Landscape genomics highlights the adaptive evolution of chickpea

The structure of crop genetic diversity reflects spatial and ecological variations caused by population dynamics during adaptation to different agricultural environments. Landscape genomics can reveal patterns of neutral and adaptive variation related to environmental and spatial heterogeneity. We assembled a collection of 532 chickpea accessions and genotyped them by whole-genome sequencing. We then assessed their genetic diversity and population structure and coupled these data to environmental variables. We applied redundancy analysis as a multivariate landscape genomics method to describe the distribution of genetic diversity according to spatial and environmental factors. Environmental and geographic factors played a key role in the diversification of chickpea germplasm. We also identified a set of candidate adaptive loci, which were enriched for genes mainly involved in responses to abiotic stress factors such as heat and drought. Our study provides new insight into the evolution, dispersal and adaptation of chickpea to different agricultural environments, and will also facilitate the efficient use of genetic resources in gene discovery and breeding programs.