Admixture and selection offer insights for the conservation and breeding of Guyuan cattle.

Background: The admixture between taurine and indicine cattle increases breed diversity and provides new genetic resources for human and natural selection. The climate of northwestern China is typified by cold and arid conditions, and cattle in this region are primarily taurine breeds. However, Guyuan cattle inhabit a transitional zone in northwestern China, typified by semi-arid and semi-humid climates. It is hypothesized that Guyuan cattle have a little of indicine ancestry. These results suggest that Guyuan cattle are a valuable genetic resource.

Results: We established a conservation population of Guyuan cattle in their native habitat. We found that Guyuan cattle were an admixture between 78.09% East Asian taurine (EAT) and 20.26% East Asian indicine (EAI) ancestries. The admixture in Guyuan cattle was dated to 255 years ago. Notably, we identified Guyuan cattle as a unique genetic resource, representing a transitional breed between northern and central Chinese cattle with distinct admixture proportions. We revealed that the selection signals in Guyuan cattle with excess EAT ancestry were associated with reproduction, immunity, body length, cold climate adaptation, pigmentation, muscle development, residual feed intake, and fat deposition and that the selection signals in Guyuan cattle with excess EAI ancestry were associated with disease resistance. Remarkably, we discovered valuable single nucleotide polymorphisms (SNPs) in the promoter regions of the RBM39 and NEK6 genes, which may play key roles in regulating muscle development and disease resistance.

Conclusions: Our results suggest that Guyuan cattle are a newly identified genetic resource, and the native taurine and indicine ancestries in Guyuan cattle remain a valuable genetic resource of conservation and breeding.