Genetic introgression between different groups reveals the differential process of Asian cultivated rice

The Asian cultivated rice consists of two major subspecies: indica and japonica. There are already many reports about the existence of genetic introgression between the two subspecies. They propose some possible introgression-related genes from the comparison of population parameters. This study uses the genome-wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica populations. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions, they generally get consistent results. Some previously known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays a vital role in the determination of both the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and the domestication process.