Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes

Simple Summary Copy number variations (CNVs) are a substantial fraction of the total genetic variability and have a major effect on phenotypic performance by altering gene expression patterns. However, the identification of CNVs remains challenging. Recent studies suggest that CNVs hardly fit with Mendelian segregation patterns and can be classified as segregating (shared by parents and offspring) and non-segregating. Both CNV classes have been hypothesized to be important in explaining between-populations (segregating CNVs) and between-individuals (non-segregating CNVs) differences in performance. Here, we report that the two CNV classes spanned different sets of genes, thus supporting that theory. Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance.