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 domesticated from a subgroup of wild rice in Mali, supporting a centric origin model. The genetic divergence between cultivated rice and its wild progenitor occurred approximately 3000-3500 years BP, followed by a wide geographical expansion 1500-2100 years BP. The non-shattering phenotype, a key domestication trait in cereals, was found to evolve repeatedly, likely at different times and locations. We also identified two genes (OgBh4 and OgPhr1) and six types of causal mutations responsible for the transition of hull color, another important domestication trait, and showed that these were also repeatedly selected across different local groups of rice accessions. These findings provide new insights into the evolutionary history of African cultivated rice and emphasize the importance of repeated trait evolution in crop domestication.