Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

TLDR

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, providing a substantial portion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of breeding‑associated genetic sweeps and balancing selection. The draft ∼738‑Mb genome of CDC Frontier, along with resequencing of 90 cultivated and wild lines from ten countries, offers a 28,269‑gene resource that highlights disease‑resistance and agronomic candidate genes, distinguishes desi and kabuli market classes, and provides insights into genome diversity and domestication for chickpea improvement.

Abstract

A draft sequence of the staple crop kabuli chickpea, together with resequencing and analysis of 90 additional lines from 10 countries, provides a resource for breeders. Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.