Whole-genome sequencing reveals genomic diversity and selection signatures in Xia’nan cattle

作者：Xingya Song, Zhi Yao, Zijing Zhang, Shijie Lyu, Ningbo Chen, Xingshan Qi, Xian Liu, Weidong Ma, Wu-Sheng Wang, Chuzhao Lei, Yu Jiang, Eryao Wang, Yongzhen Huang · 发表于：BMC Genomics · 年份：2024 · DOI：10.1186/s12864-024-10463-3 · 被引用次数：18 · 研究领域：Genetic and phenotypic traits in livestock、Genetic Mapping and Diversity in Plants and Animals、Livestock Farming and Management

Abstract Background The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia’nan cattle, a crossbreed of Charolais and Nanyang cattle, is China’s first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia’nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia’nan cattle using whole-genome sequencing data from 30 Xia’nan cattle and 178 published cattle genomic data. Result The ancestry estimating composition analysis showed that the ancestry proportions for Xia’nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia’nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia’nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes ( F ST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the...