Trios-based inquiry into <i>de novo</i> copy number variants in the swine genome

Abstract Copy number variation (CNV) plays an important role in determining multiple phenotypic traits due to these large genomic segments having the potential to disrupt functionally important genomic regions. The current study investigated the prevalence, distribution, and functional impacts of de novo CNVs in swine genomes and compared them with those that were inherited. CNV patterns showed high similarity within nuclear families, indicating that most CNVs are inherited, yet 9% arose de novo and contributed to individual variation. The underlying systematic pattern indicated that de novo deletions are shorter than inherited ones, which has essential meaning, especially for functionally important genomic locations. Moreover, de novo deletions were not uniformly distributed along the genome, forming clusters. Despite the potentially more severe impact of deletions, more de novo deletions than duplications were present in offspring genomes. The highest CNV-QTL (quantitative trait loci) overlap was found for teat number, reflecting strong selection for this trait. Overlaps also occurred in key reproductive and production traits. Multiple CNVs in the same gene may suggest regions prone to structural variation, as seen in testis-expressed 14 ( TEX14 ), linked to pig infertility, and as parkin RBR E3 ubiquitin protein ligase ( PRKN ), a known CNV hotspot in humans. Deletions were primarily located in introns, with no significant enrichment of the Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. De novo duplications mainly affected genes related to environmental interactions, such as the immune response and olfactory receptors.