Chickpea is the world’s third most widely grown legume crop, cultivated in semi-arid environments. It is an important source of protein for human consumption in more than 50 countries. Despite its importance, chickpea was previously defined as a neglected crop because of limited research and breeding efforts. By using BGI’s sequencing platform advanced research on collected germplasms genome as well as effective breeding practices in chickpea have occurred, establishing an example for the improvement of neglected crops.

In the article published on November 10 in Nature, an international team led by ICRISAT (International Crops Research Institute for the Semi-Arid Tropics) reported the sequencing of 3,366 chickpea genomes, representing the largest effort of its kind for crops. With this unprecedented genome dataset, the team assembled a pan-genome with 1,582 novel genes that were previously unreported, as well as constructed a comprehensive genomic variation map with different types of variations. Based on the genomic variation map, the study revealed that chickpea was cultivated from its wild progenitor species, Cicer reticulatum, around 12,600 years ago. After a breeding bottleneck that began around 10,000 years ago and lasted until about 1,000 years ago, a revival noted around 400 years ago suggests renewed interest in chickpea agriculture. 

“By employing whole genome sequencing, we have been able to affirm the history of chickpea’s origin in the Fertile Crescent and identify two paths of diffusion or migration of chickpea to the rest of the world. One path indicates diffusion to South Asia and East Africa, and the other suggests diffusion to the Mediterranean region (probably through Turkey) as well as to the Black Sea and Central Asia (up to Afghanistan),” said Prof. Rajeev Varshney, a Research Program Director at ICRISAT and leader of the study. He added, “More importantly, this research provides a complete picture of genetic variation within chickpea and a validated roadmap for using the knowledge and genomic resources to improve the crop.”

Genomic data can further aid breeding practices. Comparing the cultivated chickpea to its wild progenitor, C. reticulatum, the researchers identify deleterious genes responsible for lowering crop performance. Meanwhile, the study identified blocks of genes in landraces (domesticated varieties developed by farmers), responsible for improving agricultural traits including yield, climate resilience, seed characters and others. These blocks of genes (haplotypes) are advantage genotypes that breeders strive to bring into cultivars. Researchers further checked these haplotypes in all chickpea varieties between 1948 and 2012. 

“We examined the 129 chickpea varieties that were developed and released between 1948 and 2012. Though a few superior haplotypes were detected in some of these varieties, we found that most varieties lacked many of them. We have arrived at 56 promising lines that can bring these haplotypes into breeding programs to develop high-yielding varieties,” said Manish Roorkiwal, Senior Scientist with ICRISAT.

This study belongs to a chickpea genome project initiated in 2013 to first finish the construction of reference genome (Varshney et al. 2013), and then report the core germplasm resequencing of chickpea (Thudi et al. 2016; Varshney et al. 2019) (Figure 1). From this genome data, ICRISAT and other organizations have been using genomics-assisted breeding approaches to obtain as many as seven chickpea varieties in the last three years in India and Ethiopia, which have shown marked improvements over varieties released earlier. “Genomic resources are crucial for accelerating the rate of genetic gains in crop improvement programs. By developing many resources for chickpea over the last decade, ICRISAT has helped the crop shed its ‘orphan’ tag. It is hoped that the knowledge and resources made available through this study will help breeders across the world revolutionizing chickpea breeding without eroding its genetic diversity,” said Dr Arvind Kumar, Deputy Director General, ICRISAT. 

The current study, covered more varieties and provided direct information for breeding, benefiting breeding practice and ensuring food security in many developing countries. “We are happy to provide our sequencing platform for this kind of large-scale genome study. Along with our collaborators, we are setting up the example for genome data based effective breeding for more crops,” said Xin Liu, associate director of BGI Research. “Together with this international team, we have further pushed forward genome studies in chickpea, which we believe will benefit both research communities and farmers.”

Figure 1. Since 2013 there have been a series of genomic research and milestones that BGI has participated in and achieved. Breeding methods based on genomic data have further promoted the development of chickpea breeding practices, and have assisted ICRISAT to breed multiple chickpea varieties (the seed photos of the new varieties are provided by ICRISAT).

Article Link: https://www.nature.com/articles/s41586-021-04066-1


References:
Varshney, Rajeev K, Chi Song, Rachit K Saxena, Sarwar Azam, Sheng Yu, Andrew G Sharpe, Steven Cannon, et al. 2013. “Draft Genome Sequence of Chickpea (Cicer Arietinum) Provides a Resource for Trait Improvement.” Nature Biotechnology 31 (3): 240-46. https://doi.org/10.1038/nbt.2491.

Thudi, Mahendar, Annapurna Chitikineni, Xin Liu, Weiming He, Manish Roorkiwal, Wei Yang, Jianbo Jian, et al. 2016. “Recent Breeding Programs Enhanced Genetic Diversity in Both Desi and Kabuli Varieties of Chickpea (Cicer Arietinum L.).” Scientific Reports 6 (November): 1-10. https://doi.org/10.1038/srep38636.

Varshney, Rajeev K., Mahendar Thudi, Manish Roorkiwal, Weiming He, Hari D. Upadhyaya, Wei Yang, Prasad Bajaj, et al. 2019. “Resequencing of 429 Chickpea Accessions from 45 Countries Provides Insights into Genome Diversity, Domestication and Agronomic Traits.” Nature Genetics 51 (5): 857-64. https://doi.org/10.1038/s41588-019-0401-3.