Genome-wide linkage and association analysis identifies major gene loci for guttural pouch tympany in Arabian and German warmblood horses.
Abstract: Equine guttural pouch tympany (GPT) is a hereditary condition affecting foals in their first months of life. Complex segregation analyses in Arabian and German warmblood horses showed the involvement of a major gene as very likely. Genome-wide linkage and association analyses including a high density marker set of single nucleotide polymorphisms (SNPs) were performed to map the genomic region harbouring the potential major gene for GPT. A total of 85 Arabian and 373 German warmblood horses were genotyped on the Illumina equine SNP50 beadchip. Non-parametric multipoint linkage analyses showed genome-wide significance on horse chromosomes (ECA) 3 for German warmblood at 16-26 Mb and 34-55 Mb and for Arabian on ECA15 at 64-65 Mb. Genome-wide association analyses confirmed the linked regions for both breeds. In Arabian, genome-wide association was detected at 64 Mb within the region with the highest linkage peak on ECA15. For German warmblood, signals for genome-wide association were close to the peak region of linkage at 52 Mb on ECA3. The odds ratio for the SNP with the highest genome-wide association was 0.12 for the Arabian. In conclusion, the refinement of the regions with the Illumina equine SNP50 beadchip is an important step to unravel the responsible mutations for GPT.
Publication Date: 2012-07-27 PubMed ID: 22848553PubMed Central: PMC3407181DOI: 10.1371/journal.pone.0041640Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research investigates the genetic basis behind guttural pouch tympany (GPT) in Arabian and German warmblood horses. The study identifies significant genetic loci linked to this hereditary condition through genome-wide linkage and association analyses on a set of single nucleotide polymorphisms (SNPs).
Research Context
- Guttural pouch tympany (GPT) is a hereditary condition affecting foals during their first few months. This condition was previously identified as probable involving a major gene in Arabian and German warmblood horses.
- To better understand the genetic localization of GPT, the research team used genome-wide linkage and association analyses, utilizing a dense set of single nucleotide polymorphisms (SNPs), which are variations at a single position in a DNA sequence among individuals.
- The target population of this study was 85 Arabian and 373 German warmblood horses, which were genotyped with the Illumina equine SNP50 beadchip, a tool commonly used in genetic studies in horses.
Research Findings
- The non-parametric multipoint linkage analyses suggested significant connections on certain horse chromosomes for both horse breeds. For German warmbloods, significance appeared on chromosomes 3 (in the regions of 16-26 Mb and 34-55 Mb). For Arabians, it was on chromosome 15 (at the 64-65 Mb).
- The genome-wide association analyses confirmed these linked regions and detected significant signals close to the regions of highest linkage peak: 64 Mb on ECA15 for Arabians and 52 Mb on ECA3 for German warmbloods.
- The odds ratio for the SNP with the most significant genome-wide association was 0.12 for the Arabian breed. An odds ratio is a statistic that quantifies the strength of the association between two events. In this context, it reflects the strength of the association between the presence of a specific SNP and the occurrence of GPT in Arabian horses.
Conclusion and Implications
- This study provides critical genetic context to the condition of GPT in horses. By refining the regions with the Illumina equine SNP50 beadchip, the researchers increase the chances of identifying the responsible mutations for GPT.
- The identified genetic loci can focus future research on these regions to possibly uncover the exact genetic mutations responsible for GPT in Arabian and German warmblood horses.
Cite This Article
APA
Metzger J, Ohnesorge B, Distl O.
(2012).
Genome-wide linkage and association analysis identifies major gene loci for guttural pouch tympany in Arabian and German warmblood horses.
PLoS One, 7(7), e41640.
https://doi.org/10.1371/journal.pone.0041640 Publication
Researcher Affiliations
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
MeSH Terms
- Animals
- Chromosome Mapping
- Genetic Loci / genetics
- Genome-Wide Association Study
- Horse Diseases / genetics
- Horses / anatomy & histology
- Horses / genetics
- Polymorphism, Single Nucleotide
Conflict of Interest Statement
Competing Interests: The authors have declared that no competing interests exist.
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Citations
This article has been cited 7 times.- van der Vossen N, Cavalcante P, Glynn S, Achappa D, Mehmood W, Oikawa M, Vinardell T, Jamieson C. A case-control study of atypical guttural pouch empyema in Arabian foals. Vet Med Sci 2023 Jul;9(4):1599-1609.
- Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. J Genet Mutat Disord 2022 Jan;1(1).
- Mancin E, Ablondi M, Mantovani R, Pigozzi G, Sabbioni A, Sartori C. Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information. Animals (Basel) 2020 Jul 30;10(8).
- Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020 Jun 8;10(6).
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