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. 2012;7(11):e49782.
doi: 10.1371/journal.pone.0049782. Epub 2012 Nov 26.

Identification of quantitative trait loci (QTL) for canine hip dysplasia and canine elbow dysplasia in Bernese mountain dogs

Sophia Pfahler  1 , Ottmar Distl
Affiliations

Identification of quantitative trait loci (QTL) for canine hip dysplasia and canine elbow dysplasia in Bernese mountain dogs

Sophia Pfahler et al. PLoS One. 2012.

Abstract

A genome-wide association study for canine hip dysplasia (CHD) and canine elbow dysplasia (CED) using the Illumina canine high density bead chip had been performed for 174 Bernese mountain dogs. General and mixed linear model analysis identified two different regions with single nucleotide polymorphisms (SNPs) on dog chromosome (CFA) 14 significantly associated with CHD and a further significantly CHD-associated region on CFA37. For CED, four SNPs on CFA11 and 27 were significantly associated. The identified SNPs of four associated regions included nearby candidate genes. These possible positional candidates were the genes PON2 on CFA14 and FN1 on CFA37 for CHD and the genes LMNB1 on CFA11 and WNT10B on CFA27 for CED.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Manhattan plot of −log10P-values of the genome-wide association study for the canine hip dysplasia score in Bernese mountain dogs using a general model analysis.
On the X-axis, the SNPs are given by dog chromosome number. The −log10P-values for each SNP genotype effect are plotted against the SNP position on each chromosome. Chromosomes are differentiated by colors. The color keys are given below the plot. The blue line indicates the threshold of the −log10P-values for genome-wide significance after correcting for multiple testing.
Figure 2
Figure 2. Manhattan plot of −log10P-values of the genome-wide association study for the canine elbow dysplasia score in Bernese mountain dogs using a general model analysis.
On the X-axis, the SNPs are given by dog chromosome number. The −log10P-values for each SNP genotype effect are plotted against the SNP position on each chromosome. Chromosomes are differentiated by colors. The color keys are given below the plot. The blue line indicates the threshold of the −log10P-values for genome-wide significance after correcting for multiple testing.
Figure 3
Figure 3. Q-Q-plot of expected −log10P-values versus observed−log10P-values from the general model analysis for canine hip dysplasia score in Bernese mountain dogs.
Shown are all 96,412 SNPs included in the genome-wide association analysis with the grey line corresponding to the null hypothesis of no association.
Figure 4
Figure 4. Q-Q-plot of expected −log10P-values versus observed−log10P-values from the general model analysis for canine elbow dysplasia score in Bernese mountain dogs.
Shown are all 96,412 SNPs included in the genome-wide association analysis with the grey line corresponding to the null hypothesis of no association.
Figure 5
Figure 5. Genomic region with a significant association for canine hip dysplasia on dog chromosome (CFA) 14 at 23.25–24.5 Mb.
The −log10P-values of all 62 SNPs in this region and the genes annotated according to the dog genome assembly build 2.1 are shown.
Figure 6
Figure 6. Genomic region with a significant association for canine hip dysplasia on dog chromosome (CFA) 14 at 59.5–60.0 Mb.
The −log10P-values of all 41 SNPs in this region and the genes annotated according to the dog genome assembly build 2.1 are shown.
Figure 7
Figure 7. Genomic region with a significant association for canine hip dysplasia on dog chromosome (CFA) 37 at
24.75–26.0 Mb. The −log10P-values of all 58 SNPs in this region and the genes annotated according to the dog genome assembly build 2.1 are shown.
Figure 8
Figure 8. Genomic region with a significant association for canine elbow dysplasia on dog chromosome (CFA) 11 at 17.0–24.0 Mb.
The −log10P-values of all 314 SNPs in this region and the genes annotated according to the dog genome assembly build 2.1 are shown.
Figure 9
Figure 9. Genomic region with a significant association for canine elbow dysplasia on dog chromosome (CFA) 27 at 4.0–8.5 Mb.
The −log10P-values of all 241 SNPs in this region and the genes annotated according to the dog genome assembly build 2.1 are shown.
See this image and copyright information in PMC

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