Date of this Version
Anderson, Rebecca. Copy Number Variation in the Porcine Genome Detected from Whole-Genome Sequence. University of Nebraska-Lincoln. 2018.
Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace) and 48 sows (Yorkshire-Landrace composites) for a total of 72 swine animals. Copy number variations were identified and analyzed using next generation sequencing and bioinformatics software. A total of 4566 copy number variations regions (CNVRs) were discovered in this study, covering 3.02% of the swine genome. A total of 593 genes were overlapped by CNVRs. These genes were further analyzed to determine function and relevance. Enrichment analysis determine function of CNVRs included sensory perception of smell (OR4D10), G-protein coupled receptor signaling pathway, cellular response to stimulus, and cell communication Quantitative trait loci (QTL) that were discovered included carcass weight (hot), average daily gain, fat-to-meat ratio, estimated carcass lean content, and birth weight.