Genomic Studies on the Origin, Hybridization and Dispersal of Asian Rice

The cultivated rice, Oryza sativa, originating from Asia, is one of the most important cereals and has been extensively studied over several decades. It has the smallest genome size among major cereals and was the first to construct a complete reference genome. Furthermore, genetic polymorphism data have been analyzed in numerous studies, focusing on the geographical origin and relationships between cultivated and wild species. The classification of Asian rice into two subspecies, Oryza sativa L. ssp. japonica and ssp. indica, is well established, and the elucidation of their genomic backgrounds has revealed intricate relationships between these two varietal groups. Despite advancements in the amount of data and analytical techniques, the mysteries surrounding the origin and domestication processes remain subjects of ongoing debate owing to the complexity of the genomic backgrounds. Moreover, several studies utilizing genomic data from over 1000 cultivated and wild rice samples, represented by the 3000 Rice Genomes Project, have initiated discussions regarding the dispersal history of regional populations, transitions of genomic backgrounds during domestication, and genome-wide scans for selection signatures. This paper provides an overview of the classification of rice varietal groups, controversies surrounding the origin and domestication processes of japonica and indica, and recent findings on population histories revealed by population genomic analyses.