Analysis of Population Structure and Selective Signatures for Milk Production Traits in Xinjiang Brown Cattle and Chinese Simmental Cattle

作者：Ke Ma, Xue Li, Shengchao Ma, Menghua Zhang, Dan Wang, Lei Xu, Hong Chen, Xuguang Wang, Aladaer Qi, Yifan Ren, Xixia Huang, Qiuming Chen · 发表于：International Journal of Molecular Sciences · 年份：2025 · DOI：10.3390/ijms26052003 · 被引用次数：3 · 研究领域：Genetic and phenotypic traits in livestock、Cancer-related molecular mechanisms research、Genetic Mapping and Diversity in Plants and Animals

This study aims to elucidate the population structure and genetic diversity of Xinjiang brown cattle (XJBC) and Chinese Simmental cattle (CSC) while conducting genome-wide selective signatures analyses to identify selected genes associated with milk production traits in both breeds. Based on whole-genome resequencing technology, whole-genome single nucleotide polymorphisms (SNPs) of 83 Xinjiang brown cattle and 80 Chinese Simmental cattle were detected to resolve the genetic diversity and genetic structure of the two populations, whole-genome selective elimination analysis was performed for the two breeds of cattle using the fixation index (Fst) and nucleotide diversity (θπ ratio), and enrichment analysis was performed to explore their biological functions further. Both breeds exhibited relatively rich genetic diversity, with the Chinese Simmental cattle demonstrating higher genetic diversity than Xinjiang brown cattle. The IBS and G matrix results indicated that most individuals in the two populations were farther apart from each other. The PCA and neighbor-joining tree revealed no hybridization between the two breeds, but there was a certain degree of genetic differences among the individuals in the two breeds. Population structure analysis revealed that the optimal number of ancestors was three when K = 3. This resulted in clear genetic differentiation between the two populations, with only a few individuals having one ancestor and the majority having two or three common a...