Ecology and Community Genomics of an Important Crop Wild Relative As a Prelude to Agricultural Innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, among the world’s most important pulse legumes, by conserving, characterizing and harnessing the diversity of wild crop relatives and their associated microbes. We document an extreme genetic bottleneck between modern breeding lines and the wild progenitor species, while also deciphering the genetic history of wild populations. We provide evidence of ancestral adaptations in wild populations for seed coat color crypsis and demonstrate variation between wild and cultivated accessions for agronomic properties including flowering time, seed shattering, seed nutrient density, nitrogen responsiveness, insect pest resistance and drought adaptation. The assembled germplasm will serve as an essential resource for future chickpea breeding, while our methods may inform collection of other wild crop progenitor species.