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A genome‐wide association study of copy number variations with umbilical hernia in swine
Author(s) -
Long Yi,
Su Ying,
Ai Huashui,
Zhang Zhiyan,
Yang Bin,
Ruan Guorong,
Xiao Shijun,
Liao Xinjun,
Ren Jun,
Huang Lusheng,
Ding Nengshui
Publication year - 2016
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.12402
Subject(s) - copy number variation , biology , snp , single nucleotide polymorphism , genetics , snp array , inguinal hernia , gene , genome , hernia , genotype , medicine , surgery
Summary Umbilical hernia ( UH ) is one of the most common congenital defects in pigs, leading to considerable economic loss and serious animal welfare problems. To test whether copy number variations ( CNV s) contribute to pig UH , we performed a case–control genome‐wide CNV association study on 905 pigs from the Duroc, Landrace and Yorkshire breeds using the Porcine SNP 60 BeadChip and penncnv algorithm. We first constructed a genomic map comprising 6193 CNV s that pertain to 737 CNV regions. Then, we identified eight CNV s significantly associated with the risk for UH in the three pig breeds. Six of seven significantly associated CNV s were validated using quantitative real‐time PCR . Notably, a rare CNV ( CNV 14:13030843–13059455) encompassing the NUGGC gene was strongly associated with UH (permutation‐corrected P = 0.0015) in Duroc pigs. This CNV occurred exclusively in seven Duroc UH‐affected individuals. SNP s surrounding the CNV did not show association signals, indicating that rare CNV s may play an important role in complex pig diseases such as UH . The NUGGC gene has been implicated in human omphalocele and inguinal hernia. Our finding supports that CNV s, including the NUGGC CNV , contribute to the pathogenesis of pig UH .