Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Rajeev K. VarshneyInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Mahendar ThudiInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Manish RoorkiwalInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Weiming HeBGI-Shenzhen, Shenzhen, China , Hari D. UpadhyayaInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Wei YangBGI-Shenzhen, Shenzhen, China , |
Prasad BajajInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Philippe CubryInstitut de recherche pour le développement (IRD), Montpellier, France , Abhishek RathoreInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Jianbo JianBGI-Shenzhen, Shenzhen, China , Dadakhalandar DoddamaniInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , |
Aamir W. KhanInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India, The University of Western Australia (UWA), Crawley, Western Australia, Australia , Vanika GargInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India, Osmania University, Hyderabad, India , Annapurna ChitikineniInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Dawen XuBGI-Shenzhen, Shenzhen, China , Pooran M. GaurInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , Narendra P. SinghIndian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, India , |
Sushil K. ChaturvediIndian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, India, Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, India , Gangarao V.P.R. NadigatlaInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya , Lakshmanan KrishnamurthyInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India , G. P. DixitIndian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, India , |
Asnake FikreEthiopian Institute of Agricultural Research (EIAR), Debre Ziet, Ethiopia, Present address: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia , Paul K. KimurtoEgerton University, Njoro, Kenya , Sheshshayee M. SreemanUniversity of Agricultural Sciences-Bangalore, Bangalore, India , Chellapilla BharadwajICAR-Indian Agricultural Research Institute (IARI), Delhi, India , Shailesh TripathiICAR-Indian Agricultural Research Institute (IARI), Delhi, India , |
Jun WangBGI-Shenzhen, Shenzhen, China, iCarbonX, Shenzhen, China , Suk-Ha LeeSeoul National University, Seoul, South Korea , David EdwardsThe University of Western Australia (UWA), Crawley, Western Australia, Australia , Kavi Kishor Bilhan PolavarapuOsmania University, Hyderabad, India , R. Varma PenmetsaUniversity of California-Davis, Davis, CA, USA , |
Jose CrossaInternational Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico , Henry T. NguyenUniversity of Missouri, National Center for Soybean Biotechnology, Columbia, SC, USA , Kadambot H. M. SiddiqueThe University of Western Australia (UWA), Crawley, Western Australia, Australia , Timothy D. ColmerThe University of Western Australia (UWA), Crawley, Western Australia, Australia , Tim SuttonSouth Australian Research and Development Institute, Adelaide, Australia, University of Adelaide, Glen Osmond, Australia , |
Eric von WettbergUniversity of Vermont, Burlington, VT, USA , Yves VigourouxInstitut de recherche pour le développement (IRD), Montpellier, France , Xun XuBGI-Shenzhen, Shenzhen, China, China National Gene Bank (CNGB), Shenzhen, China , Xin LiuBGI-Shenzhen, Shenzhen, China, State Key Laboratory of Agricultural Genomics, Shenzhen, China |
*E-mail: r.k.varshney@cgiar.org, xuxun@genomics.cn, liuxin@genomics.cn
Abstract
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 dis-section, accelerating genetic gains in future chickpea breeding.