Extensive admixture and introgression shape genetic diversity and evolutionary adaptation in indigenous East Asian cattle

The complex introgression history of indigenous East Asian cattle is at the root of their remarkable diversity. Characterization of this diversity is a crucial step in understanding the genomic basis of adaptation to East Asian agricultural systems. However, the evolutionary history of indigenous East Asian cattle has remained poorly documented. Here, we present the largest short-read whole-genome sequencing dataset to date, including 802 indigenous Chinese cattle of 55 breeds/populations from diverse geographic regions, to address the population structure, genetic origins, and biological adaptations of this underrepresented population. We identify seven distinct genetic populations within Chinese cattle that were influenced by inter- and intraspecific introgression. We review introgression from Asian bovine species and reveal its geographical distribution characteristics in Chinese cattle. We identify a major taurine × indicine cattle admixture event during the Tang and Song dynasties (894–1210 AD ), which facilitated rapid local adaptation with a predominant effect on the immune system. Moreover, we present a comprehensive catalog of loci that underwent divergent selection across East Asian agroecological zones, including genes associated with cold tolerance, heat tolerance and meat production. Our findings indicate that admixture between taurine and indicine cattle, together with introgression from other Asian bovine species, contributed to the adaptive evolution of indigenous East Asian cattle.