Copy number variants in Italian Large White pigs detected using high‐density single nucleotide polymorphisms and their association with back fat thickness

Summary The aim of this study was to identify copy number variants ( CNV s) in Italian Large White pigs and test them for association with back fat thickness ( BFT ). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values ( EBV s; 147 with negative and 150 with positive EBV s) were genotyped with the Illumina Porcine SNP 60 BeadChip. CNV s were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions ( CNVR s) located on 15 porcine autosomes. Validation of detected CNVR s was carried out (i) by comparing CNVR s already detected by other studies and (ii) by semiquantitative fluorescent multiplex ( SQFM ) PCR of a few CNVR s. Most of CNVR s detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR . For each CNVR , we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P  <   0.10, and seven were significant at P  <   0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNV s could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVR s encompassed the ZPLD 1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNV s in pigs could assist in elucidating the genetic mechanisms underlying human obesity.