| QTL Map Information |
|---|
| Chromosome: | 14 |
| QTL Peak Location: | n/a |
| QTL Span: | n/a
|
 |
Upper, "Suggestive": | n/a |
| Upper, "Significant": | rs134633932 |
| Peak: | |
| Lower, "Significant": | rs42270651 |
| Lower, "Suggestive": | n/a |
| Marker type: | SNP |
| Analysis type: | QTL |
| Model tested: | n/a |
| Test base: | Experiment-wise |
| Threshold significance level: | Significant |
 |
VARIANCE | 1.447% | | Dominance effect: | n/a |
| Additive effect: | n/a |
| Associated Gene: | n/a |
| Cis/Trans acting type: |  |
| Links:
Edit |
Map view
|
| Extended information: |
|---|
| (none) |
User inputs on QTL #288164
Add your annotations
Add your comments
Report problems
|
| QTL Experiment in Brief |
|---|
| Animals: | The data set consisted of 388 Holstein cows. |
| Breeds associated:
|
| Design: | Animal were genotyped at 78,985 SNP markers across the genome. Marker positions were obtained for the ARS-UCD 1.2 bovine genome build. Genotype data quality control required a SNP marker call rate greater than 95% and minor allele frequency greater than 5%. A total of 388 animals and 75,823 SNPs remained in the dataset following quality control. Animals were phenotyped for 16 complete blood count (CBC) measures, which were analyzed using genotype information. |
| Analysis: | A univariate marker-based Bayes B model was used to identify 1 Mb genomic regions associated with CBC count measures. Prior probability of exclusion (π) and prior variances were estimated using a Bayes-Cπ model. A Monte Carlo Markov Chain of 80,000 iterations was used for all CBC traits except platelets, which required a chain length of 150,000 to reach convergence. A burn-in of 5000 samples was used for all analyses. |
| Software: | Julia for Whole Genome Analysis (JWAS) |
| Notes: | Some CBC measures were transformed to better approximate a normal distribution. The transformations utilized were as follows:
White blood cell count: log
Neutrophil count: log
Lymphocyte count: log
Monocyte count: none
Eosinophil count: log
Basophil count: log
Large unstained cells count: log
Red blood cell count: none
Hemoglobin content: none
Hematocrit percentage: none
Mean corpuscular volume: log
Mean corpuscular hemoglobin amount: log
Mean corpuscular hemoglobin concentration: none
Red cell distribution width: box-cox (lambda = -2)
Platelet count: none
Mean platelet volume: box-cox (lambda = -2) |
| Links: | Edit |
| Reference |
|---|
| Authors: | Siberski-Cooper CJ, Mayes MS, Gorden PJ, Kramer L, Bhatia V, Koltes JE |
| Affiliation: | Department of Animal Science, Iowa State University, Ames, IA 50011; Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, IA 50011 |
| Title: | The genetic architecture of complete blood counts in lactating Holstein dairy cows |
| Journal: | Frontiers in Genetics, 2024, 15:1360295 |
| Links: |
PubMed | Abstract | List all data
| Edit |
User inputs on reference #38601075
Add your comments
Note similar findings
Note contradictions
|
