘mask’ the presence on another Avr gene. These complicated types of interactions have led to difficulties in identifying R genes in the past and highlight the need to understand both the pathogen and host sides of the equation. Things are complicated further by the absence of resistance genes from the genome sequences of the cultivar used in the international reference genome sequencing project thereby highlighting a need for the ‘pan genome’. Novel resistance already exists in cultivated and wild Brassicas. Hence, this project will identify and characterise new sources of resistance and provide this information to breeders. We are sequencing the genomes of the pathogen and the host to understand the population structure and identify the genes present. So far we are excited to have identified Rlm4 and Rlm7, with further candidates currently undergoing validation for a further 5 genes. Two novel sources of resistance have also been identified, which we are further investigating to identify the underlying gene.

Modifying plant sterol metabolism to combat insect pests for crop protection

We have been developing a novel biotechnological strategy to control insect pests for crop protection. This strategy is based on the principle that insects rely on converting host phytosterols to cholesterol which is essential for their growth and development.

New approaches are required to control insect pests which cause enormous global crop losses. Phytophagous insects are incapable of synthesizing cholesterol. Cholesterol is a precursor of the molting hormone. Insects rely on converting host phytosterols to cholesterol via a unique dealkylation pathway. There are stringent structural demands if the phytosterol is to be used as substrate for dealkylation, therefore some phytosterols cannot be utilised by insects.

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Mentions of our research in the press and the media are an important way to build recognition and awareness for our work. Read on below to see a selection of the latest coverage we have received.

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William Thomas a Canadian field trip

Will is a 3rd Year PhD student whose project is focussed on identifying new sources of resistance against blackleg. This year he travelled to Winnipeg which is the capital city of Manitoba, one of the “prairie” provinces and the third largest canola producing province in Canada. While in Winnipeg, Will was based at the University of Manitoba (UofM), where he undertook a 4-month research internship with Prof. Dilantha Fernando to expand his work on identifying resistance genes. Canada is the world’s largest producer of canola and is also severely affected by blackleg. Will was able to gain valuable insight into blackleg management from a Canadian perspective and was exposed to new research ideas about preventing the disease. The main purpose for visiting the Fernando Lab in Winnipeg was to take advantage of their diverse collection of blackleg fungal isolates, that are genetically different to those in Australia. Will was able to phenotypically screen hundreds of canola plants with blackleg isolates stored at UofM and obtained exciting phenotyping results that will be combined with genotyping data in order to narrow down the genomic location of the resistance gene. The data that Will gathered while at UofM is a vital component of his PhD thesis, but more importantly has advanced his progress towards identifying a new source of resistance that can be deployed in Australian canola cultivars to ensure sustainable and profitable canola production

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Junrey Amas: University of Bonn, Germany internship

One of the aims of Junrey’s PhD project is to identify and characterise novel resistance genes against pathogens in Brassica species. Previous phenotyping against several blackleg isolates found a number of Brassica napus lines showing novel resistance. However, some of these lines show genetic incompatibility when crossed to cultivated species, thereby hindering the production of mapping populations for further genetic analyses. This problem can be addressed by employing tissue culture techniques, including embryo rescue to increase the chances of obtaining fertile offsprings for population development. Thus, the main objective of Junrey for visiting Prof Annaliese Mason’s Lab at the University of Bonn in Germany is to learn the protocol for conducting embryo rescue in Brassica species. Prof. Mason’s lab is a world authority in Brassica cytogenetic research and one of the pioneers in creating allohexaploid Brassica species showing novel traits, including disease resistance. Junrey also obtained complementary skills in cytogenetic analysis including fluorescence/genomic in situ hybridisation (FISH/GISH). These skills are relevant to the research objectives of the Batley lab, which Junrey hopes to transfer to other members of the team.

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Jaco Zandberg visiting Western Australia’s blackleg nurseries

The blackleg pathogen is a devastating fungal disease that attacks canola. The resulting damage on average every year is ~10-15% yield loss globally, however, in some cases it can result in up to 90% loss. As such, the Australian government along with the Grains Research Development Corporation (GRDC) and Marcoft Grains Pathology group have setup a national trial in which the disease pressure is monitored for a wide range of canola cultivars (commercial, experimental and old) to provide growers and breeders with accurate information of the breakdown of resistance in-field. Jaco Zandberg has recently returned from his trip to three of trials based in Western Australia with over a hundred samples for analysis. He hopes to perform a cutting edge method of analysis known as multi-omics to identify and characterise new disease markers. These new disease markers will provide growers and breeders with a wider range of cultivars to grow that are more resistant to the growing threat of the blackleg pathogen.

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New Research Paper

We are excited to share our pre-print describing the identification and validation of two important blackleg resistance genes. The mystery of Rlm4 and Rlm7 has now been unravelled! Well done to Yueqi Zhang, Tina Neik, Philipp Bayer and Dave Edwards (UWA Applied Bioinformatics Group), Angela Van de Wouw (University of Melbourne) and our collaborators from Hossein Borhan’s group.

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School of Biological Sciences, University of Western Australia
35 Stirling Hwy, Crawley WA 6009

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