A selective genotyping approach identifies copy number variants associated with backfat thickness in Italian Large White pigs.

Copy number variants (CNVs) are a major source of genetic variability in mammalian genomes. CNVs are involved in many human disorders, including obesity. For several biological reasons pig could be a biomedical model for human obesity and associated diseases. Fat deposition is a key process with practical and economical implications in pig breeding. This trait determines carcass value and consumers’ acceptance of pork. In this study we applied a selective genotyping approach to identify CNVs associated with backfat thickness (BFT) in Italian Large White pigs. Pigs with extreme and divergent estimated breeding values (EBVs) for BFT were selected among a performance-tested population of ≈12,000 animals and genotyped with the Illumina PorcineSNP60k Beadchip. CNVs were called using pennCNV using strict criteria. Fifteen copy number variation regions (CNVRs) (in at least 4 pigs) were present only in the positive BFT-EBV group whereas 12 CNVRs were reported only in the negative BFT-EBV tail. Other CNVRs differed in frequency (P < 0.05) between the tails. Identified CNVRs include genes involved in fat metabolism, growth regulation, immune system, and neuronal regulation of eating behavior. These results provide additional insights into mechanisms affecting fat deposition in pigs