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Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip
Author(s) -
Wang Yuan,
Zhang Tingrong,
Wang Chuduan
Publication year - 2020
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12435
Subject(s) - biology , copy number variation , genome , genetics , bovine genome , genotyping , autosome , snp genotyping , genome wide association study , snp array , structural variation , comparative genomic hybridization , gene , computational biology , single nucleotide polymorphism , genotype , chromosome
Abstract Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome‐wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.