Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds.