Susceptibility Loci for Umbilical Hernia in Swine Detected by Genome-Wide Association

Abstract

Umbilical hernia (UH) is a complex disorder caused by both genetic and environmental factors. UH brings animal welfare problems and severe economic loss to the pig industry. Until now, the genetic basis of UH is poorly understood. The high-density 60K porcine SNP array enables the rapid application of genome-wide association study (GWAS) to identify genetic loci for phenotypic traits at genome wide scale in pigs. The objective of this research was to identify susceptibility loci for swine umbilical hernia using the GWAS approach. We genotyped 478 piglets from 142 families representing three Western commercial breeds with the Illumina PorcineSNP60 BeadChip. Then significant SNPs were detected by GWAS using ROADTRIPS (Robust Association-Detection Test for Related Individuals with Population Substructure) software base on a Bonferroni corrected threshold (P = 1.67E-06) or suggestive threshold (P = 3.34E-05) and false discovery rate (FDR = 0.05). After quality control, 29,924 qualified SNPs and 472 piglets were used for GWAS. Two suggestive loci predisposing to pig UH were identified at 44.25MB on SSC2 (rs81358018, P = 3.34E-06, FDR = 0.049933) and at 45.90MB on SSC17 (rs81479278, P = 3.30E-06, FDR = 0.049933) in Duroc population, respectively. And no SNP was detected to be associated with pig UH at significant level in neither Landrace nor Large White population. Furthermore, we carried out a meta-analysis in the combined pure-breed population containing all the 472 piglets. rs81479278 (P = 1.16E-06, FDR = 0.022475) was identified to associate with pig UH at genome-wide significant level. SRC was characterized as plausible candidate gene for susceptibility to pig UH according to its genomic position and biological functions. To our knowledge, this study gives the first description of GWAS identifying susceptibility loci for umbilical hernia in pigs. Our findings provide deeper insights to the genetic architecture of umbilical hernia in pigs.

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs

“…Ding et al (2009) [11] were the first to identify regions related to the occurrence of umbilical hernias in pigs. Afterwards, other studies also identified regions related to umbilical hernias in pigs [5,12,13]. Six of the genes DE in our study were mapped to QTL regions already described in the literature for umbilical hernias in pigs: ACER2, SLC2A6, PTGS1, LGALS3, KANK3 and FOS.…”

“…Some studies have been performed to identify the genetic factors involved in the development of umbilical hernias, and QTL regions, SNPs and candidate genes associated with the appearance of this defect have been detected [5,[11][12][13]. In this study, using RNA-Seq, we sequenced the umbilical ring transcriptome to discover possible genes involved in the occurrence of umbilical hernias in pigs.…”

“…UH prevalence in pigs ranges from 0.40 to 2.25%, varying according to the breed, farm and production system [3,4]. Animals affected with UH experience generally reduced performance, with low growth rates, poor feed conversion, low meat quality and pain and discomfort, which could also lead to death [5,6]. Although it is known that economic losses caused by umbilical hernia have a huge impact in the pig industry, it is really hard to find reports with their estimates.…”

“…The development of umbilical hernia can be caused by external factors, such as physical lesions, high pressure in the abdomen, inappropriate removal of the umbilical cord, infections and management [5]. Meanwhile, it has been observed that related animals with the same management practices could present different phenotypes, i.e., being normal or affected with hernias [5], indicating that a genetic factor is also present [8]. Moreover, the heritability estimate of 0.25 for UH in pigs [9] and 0.40 in cattle [10] reinforce the genetic component regulating this trait.…”

Genome‐wide association study identifies variants in theCAPN9gene associated with umbilical hernia in pigs

“…), single nucleotide polymorphisms (SNPs; Liao et al . ) and copy number variations (CNVs; Long et al . ).…”