Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits.
Rajeev Kumar VarshneyMahendar ThudiManish RoorkiwalWei-Ming HeHari D UpadhyayaWei YangPrasad BajajPhilippe CubryAbhishek RathoreJianbo JianDadakhalandar DoddamaniMohammad Aamir Waseem KhanVanika GargAnnapurna ChitikineniDawen XuPooran M GaurNarendra P SinghSushil K ChaturvediGangarao V P R NadigatlaLakshmanan KrishnamurthyG P DixitAsnake FikrePaul K KimurtoSheshshayee M SreemanChellapilla BharadwajShailesh TripathiJun WangSuk-Ha LeeDavid EdwardsKavi Kishor Bilhan PolavarapuR Varma PenmetsaJosé CrossaHenry T NguyenKadambot H M SiddiqueTimothy D ColmerTim SuttonEric Bishop von WettbergYves VigourouxXue LiuXin LiuPublished in: Nature genetics (2019)
We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.