Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays

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Date: July 23, 2013
From: PLoS ONE(Vol. 8, Issue 7)
Publisher: Public Library of Science
Document Type: Article
Length: 5,427 words
Lexile Measure: 1560L

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Author(s): Jiying Wang 1,2, Haifei Wang 1, Jicai Jiang 1, Huimin Kang 1, Xiaotian Feng 1, Qin Zhang 1, Jian-Feng Liu 1,*

Introduction

Copy number variations (CNVs) are gains and losses of genomic sequence greater than 50 bp between two individuals of a species [1], [2]. The milestone work by Iafrate et al. and Sebat et al. 2004 [3], [4] firstly revealed CNVs distribute ubiquitously in the human genome. Since then, thousands of novel CNVs were detected in the human genome [5], [6], [7]. Compared with the most frequent SNP marker, CNVs cover wider genomic regions in terms of total bases involved and have potentially larger effects by changing gene structure and dosage, alternating gene regulation, exposing recessive alleles and other mechanisms [8], [9]. As an important form of genetic variation, CNVs are becoming an important source of genetic variance [10] and may account for some of the missing heritability for complex traits [11].

In domestic animals, phenotype variations caused by CNVs were also observed, for instance, the white coat phenotype in pigs caused by the duplication of the KIT gene [12], [13], the pea-comb phenotype in chickens caused by the copy number alteration in intron 1 of the SOX5 gene [13] and hair greying and melanoma in horses caused by a 4.6-kb duplication in intron 6 of STX17 [14]. Additionally, the study by Seroussi et al. [15] showed there were significant associations between the loss of this region and total merit, and between copy number of this region with the genetic evaluations for protein production, fat production and herd life. These findings demonstrate that CNVs can be considered as promising markers for some phenotypic and economically important traits or diseases in domestic animals.

Different methodologies can be applied to identify or genotype CNVs at a genome-wide scale. So far, there are three main approaches: array comparative genomic hybridization (aCGH), SNP genotyping array and high-throughput sequencing [16], [17]. Among these technologies, the SNP genotyping array has the advantage of performing both genome-wide association studies (GWAS) and CNV detection. SNP arrays can simultaneously measure both total signal intensity (Log R ratio - LRR) and allelic intensity ratios (B allele frequency - BAF) in a genomic sample, and allows both DNA copy number and copy-neutral LOH to be assessed [18]. Additionally, SNP arrays use less sample per experiment compared to aCGH, and it is a cost effective technique which allows users to increase the number of samples tested on a limited budget [19].

As one of the most economically important livestock worldwide, pig also represents one of the most important research models for various human diseases [20]. In the past few years, many efforts have been used to detect CNVs in pig genome using different technological platforms, i.e. , aCGH [21], [22], PorcineSNP60 BeadChip [23], [24], [25] and high-throughput sequencing [26]. Previous CNV studies in other species at genome scale suggest that CNVs comprise up to ~12%, 4% and 4.6% of human [5], dog [27] and cattle [28] genome sequence, respectively. Compared with...

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Gale Document Number: GALE|A478148509