Genome Diversity and Domestication in African Rice: A Genome-Wide Analysis By High-Depth Sequencing of Wild and Cultivated African Rice

African rice, Oryza glaberrima, and Asian rice, Oryza sativa, have independent domestication processes. O. glaberrima is thought to have been domesticated in West Africa from the wild progenitor Oryza Barthii. Asian rice was introduced from the 16^th century and has partly replaced O. glaberrima.

To gain insight into the rice domestication process in Africa, we re-sequenced a unique dataset of 162 cultivated and 87 wild accessions. This sequencing was performed at a high depth with a 35x mean coverage. This high-quality sequencing allowed to identify 5.537.879 high-quality single-nucleotide polymorphisms (SNPs). Strong population structure was observed between the wild accessions, while structure was much lower in the cultivated group. We identified strong domestication-selective sweeps. Finally, approximate bayesian analysis and spatial modeling were performed to understand where and when domestication occurred and how the domesticated crops have spread. We identified both a strong bottleneck associated with the domestication, and a recent crash in the cultivated population certainly associated with the replacement of cultivated African rice by Asian rice.

The final output of this study provides genome-wide variations for wild and cultivated African rice useful for the identification of new genes and for the development of genome-wide association studies. Such resources will help speed up rice improvement in Africa.