Abstract
Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.
Highlights
One of the important challenges in post-genomic biology is relating observed phenotypic variation to the underlying genotypic variation
The purpose of this study is to identify and characterize Copy number variations (CNVs) regions detected from whole-genome sequence of 240 members of an experimental swine herd at the U.S Meat Animal Research Center (USMARC), a resource representative of commercial swine germplasm, utilizing the newly released, highquality Sscrofa 11.1 genome assembly
When generating our sequence data, we targeted a minimum of 3× coverage for each of the founding sows and 10× coverage for the remaining 168 animals
Summary
One of the important challenges in post-genomic biology is relating observed phenotypic variation to the underlying genotypic variation. Genome-wide association studies (GWAS) have made thousands of connections between single-nucleotide polymorphisms (SNPs) and phenotypes, implicating regions of the genome that may play a causal role in a variety of complex traits. Despite their success in identifying associated variants, association studies account for only a small percentage of the total heritability (Maher, 2008). Significant overlap between protein-coding genes and CNV has been reported in a number of species, including human (Bailey et al, 2009), mouse (Locke et al, 2015), cattle (Keel et al, 2016b), and pig (Paudel et al, 2013). CNVs appear to influence gene expression levels (Stranger et al, 2007; Henrichsen et al, 2009)
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