A genome‐wide association study of copy number variations with umbilical hernia in swine

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 .