Abstract
BackgroundUmbilical hernia is one of the most prevalent congenital defect in pigs, causing economic losses and substantial animal welfare problems. Identification and implementation of genomic regions controlling umbilical hernia in breeding is of great interest to reduce incidences of hernia in commercial pig production. The aim of this study was to identify such regions and possibly identify causative variation affecting umbilical hernia in pigs. A case/control material consisting of 739 Norwegian Landrace pigs was collected and applied in a GWAS study with a genome-wide distributed panel of 60 K SNPs. Additionally candidate genes were sequenced to detect additional polymorphisms that were used for single SNP and haplotype association analyses in 453 of the pigs.ResultsThe GWAS in this report detected a highly significant region affecting umbilical hernia around 50 Mb on SSC14 (P < 0.0001) explaining up to 8.6% of the phenotypic variance of the trait. The region is rather broad and includes 62 significant SNPs in high linkage disequilibrium with each other. Targeted sequencing of candidate genes within the region revealed polymorphisms within the Leukemia inhibitory factor (LIF) and Oncostatin M (OSM) that were significantly associated with umbilical hernia (P < 0.001).ConclusionsA highly significant QTL for umbilical hernia in Norwegian Landrace pigs was detected around 50 Mb on SSC14. Resequencing of candidate genes within the region revealed SNPs within LIF and OSM highly associated with the trait. However, because of extended LD within the region, studies in other populations and functional studies are needed to determine whether these variants are causal or not. Still without this knowledge, SNPs within the region can be used as genetic markers to reduce incidences of umbilical hernia in Norwegian Landrace pigs.
Highlights
Umbilical hernia is one of the most prevalent congenital defect in pigs, causing economic losses and substantial animal welfare problems
It is generally accepted that genetics influence congenital umbilical hernias, but mode of inheritance and Grindflek et al BMC Genomics (2018) 19:412 genetic architecture are more or less undiscovered, and h2 estimates of umbilical hernia are reported to be very low in pigs (0.06–0.08) [1, 8]
The aim of this study was to collect a proper case/control material and identify genomic regions affecting the frequency of umbilical hernia in pigs, using Genome wide association study (GWAS) on a high resolution SNP panel followed up by candidate gene approaches
Summary
Umbilical hernia is one of the most prevalent congenital defect in pigs, causing economic losses and substantial animal welfare problems. The aim of this study was to identify such regions and possibly identify causative variation affecting umbilical hernia in pigs. Hernias are of the most common congenital defects in pigs which often leads to poor animal welfare and severe economic losses for pig producers. The frequencies and heritabilities of umbilical hernia differs between species. In humans some studies have been done on structural variations like deletions and duplications, suggesting that such variations could play a role in occurrence of umbilical hernia [13,14,15]. Two studies in other species suggest that umbilical hernia is associated with the function of cyclin-dependent kinase inhibitory protein p57KIP2, a regulator of cell proliferation [16, 17]
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