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.
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R.K.V. acknowledges the funding support from CGIAR Generation Challenge Programme, Department of Science and Technology Government of India under the Australia-India Strategic Research Fund, Ministry of Agriculture and Farmers Welfare, Government of India and Bill & Melinda Gates Foundation, USA. Shenzhen Municipal Government of China (grant no. JCYJ20150831201643396 and no. JCYJ20170817145512476 under the Basic Research Program) and the Guangdong Provincial Key Laboratory of Genome Read and Write (grant no. 2017B030301011) are acknowledged to provide support to X.X. and X.L. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of the CGIAR Consortium.