Enhancing Genome-Wide Copy Number Variation Identification by High Density Array CGH Using Diverse Resources of Pig Breeds

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Date: Jan. 27, 2014
From: PLoS ONE(Vol. 9, Issue 1)
Publisher: Public Library of Science
Document Type: Article
Length: 5,314 words
Lexile Measure: 1650L

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

Introduction

Pigs have been one of the most economically important livestock worldwide for over 10,000 years as an important animal supplying meat [1]. Pigs are also closely related to humans in terms of anatomy, genetics and physiology, and represent an excellent animal model to study various human diseases [2], [3]. Because of the economic and medical importance of pigs, the Swine Genome Sequencing Consortium (SGSC) has decoded swine whole-genomic information. The porcine genome consists of 18 autosomes and sex chromosomes with a genome size estimated to be around 2.8 Gbp and a minimum of 21,640 protein-coding genes involved [4]. The completion of porcine genome and its annotation, together with chips and high throughput sequencing technologies, make it possible to study the genomic variations in-depth.

So far a wide range of genomic variations have been found existing across genome, from single nucleotide polymorphisms (SNPs) to structure variations with sizes ranging from kilobases (Kb) to megabases (Mb). As a major form of genomic variations, copy number variations (CNVs) are defined as gains and losses of genomic sequence greater than 50 bp between two or more individuals of a species [5], [6]. Compared with the most frequent polymorphisms of SNPs, 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 [7], [8]. In humans, since the milestone works by Iafrate et al. and Sebat et al. 2004 [9], [10], CNVs have attracted extensive attentions and 109,863 CNVs have been identified (http://dgv.tcag.ca/dgv/app/, July 2013). Studies in domestic animals have shown that a suite of genes with copy number alteration were found contributing to variation of either phenotypic variability or disease susceptibility, such as the KIT gene for white coat phenotype in pigs [11], SOX5 gene for the pea-comb phenotype in chickens [12], STX17 gene for hair greying and susceptibility to melanoma in horses [13]. Additionally, the study by Seroussi et al. [14] indicated there were close associations between CNVR, located on BTA18, and index of total merit and genetic evaluations for protein production, fat production and herd life in Holstein cattle.

Using different technological platforms, substantial progress has been made in identifying CNVs in pigs. For example, based on Porcine SNP60 BeadChip and aCGH, Ramayo-Caldas et al. [15], Wang et al. [16], [17], Chen et al.[18], Fadista et al. [19] and Li et al.[20] identified hundreds of CNVRs. Recently, based on genome re-sequencing, Rubin et al. [21] and Paudel et al. [22] also detected a large amount of CNVs. However, compared to humans and other model organisms, relatively few studies have investigated CNVs in pigs and little is known about how CNVs contribute to normal phenotypic variation and to disease susceptibility in this species. Findings from previous studies also indicate that besides the platforms employed in CNV detection, a considerable proportion of CNVs segregate...

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Gale Document Number: GALE|A478845427