Genetic Diversification and Population Admixture Signatures in Yunnan Native Cattle

Area of Science:

• Genomics
• Animal Genetics
• Evolutionary Biology

Background:

• Yunnan native cattle (YNC) are vital indigenous bovine genetic resources in Southwest China.
• Understanding their genetic diversity and adaptive differentiation is crucial for conservation and breeding strategies.

Purpose of the Study:

• To investigate the genetic diversity, population structure, and adaptive differentiation of YNC using whole-genome SNP data.
• To identify candidate genes associated with local adaptation, including climate and trait-specific adaptations.

Main Methods:

• Whole-genome SNP data analysis of 457 individuals from eight YNC populations and two related species.
• Population structure analysis, genome-wide selective sweep scans, and balancing selection analyses.
• Identification of candidate genes related to cold tolerance, heat stress, milk traits, and high-altitude adaptation.

Main Results:

• A distinct latitudinal gradient in genetic diversity was observed, with higher diversity in northern populations.
• Population structure correlated with geographic distribution, revealing complex admixture patterns.
• Candidate genes like GRIA4, DUOXA2, ST3GAL3, MST1, MGST1, SLC36A1, and SLIT3 were identified for various adaptive traits, including cold/heat tolerance and milk production.
• Historical introgression from Zhongdian yak into Diqing cattle was detected, with SLIT3 implicated in high-altitude adaptation.

Conclusions:

• The study provides a comprehensive genomic framework for YNC.
• Genomic insights support targeted management and conservation of these valuable indigenous bovine resources.
• Adaptive differentiation and introgression highlight the evolutionary history and potential of YNC populations.