Rice Genome Variations and Domestication Study

The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. The cultivated rice is considered to be domesticated from wild rice (Oryza rufipogon) thousands of years ago. The differences are reflected in a wide range of morphological and physiological traits.

We performed large-scale genome sequencing for analyzing genome-wide genetic variations to further understanding of rice gene functions in agronomic traits and for bridging the knowledge gap between genotype and phenotype in rice. We construct a comprehensive map of rice genome variation based on the genome sequences from geographically diverse accessions of the wild rice species O.rufipogon, and from indica and japonica varieties of O.sativa. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that O. sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in Southern China, and that O. sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into Southeast and South Asia. The domestication-associated traits are analyzed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.