Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14

BMC Genomics
E GrindflekM van Son

Abstract

Umbilical 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. The 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 ...Continue Reading

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Citations

Jan 31, 2021·Genes·Ariene Fernanda Grando RodriguesMônica Corrêa Ledur
Apr 23, 2021·Preventive Veterinary Medicine·Trine Hovmand-HansenHenrik E Jensen
Nov 30, 2021·Animal Health Research Reviews·Eymen DemirTaki Karsli

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Methods Mentioned

BETA
genotyping
PCR
Assay

Software Mentioned

PolyPhred
MODEL
Haploview
MassARRAY Assay Design
GROMOS
Phred
Ensembl
Phrap
Genome Studio
SWISS

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