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Chickpea Traits, Domestication History Revealed through Global Sequencing Effort

NEW YORK (GenomeWeb) – An international team led by investigators in India and China has sequenced hundreds of global chickpea accessions, uncovering clues to the crop plant's domestication and spread around the world. 

The researchers resequenced the genomes of more than 400 chickpea lines from 45 countries to narrow in on some 4.97 million SNPs that were subsequently used for a genome-wide association analysis highlighting SNP markers and genes with ties to more than a dozen agriculturally important traits, such as drought or pest resistance.

In addition to placing the chickpea's origins in the Eastern Mediterranean, the team retraced its spread from the Fertile Crescent to Central Asia, East Africa, and South Asia, and focused in on more than 100 parts of the genome that seem to have been subject to selection during chickpea domestication and breeding. The findings appeared online yesterday in Nature Genetics.

"Our study indicates that in terms of center of origin of chickpea, Fertile Crescent/Mediterranean is the possible primary center with Ethiopia as a secondary center of diversity," co-first and co-corresponding author Rajeev Varshney, research program director for genetic gains at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, India, said in a statement.

He further noted that the current results point to "a migration route from Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India)."

"The new study established a foundation for large-scale characterization of germplasm, population genetics, and crop breeding," co-senior and co-corresponding author Liu Xin, deputy director of BGI Research, said in a statement, noting that the work "helped understand domestication and post-domestication divergence of chickpea."

For the analysis, researchers at dozens of centers around the world brought together available genome sequence data for 129 lines or varieties sequenced in the past and new whole-genome re-sequencing data for 300 chickpea genotypes from a reference set Varshney and colleagues assembled more than a decade ago and described in BMC Plant Biology.

By comparing the chickpea sequences to one another and to a reference genome representing a Canadian chickpea genotype first sequenced in 2013, the team identified more than 4.97 million SNPs, some 596,100 small insertions or deletions, more than 4,900 copy number variants, and tens of thousands of sequences that were present in some accessions and missing in others.

The researchers saw three genetic clusters for the accessions analyzed, using the variants identified to explore chickpea relationships, genetic diversity, and migration patterns. With information at 3.65 million chickpea SNPs, meanwhile, they performed a GWAS focused on 20 drought- or heat tolerance-related traits, which led to 262 proposed SNP markers for 13 of those traits.

The authors noted that the study led to "marker-trait associations (MTAs) for drought and heat tolerance-related traits that can be used in marker-assisted breeding to develop new chickpea varieties with enhanced yield and climate resilience."

The sequences also provided a look into chickpea's past, revealing 204 genes and 122 parts of the genome that appear to have been subject to selection in the process of chickpea domestication, breeding, and spread throughout the world.