Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.

Yanan Wang,Hongyang Wang,Zhonglin Tang,Bin Fan,Jing Liu,Yu Zhang,Bang Liu,Shaobo Yu,Kui Li,Chao Wang,Yaqi Sun,Marinus Fw Te Pas

doi:10.1371/journal.pone.0106780

Yanan Wang, Hongyang Wang + Show 10 more

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https://doi.org/10.1371/journal.pone.0106780

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Abstract

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.

Highlights

Copy number variations (CNVs) refer to the structurally genomic variations from hundreds of bases to several kilo-bases and the relevant complex mutations in the construction of chromosomes
The comparative genomic hybridization (CGH) based approach and high-throughput sequencing have excellent performance in refined resolution and relative signal intensities, while the SNP genotyping array has the advantage in both genome-wide association studies (GWAS) and CNV detection
SNP arrays have been routinely used for CNV detection in humans and other organisms, and manufacturers of SNP genotyping arrays have incorporated nonpolymorphic markers into their arrays to improve the coverage of SNP arrays for CNV analysis [27]

Summary

Introduction

Copy number variations (CNVs) refer to the structurally genomic variations from hundreds of bases to several kilo-bases and the relevant complex mutations in the construction of chromosomes. We analyzed the difference in CNVs between Chinese indigenous breeds and western breeds by using Porcine SNP60 BeadChip and PennCNV algorithm, and performed a genome-wide CNV detection in 302 pigs from six Chinese indigenous breeds, three European breeds and one hybrid. PennCNV was used for CNV identification by integrating a Hidden Markov Model (HMM) for high resolution copy number variation detection with whole-genome SNP genotyping data [38]. This algorithm incorporates multiple sources of information, including total signal intensity data of log R Ratio (LRR) and B allele frequency (BAF) at each SNP marker, the distance between neighboring SNPs, the population frequency of B allele (PFB) of SNPs, and the pedigree information where available. Statistical significance was assessed by using P value of a modified Fisher’s exact test and Benjamini correction for multiple testing

Ethics Statement

Results and Discussion

Conclusions