A Comprehensive Survey Of Copy Number Variation In18Diverse Pig Populations And Analysis Of Its Association With Gene Expression And Complex Traits

Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike human, rat or mice genome where CNVs have been well annotated, studies of porcine CNV are still limited. To our knowledge, the investigation of CNV effects on global gene expression and phenotypic traits remains unexplored in pigs.Here we used Porcine SNP60BeadChip and PennCNV algorithm to identify1,243putative CNVs belonging to341CNV regions (CNVRs) in1,557pigs from18diverse populations. Quantitative real time PCR confirmed76.9%of randomly selected CNVRs. We found that the CNVRs were non-randomly distributed in the pig genome. Among the341CNVRs,27overlapped with recombination hotspots, and492genes out of1,340transcripts located within the CNVRs have been reported to be copy number variable genes in the human genome. We analyzed the association of CNV variants with gene expression levels and identified1,266and741significant associations targeting969and537distinct transcripts including52and48cis-eQTLs in liver and muscle, respectively. We observed an obvious enrichment of SNP-based eQTLs within CNVRs. An enrichment of trait-associated SNPs was also detectedwithin CNVRs where total243significant QTLs for118traits were located within85CNVRs.In conclusion, we revealed the distribution of the unprecedented number of341CNVRs in pig genome and detected the association of CNVs with gene expressionand phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to further elucidate the regulating mechanisms of CNV on gene expression and to facilitate the identification of trait-related CNVs.