Population genomic analysis unravels the repeated trait evolution after the centric origin of African cultivated rice.

Abstract

The origin of African cultivated rice (Oryza glaberrima) has been debated for over half a century, with many aspects of its domestication process remaining unclear. Through an extensive population analysis of 494 accessions, we found that African cultivated rice was initially domesticated from a subgroup of wild rice in Mali, supporting a centric model of origin. The genetic divergence between the cultivated rice and its wild progenitor was estimated to have occurred approximately 3,000 to 3,500 years BP, followed by a wide geographical expansion between 1,500 and 2,100 years BP. The non-shattering phenotype, a crucial domestication trait in cereal crops, was found to evolve repeatedly, probably at different times and locations. Similarly, we identified two genes (OgBh4 and OgPhr1) and six types of causal mutations responsible for the transition of hull colour, another important domestication trait, which were also repeatedly selected across different local groups. These findings shed new light on the evolutionary history of African cultivated rice and emphasize the significance of repeated trait evolution in crop domestication.