Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle

BACKGROUND: Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. RESULTS: We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. CONCLUSIONS: Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.