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Background <p>Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N’Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds.</p> Results <p>Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from <i>Bos taurus</i> and <i>Bos indicus</i>. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1).</p> Conclusions <p>This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.</p>

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Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年2月28日

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  • Xiaoyun Wu,
  • Jie Pei,
  • Lin Xiong,
  • Qianyun Ge,
  • Pengjia Bao,
  • Chunnian Liang,
  • Ping Yan,
  • Xian Guo

摘要

Background

Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N’Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds.

Results

Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from Bos taurus and Bos indicus. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1).

Conclusions

This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.