Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Rajeev Varshney, Mahendar Thudi, Manish Roorkiwal, Weiming He, Hari D. Upadhyaya, Wei Yang, Prasad Bajaj, Philippe Cubry, Abhishek Rathore, Jianbo Jian, Dadakhalandar Doddamani, Aamir Khan, Garg Vanika, Annapurna Chitikineni, Dawen Xu, Pooran Gaur, Narendra Pratap Singh, Sushil k. Chaturvedi, NVPR Ganga Rao, Lakshmanan Krishnamurty, Girish Dixit, Asnake Fikre, Paul Kimurto, Sheshshayee Sreeman, Bharadwaj Chellapilla, Shailesh Tripathi, Jun Wang, Suk-Ha Lee, David Edwards, Polavarapu B. Kavi Kishor, R. Varma Penmetsa, Jose Crossa, Henry T. Nguyen, Kadambot H M Siddique, Timothy Colmer, Tim Sutton, Eric J. B. von Wettberg, Vigouroux Yves, Xun Xu, Xin Liu. (29/4/2019). Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics, 5(51), pp. 857-864.

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 dissection, accelerating genetic gains in future chickpea breeding.