The entire chickpea genome has just been sequenced, providing chickpea breeders with a powerful tool for lifting the performance of this increasingly important crop – both in Australia and internationally.
The genome sequencing project was designed especially to help breeders improve cultivated varieties by sampling the whole gene pool – elite varieties, landraces and wild species. In total 90 genomes were sequenced.
Crop plant sequencing is often limited to just one example of the species. By sequencing across the whole species the genetic differences that drive breeding programs for lifts in yield, quality, stress tolerance and disease resistance are more rapidly identified. The project was undertaken by the International Chickpea Genome Sequencing Consortium (ICGSC) led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) based in Hyderabad, India.
The project generated thousands of DNA markers that can be used to broaden the otherwise narrow genetic base of cultivated chickpea varieties, and to subsequently develop superior varieties.
The research milestone involved 49 scientists from 23 organisations in 10 countries. Funding also had an international base that included GRDC and the Consultative Group on International Agricultural Research and organisations in India, China, the US, Europe and Canada.
Among the varieties sequenced were 29 elite varieties (19 desi and 10 Kabuli) sourced from leading chickpea-growing countries. The first genome sequenced was that of the Canadian Kabuli variety CDC Frontier which is resistant to the fungal disease ascochyta blight. The remainder were breeding lines, landraces and five wild species.
Chickpea was found to contain a comparatively small number of genes (187) that confer resistance to pests and diseases (the so-called NBS-LRR genes). This explains why the Australian industry has struggled in the past with disease. In comparison, other legume industries, such as soybean, have 506 such genes to draw on.
Dr Rajeev Varshney, ICGSC coordinator and director of ICRISAT’s Center of Excellence in Genomics, says that genetic diversity is an important prerequisite for crop improvement, but to date this has been limited in chickpeas.
“This study will provide access to ‘good genes’ to speed up breeding, and to genomic regions that will bring genetic diversity back from landraces or wild species into breeding lines. It could halve the time (currently four to eight years) needed to breed a new variety with market-preferred traits.”
In all, 28,269 chickpea genes were detected, with most demonstrating similarities to known genes in other species. This has allowed researchers to tentatively attribute a biological function to almost 90 per cent of the chickpea genes.
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