Copy number variants selected during pig domestication inferred from whole genome resequencing

Abstract

Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (~30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

“…Vasoactive intestinal peptide receptor 2 (VIPR2), a transmembrane glycoprotein, was selected in this study. The VIPR2 was found as selected in pigs in our previous study [30]. In humans, VIPR2 plays an important role in controlling fat deposition [68]; in mice, VIPR2-knockout results in growth inhibition, decreased fat mass, and increased lean mass [69]; and in pigs, VIPR2 is associated with feeding efficiency [70].…”

“…These genotypes were used to calculate the allele frequency of each CNV locus. The genetic differentiation of the two populations based on CNVs was calculated using the "-weir-fst-pop" in VCFtools [27] with the fixation index (Fst) method [28], which is a widely used statistic in CNV studies [29,30]. The value of Fst ranged from 0 to 1.…”