An atlas of CNV maps in cattle, goat and sheep

Abstract

Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31822052, 31572381) and the National Thousand Youth Talents Plan, and the Program of the National Beef Cattle and Yak Industrial Technology System (CARS-37). We thank the High-Performance Computing platform of Northwest A&F University. We thank Yu Wang, Xiangyu Pan, Ming Li, Xiaomeng Tian, Dongke Zhou, Zhirui Yang, Han Xu, Chunna Cao and other members of the genome of big data laboratory for discussions. We also thank members of the NextGen project for sharing their data.

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Correspondence to Yu Jiang.

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The author(s) declare that they have no conflict of interest. Animal care and the experiments were conducted according to the guidelines established by the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004) and approved by the Institutional Animal Care and Use Committee (College of Animal Science and Technology, Northwest A&F University, China). Every effort was made to minimize animal pain, suffering, and distress and to reduce the number of animals used.

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Huang, Y., Li, Y., Wang, X. et al. An atlas of CNV maps in cattle, goat and sheep. Sci. China Life Sci. (2021). https://doi.org/10.1007/s11427-020-1850-x

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Keywords

  • copy number variation
  • species-shared
  • balancing selection
  • ruminant livestock