Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Phenotyping
2.2.1. Photograph Selection
2.2.2. Horse Shape Data
2.2.3. Phenotype Concordance
2.2.4. Quality Control of the Phenotype
2.3. Genetic Analyses
2.3.1. Franches-Montagnes Horses
2.3.2. Lipizzan Horses
2.3.3. Merging the Genetic Data Sets (Franches-Montagnes and Lipizzan Horses)
2.4. Genome-Wide Association Studies
2.5. Functional Annotation
3. Results
3.1. Phenotypic Analyses
3.2. Population Structure
3.3. Genome-Wide Association Studies for Joint Angle Measurements
3.3.1. Poll Angle Associations
3.3.2. Elbow Joint Angle Association
3.3.3. Stifle Joint Angle Association
3.3.4. Fetlock Joint Angle of the Hind Limb Association
3.3.5. Carpal Joint Angle Associations
4. Discussion
4.1. Phenotypes
4.2. Genome-Wide Association Studies
4.2.1. Identification and Interpretation of Relevant Quantitative Trait Loci
4.2.2. Poll Angle
4.2.3. Elbow Joint Angle
4.2.4. Stifle Joint Angle
4.2.5. Fetlock Joint Angle of the Hind Limb
4.2.6. Carpal Joint Angle
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Joint Angle | Mean | SD | Min | Max | h2 | SE | ICC (20 LIP) |
---|---|---|---|---|---|---|---|
Poll | 102.55 | 4.70 | 85.35 | 117.29 | 0.38 | 0.098 | 0.92 |
Neck–shoulder blade | 81.86 | 6.56 | 62.77 | 99.47 | 0.42 | 0.086 | 0.16 |
Shoulder joint | 94.00 | 6.61 | 77.09 | 114.94 | 0.42 | 0.090 | 0.13 |
Elbow joint | 129.50 | 5.79 | 112.60 | 147.50 | 0.22 | 0.076 | 0.52 |
Carpal joint | 177.30 | 1.81 | 170.00 | 179.90 | 0.35 | 0.088 | 0.49 |
Fetlock joint of the forelimb | 149.10 | 4.08 | 136.80 | 162.00 | 0.32 | 0.089 | 0.79 |
Hip joint | 78.22 | 3.01 | 68.80 | 91.17 | 0.24 | 0.092 | 0.58 |
Stifle joint | 99.76 | 4.08 | 89.28 | 115.26 | 0.40 | 0.089 | 0.90 |
Hock | 152.90 | 2.30 | 145.00 | 159.50 | 0.25 | 0.095 | 0.96 |
Fetlock joint of the hind limb | 155.80 | 6.43 | 137.60 | 177.90 | 0.58 | 0.086 | 0.81 |
Joint Angle | Stud Farm | Birth Year Category | Age Category | Sex | Head in Relation to Camera | Position of Front Limb | Position of Hind Limb | Body Alignment to the Camera | Tail Position |
---|---|---|---|---|---|---|---|---|---|
Poll | ** | * | ** | * | ** | ||||
Elbow joint | *** | ** | |||||||
Carpal joint | *** | ||||||||
Fetlock joint of the forelimb | ** | * | |||||||
Hip joint | ** | * | *** | *** | |||||
Stifle joint | *** | * | *** | *** | |||||
Hock | *** | ||||||||
Fetlock joint of the hind limb | * | *** | ** |
Joint Angle | ECA | Position on EquCab2.0 | Position on EquCab 3.0 | #SNP | SNP with the Lowest p-Value | p-Value | Number of Genotyped Horses | Allele Frequency | ||
---|---|---|---|---|---|---|---|---|---|---|
AAFM,LIP | ABFM,LIP | BBFM,LIP | ||||||||
Poll | 28 | 12,101,898–12,106,363 | 13,129,017–13,133,483 | 3 | AX-103978374 | 1.36 × 10−07 | 495 | 4911,38 | 19797,100 | 249176,73 |
1 | 124,405,158 | 125,551,151 | 1 | AX-103779310 | 6.83 × 10−07 | 495 | 138,5 | 13370,63 | 349206,143 | |
Elbow joint | 29 | 18,799,958 | 19,878,299 | 1 | AX-103649839 | 1.69 × 10−07 | 490 | 3712,25 | 15469,85 | 299198,101 |
Stifle joint | 8 | 19,266,146 | 21,704,931 | 1 | AX-102974274 | 2.77 × 10−07 | 473 | 454,41 | 18680,106 | 242178,64 |
Fetlock joint of the hind limb | 27 | 22,021,462 | 22,068,848 | 1 | AX-103624054 | 5.42 × 10−07 | 495 | 53,2 | 10270,32 | 388211,177 |
Carpal joint | 4 | 37,412,203 | 37,460,405 | 1 | AX-104691515 | 6.07 × 10−07 | 479 | 463,43 | 16054,106 | 273211,62 |
3 | 106,128,177 | 107,955,102 | 1 | AX-105008533 | 6.24 × 10−07 | 493 | 390,39 | 14328,115 | 311254,57 | |
7 | 42,659,817 | 43,694,770 | 1 | AX-103944161 | 8.83 × 10−07 | 495 | 222,20 | 18675,111 | 287207,80 |
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Gmel, A.I.; Druml, T.; von Niederhäusern, R.; Leeb, T.; Neuditschko, M. Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses. Genes 2019, 10, 370. https://doi.org/10.3390/genes10050370
Gmel AI, Druml T, von Niederhäusern R, Leeb T, Neuditschko M. Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses. Genes. 2019; 10(5):370. https://doi.org/10.3390/genes10050370
Chicago/Turabian StyleGmel, Annik Imogen, Thomas Druml, Rudolf von Niederhäusern, Tosso Leeb, and Markus Neuditschko. 2019. "Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses" Genes 10, no. 5: 370. https://doi.org/10.3390/genes10050370
APA StyleGmel, A. I., Druml, T., von Niederhäusern, R., Leeb, T., & Neuditschko, M. (2019). Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses. Genes, 10(5), 370. https://doi.org/10.3390/genes10050370