The Origin and Domestication History of African Rice (Oryza glaberrima)

Oryza glaberrima is an African cultivated rice species that independently domesticated from its wild progenitor O. barthii around 3,000 years ago. O. glaberrima was characterized for resistance to biotic and abiotic stresses, which can be used as source of donor resistant genes in rice breeding. In contrast to Asian cultivated rice O. sativa, the domestication and selection processes of O. glaberrima remains largely unknown.

In order to identify the domestication history and origin of O. glaberrima, we generated genome sequences from 94 geographically diverse O. barthii and 20 O. glaberrima accessions to construct a comprehensive genome variation map of African rice. Oryza glaberrima contains substantially reduced genetic variations compared to O. barthii, which indicated severe genetic bottleneck during domestication. Population genetics and molecular evolution analyses identified four subgroups as well as one admixed subgroup in O. barthii accessions (from Ob-I to Ob-V). In-depth population genetic analyses between O. glaberrima and O. barthii revealed that O. glaberrima was first domesticated from Ob-V. Combined with biogeographic analysis, we determined that O. glaberrima was domesticated near the Niger River delta in West Africa. The genome wide analysis of introgression and analysis of some domestication genes provided strong evidence of independent domestication of O. glaberrima. In search of selective signatures that related to domestication process, we identified a large number of genomic regions that experienced selective sweeps in O. glaberrima during domestication. Our comprehensive genome wide analyses provide the genetic evidence of domestication history, independent domestication and domestication center of O. glaberrima.