Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds

Jiying Wang; Jicai Jiang; Haifei Wang; Huimin Kang; Qin Zhang; Jian-Feng Liu

doi:10.1371/journal.pone.0087571

Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds

PLoS One. 2014 Jan 27;9(1):e87571. doi: 10.1371/journal.pone.0087571. eCollection 2014.

Authors

Jiying Wang¹, Jicai Jiang², Haifei Wang², Huimin Kang², Qin Zhang², Jian-Feng Liu²

Affiliations

¹ Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ; Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
² Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Abstract

Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding / methods*
China
Comparative Genomic Hybridization / methods*
DNA Copy Number Variations / genetics*
Genome / genetics*
Real-Time Polymerase Chain Reaction / veterinary
Species Specificity
Sus scrofa / genetics*

Grants and funding

This work was financially supported by the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191), the National High Technology Research and Development Program of China (863 Program 2011AA100302, 2013AA102503), the National Natural Science Foundations of China (31272419) and the New-Century Training Program Foundation for the Talents by the State Education Commission of China (NETC-10-0783). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.