title: A genome-wide association study of copy number variations with umbilical hernia in swine.
abstract: 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 (CNVs) 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 SNP60 BeadChip and penncnv algorithm. We first constructed a genomic map comprising 6193 CNVs that pertain to 737 CNV regions. Then, we identified eight CNVs significantly associated with the risk for UH in the three pig breeds. Six of seven significantly associated CNVs were validated using quantitative real-time PCR. Notably, a rare CNV (CNV14:13030843-13059455) 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. SNPs surrounding the CNV did not show association signals, indicating that rare CNVs 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 CNVs, including the NUGGC CNV, contribute to the pathogenesis of pig UH.
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Long
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Su
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Huashui
authors.initials: H
authors.lastname: Ai
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Zhiyan
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.|Fujian Vocational College of Agriculture, Fuzhou, 360119, China.
authors.forename: Guorong
authors.initials: G
authors.lastname: Ruan
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: College of Life Science of Jinggangshan University, Jian, 343009, China.
authors.forename: Xinjun
authors.initials: X
authors.lastname: Liao
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
authors.forename: Nengshui
authors.initials: N
authors.lastname: Ding
mesh_terms: D000818:Animals; D001947:Breeding; D056915:DNA Copy Number Variations; D055106:Genome-Wide Association Study; D005838:Genotype; D006554:Hernia, Umbilical / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D034421:Sus scrofa / Q000235:genetics*; D013552:Swine; D013553:Swine Diseases / Q000235:genetics*
keywords: CNV; genome-wide analysis; pig; umbilical hernia