| QTL Map Information |
|---|
| Chromosome: | 3 |
| QTL Peak Location: | 143.98 (cM) |
| QTL Span: | 143.98-143.98 (cM)
130.7-130.7 (Mbp) |
 |
Upper, "Suggestive": | n/a |
| Upper, "Significant": | n/a |
| Peak: | rs326411709 |
| Lower, "Significant": | n/a |
| Lower, "Suggestive": | n/a |
| Marker type: | SNP |
| Analysis type: | Association |
| Model tested: | Mendelian |
| Test base: | Comparison-wise |
| Threshold significance level: | Significant |
 |
P_values | 3.69E-6 | | Dominance effect: | n/a |
| Additive effect: | n/a |
| Associated Gene: | n/a |
| Cis/Trans acting type: |  |
| Links:
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| Extended information: |
|---|
| (none) |
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| QTL Experiment in Brief |
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| Animals: | Animals were from a Yorkshire x Landrace terminal boar line cross. The data set consists of 786 pigs recruited from multiple farms in Ontario, Canada. |
| Breeds associated:
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| Design: | Pigs were genotyped using a custom 54K Affymetrix Axiom® myDesign™ chip designed in consultation with the Canadian Centre for Swine Improvement (Ottawa, Ontario, Canada). After quality control, 51984 SNPs were used in the analysis. |
| Analysis: | Univariable analysis of each phenotype was performed using a mixed-effects logistic regression model in Stata to assess the significance of associations between covariates and the phenotype (p < 0.05) and subsequent inclusion in the GWAS model. To account for cryptic relatedness of the pigs in a study population with no sire information, a genomic relatedness matrix (GRM) was calculated using the genome-wide efficient mixed model association algorithm (GEMMA) v0.96. Genome-wide analyses of case-control data were performed using a generalized logistic mixed model association test (GMMAT) using the GMMAT v0.9.3 package for R. The covariates analyzed in Stata and the GRM created in GEMMA were included in the GMMAT analysis. The chosen p-value threshold for suggestive and significant associations was 1.0 × 10-5 and 5.0 × 10-7, respectively based on a study by Burton et al. |
| Software: | Stat, R, GEMMA, GMMAT |
| Notes: | |
| Links: | Edit |
| Reference |
|---|
| Authors: | Schut CH, Farzan A, Fraser RS, Ainslie-Garcia MH, Friendship RM, Lillie BN |
| Affiliation: | Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada |
| Title: | Identification of single-nucleotide variants associated with susceptibility to Salmonella in pigs using a genome-wide association approach |
| Journal: | BMC Veterinary Research, 2020, 16(1):138 |
| Links: |
PubMed | Abstract | List all data
| Edit |
| Additional Information |
|---|
| Comments: | tonsils or lymph nodes |
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