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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #326502

Research Project: Genetic and Genomic Approaches to Improve Swine Reproductive Efficiency

Location: Livestock Bio-Systems

Title: Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

item Keel, Brittney
item Snelling, Warren
item Keele, John

Submitted to: International Society for Animal Genetics (ISAG)
Publication Type: Abstract Only
Publication Acceptance Date: 4/22/2016
Publication Date: 7/23/2016
Citation: Keel, B.N., Snelling, W.M., Keele, J.W. 2016. Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 83 (Abstract # P4008).

Interpretive Summary:

Technical Abstract: Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, are known to be associated with both diseases and phenotypic traits. Deeply sequenced genomes are often used to identify CNV, but deep sequence is too expensive to collect on many individuals. The random variation in coverage that occurs with current sequencing methods may make low coverage sequence unsuitable for CNV detection. A more complete catalog of important CNV might be obtained from low coverage sequence from several individuals if approaches capable of detecting CNV in low coverage sequence can be identified. Benchmark CNV data sets were simulated and used to test the performance of three modern CNV detection algorithms at varying levels of coverage. Comparison of the three methods determined that a multiple sample read depth approach is most suitable for detecting CNV in low coverage genomic sequence. As part of an effort to identify DNA sequence variation that affects beef cattle performance, this method was applied to low coverage DNA sequence from 154 influential bulls in the U.S. Meat Animal Research Center Germplasm Evaluation (GPE) project. These bulls were purebred sires sampled from seven popular beef breeds in the U.S. (Angus, Hereford, Simmental, Limousin, Charolais, Gelbvieh, and Red Angus). Sequence reads were mapped to the current bovine genome assembly; a mean of 2.9-fold coverage per bull was obtained. 1,532 copy number variable regions (CNVRs) were detected, with each being present in at least 8 different bulls. These CNVRs covered approximately 7% of the bovine genome and overlapped 2,004 protein-coding genes. A larger than expected number of genes involved in immune system processes were affected by CNV. In addition, CNV were shown to overlap several known regions of DNA that correlate with variation in cattle phenotype. Further investigation is needed to assess how much influence the coding sequence CNVs identified from this work might have on cattle performance.