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Copy number variation in the cattle genome

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Abstract

Copy number variations (CNVs) are gains and losses of genomic sequence greater than 50 bp between two individuals of a species. While single nucleotide polymorphisms (SNPs) are more frequent, CNVs impact a higher percentage of genomic sequence and have potentially greater effects, including the changing of gene structure and dosage, altering gene regulation and exposing recessive alleles. In particular, segmental duplications (SDs) were shown to be one of the catalysts and hotspots for CNV formation. Substantial progress has been made in understanding CNVs in mammals, especially in humans and rodents. CNVs have been shown to be important in both normal phenotypic variability and disease susceptibility. Recently, interest in CNV study has extended into domesticated animals, including cattle. Multiple genome-wide cattle CNV studies have been carried out using both microarray and next generation sequencing technologies. Integration of SD and CNV results with SNP and other datasets are beginning to reveal impacts of CNVs on cattle domestication, health, and production traits.

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Acknowledgments

G.E.L. was supported by NRI/AFRI grants no. 2007-35205-17869 and 2011-67015-30183 from the USDA CSREES (now NIFA) and Project 1265-31000-098-00 from USDA-ARS. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

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  1. Bovine Functional Genomics Laboratory, USDA-ARS, ANRI, Beltsville, MD, 20705, USA

    George E. Liu & Derek M. Bickhart

  2. GEL: Bovine Functional Genomics Laboratory, USDA-ARS, Building 200, Room 124B, BARC-East, Beltsville, MD, 20705, USA

    George E. Liu

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Liu, G.E., Bickhart, D.M. Copy number variation in the cattle genome. Funct Integr Genomics 12, 609–624 (2012). https://doi.org/10.1007/s10142-012-0289-9

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