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. 2018 Jan 27;5(1):15.
doi: 10.3390/vetsci5010015.

Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd

Luisa Vitória Lago  1 , Arthur Nery da Silva  2 , Eraldo L Zanella  3   4 , Mariana Groke Marques  5 , Jane O Peixoto  6 , Marcos V G B da Silva  7 , Mônica C Ledur  8 , Ricardo Zanella  9   10
Affiliations

Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd

Luisa Vitória Lago et al. Vet Sci. .

Abstract

In this paper, we have used two approaches to detect genetic associations with scrotal hernias in commercial pigs. Firstly, we have investigated the effects of runs of homozygosity (ROH) with the appearance of scrotal hernias, followed by a Genome Wide Association Study (GWAS). The phenotype classification was based on visual appearance of scrotal hernias. Each affected animal was matched to a healthy control from the same pen. In the total, 68 animals were genotyped using the Porcine SNP60 Beadchip, out of those, 41 animals had the presence of hernias and 27 were healthy animals. Fifteen animals were removed from the analysis due to differences in genetic background, leaving 18 healthy animals and 35 piglets with scrotal hernia. Further, the detection of extended haplotypes shared ROH were conducted for health (control) and affected (case) animals and a permutation test was used to test whether the ROH segments were more frequent in case/case pairs than non-case/case pairs. Using the ROH, we have identified an association (p = 0.019) on chromosome 2(SSC2) being segregated on animals with the presence of scrotal hernias. Using a GWAS, a region composed by 3 SNPs on the sexual chromosome X (SSCX) were associated with scrotal hernias (p < 1.6 × 10-5), this region harbors the Androgen Receptor Gene (AR).

Keywords: SNP; genetics; hernias; swine.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1
(A) A Multi-Dimensional scaling Plot constructed only with markers with LD < 0.2, before animal quality control. Each circle represents an individual animal; (B) A Multi-Dimensional Plot constructed only with markers with LD < 0.2, after animal quality control.
Figure 2
Figure 2
A Quantile-quantile Q-Q plot for observed P-values vs. those expected for an association of loci with scrotal hernias formation. The Q-Q plot shows no evidence of population substructure.
Figure 3
Figure 3
ROH segment sharing permutation test with the appearance of scrotal hernias in a commercial swine operation, constructed with 100 SNPs and 1000 Kb distance.
Figure 4
Figure 4
Case and Control association test with appearance of scrotal hernias with a sample population from a commercial swine operation.
See this image and copyright information in PMC

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