Study on the origin of Asian cultivated rice based on 15 domestication regions

Cultivated rice (Oryza sativa) is an important food crop worldwide, and its domestication is one of the most important events in human history. Common wild rice is the direct wild progenitor of cultivated rice, however its detailed process is still controversial. In this study, we systemically identified 15 domestication regions (DRs) in the rice genome using 461 wild and 595 cultivated rice accessions. Phylogenetic trees were constructed separately for the 15 DRs to analyze the closely affiliated wild accessions. We found that most of the closely affiliated wild accessions of temperate japonica came from southern China, and most of the closely affiliated wild accessions of tropical japonica came from China and India. Wild populations in southern China and India are the source of the temperate japonica and tropical japonica gene pools (that is, the sum of the genes carried by all wild individuals in southern China and India). In addition, most of the closely affiliated wild accessions of indica rice came from Southeast Asia, China and India, suggesting that wild populations in Southeast Asia, China and India are the source of the indica gene pools. Interestingly, wild populations in India and Burma are the source of the Aus and Bas gene pools, respectively. Our results will help to further clarify the origin and domestication history of Asian cultivated rice.

Automated summary

In this study, 15 domestication regions (DRs) in the rice genome were identified using wild and cultivated rice accessions. The closely affiliated wild accessions of temperate japonica came mainly from southern China, while those of tropical japonica came from China and India. Similarly, the closely affiliated wild accessions of indica rice came from Southeast Asia, China, and India. The results provide valuable insights into the origin and domestication history of Asian cultivated rice.