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Copy number variants in Italian Large White pigs detected using high‐density single nucleotide polymorphisms and their association with back fat thickness
Author(s) -
Schiavo G.,
Dolezal M. A.,
Scotti E.,
Bertolini F.,
Calò D. G.,
Galimberti G.,
Russo V.,
Fontanesi L.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12180
Subject(s) - copy number variation , biology , autosome , genetics , single nucleotide polymorphism , bonferroni correction , exact test , white (mutation) , candidate gene , population , gene , genotype , chromosome , medicine , genome , statistics , mathematics , environmental health
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.