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

• Published in: BMC genomics Vol. 13; no. 1; p. 733
• Main Authors: Chen, Congying, Qiao, Ruimin, Wei, Rongxing, Guo, Yuanmei, Ai, Huashui, Ma, Junwu, Ren, Jun, Huang, Lusheng
• Format: Journal Article
• Language: English
• Published: London BioMed Central 27.12.2012; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Animal Genetics and Genomics; Animal populations; Animals; Biomedical and Life Sciences; Biotechnology industry; Body Composition - genetics; Body Size - genetics; Body weight; Breeding - methods; Carcasses; China; chromosome 6; Chromosomes; Complex trait; copy number; Copy number variable gene; Copy number variation; Copy number variations; DNA Copy Number Variations - genetics; Gene expression; Gene mapping; Genes; Genetic aspects; Genetic Association Studies; Genetics; Genetics, Population; Genomes; Genomics; Genotype; Glycolysis; Hemoglobin; Hot spots; Humerus; Life Sciences; Linear Models; Mammals; Mice; Mice, Knockout; Microarrays; Microbial Genetics and Genomics; Molecular Sequence Annotation; Muscles; Mutation; Non-human and non-rodent vertebrate genomic; Phenotype; Pig; Plant Genetics and Genomics; Polymerase chain reaction; Proteins; Proteomics; QTL; Quantitative genetics; Quantitative trait loci; Quantitative Trait Loci - genetics; Real-Time Polymerase Chain Reaction; Research Article; Species Specificity; Surveys; Swine; Swine - genetics; China; United States; QTL; Complex trait; Copy number variation; Copy number variable gene; Pig
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-13-733

Background Copy 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. Result Here 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 F 2 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. Conclusion We 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.