A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits

Abstract

BackgroundCopy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited.ResultHere we used Porcine SNP60 BeadChip and PennCNV algorithm to identify 1,315 putative CNVs belonging to 565 CNV regions (CNVRs) in 1,693 pigs from 18 diverse populations. Total 538 out of 683 CNVs identified in a White Duroc × Erhualian F2 population fit Mendelian transmission and 6 out of 7 randomly selected CNVRs were confirmed by quantitative real time PCR. CNVRs were non-randomly distributed in the pig genome. Several CNV hotspots were found on pig chromosomes 6, 11, 13, 14 and 17. CNV numbers differ greatly among different pig populations. The Duroc pigs were identified to have the most number of CNVs per individual. Among 1,765 transcripts located within the CNVRs, 634 genes have been reported to be copy number variable genes in the human genome. By integrating analysis of QTL mapping, CNVRs and the description of phenotypes in knockout mice, we identified 7 copy number variable genes as candidate genes for phenotypes related to carcass length, backfat thickness, abdominal fat weight, length of scapular, intermuscle fat content of logissimus muscle, body weight at 240 day, glycolytic potential of logissimus muscle, mean corpuscular hemoglobin, mean corpuscular volume and humerus diameter.ConclusionWe revealed the distribution of the unprecedented number of 565 CNVRs in pig genome and investigated copy number variable genes as the possible candidate genes for phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to facilitate the identification of trait-related CNVs.

Global copy number analyses by next generation sequencing provide insight into pig genome variation

“…We also compared CNVRs in this study with previous pig CNV studies [24, 25, 35, 36, 39, 41, 42]. After merging the results of recent reports, a total of 849 out of 3,131 CNVRs (27.75%) with the length of 33.02 Mb in our study overlapped with those previously reported (see Table 4).…”

Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

“…CNVRs that overlap with SDs are dominated by vomeronasal receptors and olfactory genes and are enriched for processes such as the sensory perception of taste, immune response, and G-protein coupled receptor signaling pathway (Supplemental Table S2). The association of CNVs with gene families involved in these processes has also been reported in other species and in inbred mouse strains Cutler et al 2007;Guryev et al 2008;She et al 2008;Chen et al 2009Chen et al , 2012Doan et al 2012). Genes in CNVRs that do not overlap with large SDs showed enrichment for terms related to a much broader spectrum of biological processes, such as protein modification, signaling, and ion transport (Supplemental Table S3).…”

Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

“…In addition, the OvineSNP50 BeadChip has fewer probes than other mamalian BeadChips, such as those of humans [42], cattle [43]and pigs [44], and some…”