Genome-Wide Copy Number Variations Inferred from SNP Genotyping Arrays Using a Large White and Minzhu Intercross Population

Ligang Wang,Xiaojun Ma,Duxue Cheng,Xin Song,Longchao Zhang,Jing Liang,Kebin Zhao,Xin Liu,Hua Yan,Lixian Wang,Shaokang Chen,Weizhen Luo,Zongli Xu

doi:10.1371/journal.pone.0074879

Abstract

Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.

Highlights

The pig (Sus scrofa) is an economically important livestock worldwide and an ideal animal model for human disease research because its genome is similar in size and organization
copy number variant regions (CNVRs) were identified by the 4 programs (Table S1 in File S1)
By using the Porcine SNP60 Genotyping BeadChip and an F2 pig resource population, we identified 249 CNVRs and generated a powerful and comprehensive CNVR map of the pig genome

Summary

Introduction

The pig (Sus scrofa) is an economically important livestock worldwide and an ideal animal model for human disease research because its genome is similar in size and organization. Many studies have shown that CNVs play important roles in normal phenotypic variability and disease susceptibility [1,12,13,14,15,16,17,18]. They are considered promising markers for identifying economic- and disease-related traits in domestic animals [19]. Discovery (DAVID, http://david.abcc.ncifcrf.gov) [30], 7 Benjiamini correction, statistically significant Gene Ontology (GO) [31]

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Conclusion