World’s Largest Plant Genome Sequencing of Chickpea has Successfully Catalogued

Chickpea's pan-genome was produced by an international team of researchers from 41 organizations including researchers from the University of Western Australia’s Institute of Agriculture sequencing the genomes of 3,366 chickpea lines from 60 nations.

The researchers, led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), discovered 29,870 genes, including 1,582 previously unknown genes. The study is the most comprehensive of its sort for any plant, placing chickpea among a select club of crops having such a detailed genome map.

Research Findings:

A research article, published in the prestigious Nature journal, outlined how 57 scientists from 41 organizations and 11 countries used genomic sequencing to map the variation in 3,171 cultivated and 195 wild chickpea accessions (unique seed samples).

“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 Programme Director at ICRISAT and leader of the study that was published on 10 November in Nature. “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,” he added.

Chickpea is the world's third-most-cultivated legume, with over 50 countries growing it. It is a staple of many countries' cuisines and a key source of dietary protein, particularly in the Global South. In 2013, ICRISAT was the driving force behind the sequencing of the first chickpea genome (a Kabuli line). This sequence paves the path for the development of molecular resources to improve the crop.

Soon after, the need to fully understand genetic variation at the species level, especially in landraces and wild types, prompted a greater effort to sequence more lines. The authors of the new work describe sequencing 3,171 cultivated chickpea accessions and 195 wild chickpea accessions that are conserved in several gene banks. These 3,366 accessions illustrate the genetic diversity of chickpeas in a considerably larger global collection.

Cicer arietinum is the scientific name for farmed chickpea. C. arietinum diverged from its wild progenitor species, Cicer reticulatum, some 12,600 years ago, according to the study. According to the authors of the study, the method employed to analyze the divergence of eight Cicer species through time can also be used to discover misclassification or duplication of accessions in order to better manage germplasm in gene banks.

"As the world's population grows, chickpea consumption is expected to climb in the next years." Dr. Trilochan Mohapatra, Director General, Indian Council of Agricultural Research (ICAR), and one of the study's authors, stated, "Research like this is the need of the hour to enable major producing countries like India to enhance crop production while making crops climate-resilient."

Dr. Jacqueline Hughes, Director General, ICRISAT, said, “By developing many genomic resources for chickpea over the last decade, ICRISAT has helped the crop shed its ‘orphan’ tag. With our partners in agricultural research for development, we will continue to research chickpea and translate findings into crop varieties that benefit farmers, consumers, and nations.”

The researchers were able to discover detrimental genes responsible for reducing crop performance by comparing the genetic variance in cultivated chickpea with that of its wild progenitor. Because detrimental genes would have been purged to some amount in cultivated lines by selection and recombination, they were more common in the wild progenitor. According to the researchers, detrimental genes in cultivars can be further purged utilizing genomics-assisted breeding or gene editing.

Furthermore, the research discovered gene blocks in landraces (domesticated varieties established by farmers) that can greatly improve crop performance by enhancing yield, climatic resistance, and seed characteristics. These genetic blocks, known as haplotypes, are what crop breeders try to incorporate into cultivars. The research gives light on the deployment of these haplotypes in chickpea varieties using historical data from all varieties issued between 1948 and 2012.

"We looked at 129 previously released variants. Though some of these kinds had a few superior haplotypes, we discovered that the majority of them lacked many favorable haplotypes”. Dr. Manish Roorkiwal, a Senior Scientist in Genomics and Molecular Breeding at ICRISAT, said, "We've arrived at 56 potential lines that can incorporate these haplotypes into breeding programs to generate enhanced varieties."

Dr. Arvind Kumar, Deputy Director General-Research, ICRISAT, stated, "It is hoped that the knowledge and resources made available via this study would help breeders around the world revolutionize chickpea breeding without losing its genetic diversity."

To use the findings of the study on the farm, the authors offered three genomic-based breeding approaches aimed at improving 16 attributes and increasing chickpea productivity. They established that the methods work by using them to improve 100-seed weight, an important yield attribute, and forecasting increases of 12 to 12%.