Copy Number Variation in the Cattle Genome

Authors: Liu, Ge - George; Bickhart, Derek

Submitted to: Functional and Integrative Genomics
Publication Type: Review Article
Publication Acceptance Date: 6/18/2012
Publication Date: 7/13/2012
Citation: Liu, G., Bickhart, D.M. 2012. Copy Number Variation in the Cattle Genome. Functional and Integrative Genomics. DOI: 10.1007/S10142-012-0289-9.

Interpretive Summary: Copy number variation (CNV) is abundant in livestock, differing from SNPs in extent, origin and functional impact. This book chapter reviews the current status of cattle CNV studies, advocates for CNV documentation standards and provides insights into future directions. Farmers, Scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this chapter.

Technical 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.