Population genomics elucidates the trajectory of chicken domestication from Asia to Japan

Chickens were domesticated over 4,000 years ago and are now the most popular poultry species in the world. In Japan, chickens are believed to have been first introduced around 2,000 years ago. Today, approximately 45 chicken breeds can be found in Japan, and they have unique and diverse phenotypic characteristics. However, their origins and histories have largely remained unexplored. Here, we newly sequenced whole genomes of 41 populations including 21 Japanese native chickens. By integrating them with published genomes to compile a total of 133 geographically comprehensive samples, we conducted population genomic analyses to elucidate the trajectory of their domestication from Asia to Japan. Our findings indicate that Japanese native chickens were derived from Southeast and East Asia, the centers of chicken domestication, through several separate events. The whole-genome phylogenetic analyses classified Japanese chickens into several groups and clarified the geographic origins of each group. These results provide new insights into the population structure, admixture history of Asian chicken breeds, and genomic trajectory of chickens from Asia to Japan.