Scientists sequence chickpea genome which could inform crop improvement efforts

Close-up of chickpea plant. Photo by Srujan Punna.

Close-up of chickpea plant. Photo by Srujan Punna.

  • Researchers have sequenced the genome of chickpea.
  • The sequencing helped scientists identify the origin and patterns of migration of the pulse crop.
  • The research can help in the transfer of beneficial genes and the removal of deleterious ones.

Researchers have prepared an extensive genome map of the protein-rich chickpea, by sequencing its genetic material, which helped confirm its origin and migration and discover new genes to aid crop improvement.

This makes chickpea (Cicer arietinum), an important source of protein, carbohydrates and minerals, among the small group of crops with such an extensive genome map. It is extensively cultivated in more than 50 countries, mostly in South Asia and sub-Saharan Africa, and is important for nutritional security.

There is a need for improved crop varieties with higher yields, improved nutrition, and disease- and pest-resistance to meet the increasing food and nutrition security demands, particularly in South Asia and sub-Saharan Africa.  The crop also enriches soil fertility by adding significant amounts of nitrogen.

An international team of 57 researchers from 41 organisations across 11 countries assembled the pan-chickpea genome, by sequencing the genomes of 3,366 chickpea lines taken from 60 countries. The effort, described as “the largest effort of its kind for any plant” was led by the International Crops Research Institute for the Semi Arid Tropics (ICRISAT) in Hyderabad. The scientists identified 1,582 novel chickpea genes that were previously unreported, their report in Nature says.

“This is entirely new, and this is the largest plant genome sequencing project not only in chickpea but also for any plant species,” Rajeev Kumar Varshney, Director, State Agricultural Biotechnology Centre, Murdoch University, Australia. Varshney, who is one of the authors of the study, was at ICRISAT previously.

“This study highlights genetic bottlenecks, identifies genetic load, and also present haplotypes and genomic breeding stories,” Varshney said. “This was never studied before.”

The research is important also from evolutionary biology perspective as it helps understand the centre of origin and migration of chickpea, he added.

The scientists used whole-genome sequencing to confirm the history of chickpea’s origin in the Fertile Crescent — a crescent-shaped region in the Middle East spanning modern-day Iraq, Syria, Lebanon, Palestine, Israel, Jordan, northern Egypt and western Iran. The area is considered the birthplace of agriculture as its geography and climate supported crop growth which, in turn, led to a shift in lifestyle from hunter-gatherer communities to agricultural communities.

The genome sequencing helped the scientists 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, the report says.

The analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement.

“The 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,” the report in Nature adds.

The scientists also located the regions in the chromosomes, which contain the genetic material, which contain harmful mutations responsible for limited genetic diversity and decreased fitness; as well as genes for crop improvement-related traits. The information can help in the transfer of beneficial genes from one species to another, as well as help purge the deleterious genes either through genomics-assisted breeding or gene editing, the report says.

The scientists have proposed three crop breeding strategies based to enhance crop productivity for 16 traits, and at the same time avoid loss of genetic diversity.

Scientists at ICRISAT are working on improving chickpea. Photo by ICRISAT.
Scientists at ICRISAT are working on improving chickpea. Photo courtesy of ICRISAT.

Chickpea improvement efforts

Scientists at ICRISAT have been working on improving the chickpea plant. Earlier they reported in Theoretical and Applied Genetics that “modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts.” Scientists have been integrating genomic technologies with conventional breeding in recent years for chickpea improvement.

While conventional breeding methods have helped scientists develop more than 200 improved chickpea varieties previously, there is “ample scope” to increase productivity, they reported.

Chickpea is not as amenable to hybridisation as some other pulses, which is part of the challenge in breeding chickpea extensively, says Rajeswari Raina, professor at the school of humanities and social sciences at Shiv Nadar University near Delhi, who specialises in agriculture policy. “Hybridisation has not worked in this crop.”

Another reason is that it is easier for scientists to change the crop physiology, for example, shorter straw or more panicles, in crops such as rice and wheat, but not in chickpea.

Other reasons include India’s agriculture policies in recent decades, especially after the Green Revolution, with a shift towards cash crops such as cotton and sugarcane, which led to a neglect of traditional millets and pulses.

In India, chickpea is grown in about 10.75 million hectares, primarily in rainfed areas with limited external inputs. Poor seed replacement rate – percentage of area sown with high-quality seeds other than those stored in the farmers’ fields – in chickpea is often a constraint in its cultivation. In general, pulse productivity has been stagnant in India due to the widespread use of low-quality farm-saved seeds and low seed replacement rates, noted a 2021 study which also found that access to irrigation and institutional credit can increase seed replacement and result in increased chickpea productivity.

That said, India has made strides in chickpea production. According to ICRISAT, short-duration chickpea varieties, such as JG 11 and JAKI 9218, developed in collaboration with ICRISAT, contributed significantly to expanding chickpea area in southern India.

ICRISAT says that “one of the greatest success stories for pulses in India is the spectacular increase in area and productivity of chickpea in central and southern India, outperforming rest of the world (all chickpea growing countries excluding India) in chickpea production.”

During the past four decades (1979-2019), chickpea production in central and southern India increased by 445%, from 1.27 to 6.95 million MT between 1979 and 2019.

According to the Food and Agriculture Organisation (FAO), chickpea is grown on an estimated 14.56 million hectares spanning over 55 countries, which together produce 14.78 million tons. But several biotic and abiotic stresses restrict chickpea productivity to about one ton per hectare, despite a potential to produce 3.5-4 tons per hectare under optimum growing conditions.

While there has been an increase in chickpea productivity since 1961, there has also been, in parallel, a rise in its sensitivity to biotic and abiotic stresses. Another limitation is the limited number of donor parents with germplasm, which means a few number of parent plats are used and re-used.

Meanwhile, drought and heat stresses can reduce chickpea yields by up to 70%. The crop is also sensitive to biotic stresses, such as bacterial and fungal diseases such as dry root rot, collar rot, fusarium wilt, ascochyta blight, and botrytis grey mould. Seasonal weeds further reduce yields.


Banner image: Close-up of chickpea plant. Photo by Srujan Punna.

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