A team of researchers from Murdoch University’s Centre for Crop and Food Innovation (CCFI) has unveiled Australia’s first chickpea pan-genome, marking a major leap forward in efforts to future-proof one of the country’s most important pulse crops.
This landmark genetic resource, published in the Plant Biotechnology Journal, compiles high-quality genome assemblies of the 15 most popular chickpea varieties grown by Australian farmers.
The analysis has revealed previously untapped genetic diversity that is vital for improving yield, flowering time, drought and acid soil tolerance, and disease resistance.
Led by Prof. Rajeev Varshney, Director of CCFI and corresponding author of the study, the project brought together experts from Chickpea Breeding Australia, Agriculture Victoria Research, the WA Department of Primary Industries and Regional Development, UWA’s Institute of Agriculture, and BGI Research.
“The Australian chickpea pan-genome marks a significant step in safeguarding future production,” said Prof. Varshney.
“It enables us to accelerate the development of varieties tailored to each region—especially those more drought-resilient and acid soil-tolerant in Western Australia, and those with stronger resistance to diseases like Ascochyta Blight. We’re now working with breeders to get these improved varieties into the hands of Australian growers.”
Among the discoveries was the identification of 34,345 gene families, including nearly 14,000 that are “dispensable” but enriched for genes associated with critical traits. Importantly, the study pinpointed structural variations influencing flowering time, seed weight, and resilience to stress—laying the groundwork for more targeted breeding.
Researchers also identified the potential of incorporating a known “QTL-hotspot” region—previously proven to boost yields by 15–22% in India, Ethiopia, Kenya and Tanzania—into Australian chickpea lines. Work is already underway to introgress this trait into local varieties.
The research was supported by the Grains Research and Development Corporation (GRDC), which described the project as a milestone for Australian agriculture.
“GRDC is proud to have invested in this ground-breaking work on behalf of grain growers,” said Dr Francis Ogbonnaya, GRDC’s Senior Manager for Oilseeds and Pulses.
“Unlocking the genetic diversity of the crop provides a powerful foundation for breeding varieties better suited to Australia’s increasingly challenging growing conditions.”
Dr Kristy Hobson, Chickpea Breeder at Chickpea Breeding Australia, noted the importance of this genetic map for the future of an industry that produced over 2 million tonnes of chickpeas last season.
“Since the 1970s, Australian chickpea farming has grown into a billion-dollar sector,” she said.
“This pan-genome helps fill key knowledge gaps and will be essential in tackling ongoing challenges such as changing farming practices, market shifts, soil constraints and major disease pressures.”
With this new genomic toolkit in hand, Australian researchers and breeders are better equipped than ever to deliver the next generation of chickpeas that are robust, high-yielding, and resilient—ensuring the crop’s continued success at home and on the global stage.
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