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

Abstract

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.

Population dynamics of potentially harmful haplotypes: a pedigree analysis

“…Furthermore, since genetic features such as Copy Number Variations (CNV) have been shown to cause calling errors giving wrong SNP alleles [ 27 ], the LB identified were overlapped, using BedTools as well, with 344 CNV regions previously identified in the Gochu Asturcelta pig population (see Supplementary Table S5 of Arias et al [ 37 ]).…”