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Open Access Highly Accessed Research article

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

Jicai Jiang1, Jiying Wang2, Haifei Wang1, Yan Zhang3, Huimin Kang1, Xiaotian Feng1, Jiafu Wang4, Zongjun Yin5, Wenbin Bao6, Qin Zhang1 and Jian-Feng Liu1*

Author Affiliations

1 National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

2 Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China

3 Virginia Bioinformatics Institute, Virginia Tech, Washington Street, Blacksburg, Virginia MC0477, 24061, USA

4 School of Animal Science, Guizhou University, Guiyang 550025, China

5 College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China

6 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China

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BMC Genomics 2014, 15:593  doi:10.1186/1471-2164-15-593

Published: 14 July 2014

Abstract

Background

Copy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs.

Results

Using whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection.

Conclusions

Our studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.

Keywords:
Copy number variations (CNVs); Segmental duplications (SDs); Next generation sequencing (NGS); Pigs