New Australian Chickpea Pan-Genome Poised to Boost National Chickpea Production

Researchers from the Centre for Crop and Food Innovation (CCFI) at Murdoch University have led the generation of a pan-genome tailored specifically to Australian chickpea varieties, paving the way for improved chickpea production across the country.

The comprehensive genetic resource, composed of high-quality assemblies of the 15 most popular chickpea varieties grown by Australian farmers, uncovered previously uncharacterized genetic diversity that will prove essential in understanding and improving desirable agronomic traits that underpin the success of the nation’s Chickpea production, including yield, flowering time, acid soil tolerance and drought tolerance.

The pangenome analysis, published in Plant Biotechnology Journal and conducted in collaboration with Chickpea Breeding Australia (a Grains Research and Development Corporation and New South Wales Department of Primary Industries and Regional Development joint initiative), Agriculture Victoria Research, the WA Department of Primary Industries and Regional Development, the UWA Institute of Agriculture, and BGI Research, identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits.

The research pinpointed structural variations that influence flowering time, seed weight, disease resistance, drought resilience and acid toil resilience, highlighting a major opportunity to expand the genetic base of Australian chickpeas and ultimately support the long-term sustainability of chickpea production in Australia.

The researchers also discovered that Australian varieties could be further improved through the introduction of the “QTL hotspot” region for drought tolerance that has already demonstrated a 15- 22% yield advantage after its introgression in elite cultivars in India, Ethiopia, Kenya and Tanzania. CCFI is now working with industry partners to introgress the “QTL-hotspot” for drought tolerance into Australian varieties and deliver them to chickpea growers.

Reporting on the findings, Professor Rajeev Varshney, CCFI Director and corresponding author of the study, explained that:

“The Australian chickpea pangenome marks a significant step in safeguarding future production, as it enables us to accelerate the development of chickpea varieties tailored to each region. That could mean varieties that are more drought-resilient and acid soil-tolerant in Western Australia and nationally, and more resistant to diseases like Ascochyta Blight. We look forward to working with breeding organizations to get new and improved varieties into the hands of Australian farmers.

“I would like to thank all of our collaborators on this important piece of research, which we hope will ultimately boost farmer profitability and secure Australia’s position as a globally leading chickpea producer.”

GRDC is proud to have invested on behalf of Australian grain growers in this ground-breaking research. It is fantastic to see the country’s leading chickpea researchers unite to develop a significant genetic resource critical towards securing the future productivity and sustainability of chickpeas in increasingly challenging growing conditions.

This landmark GRDC investment in the development of an Australian chickpea pan-genome represents a major leap forward in our understanding of chickpea genetics that underpins Australia’s unique growing conditions. By unlocking the genetic diversity within the crop, this research provides a powerful foundation for breeding chickpea varieties with improved drought resilience and abiotic stresses, directly addressing some of the most pressing challenges for Australian grain growers. It exemplifies GRDC's commitment to delivering world-class science that drives real on-farm impact."

Dr Francis Ogbonnaya, Senior Manager for Oilseeds and Pulses, GRDC

Summarizing the findings, Dr Kristy Hobson, Chickpea Breeder at Chickpea Breeding Australia, said:

“Since the release of Australia’s first commercial chickpea variety in the 1970s, our industry has flourished into a billion-dollar sector that produced over 2 million tonnes of chickpea last season, and one of the world’s major chickpea exporters. However, there are significant challenges, including changes in agricultural practices, shifts in market demands, soil constraints, and significant disease pressures.

“These findings fill in some much-needed knowledge gaps regarding the genetic makeup of Australian chickpea varieties, which will be essential for further improvement through identifying the genes responsible for yields, stress tolerance and disease resistance.”