Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses.
Abstract: The recent completion of the horse genome and commercial availability of an equine SNP genotyping array has facilitated the mapping of disease genes. We report putative localization of the gene responsible for dwarfism, a trait in Friesian horses that is thought to have a recessive mode of inheritance, to a 2-MB region of chromosome 14 using just 10 affected animals and 10 controls. We successfully genotyped 34,429 SNPs that were tested for association with dwarfism using chi-square tests. The most significant SNP in our study, BIEC2-239376 (P(2df)=4.54 × 10(-5), P(rec)=7.74 × 10(-6)), is located close to a gene implicated in human dwarfism. Fine-mapping and resequencing analyses did not aid in further localization of the causative variant, and replication of our findings in independent sample sets will be necessary to confirm these results.
© 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.
Publication Date: 2010-11-26 PubMed ID: 21070269DOI: 10.1111/j.1365-2052.2010.02091.xGoogle Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research article discusses the use of genome-wide SNP analysis to locate a gene thought to be responsible for dwarfism in Friesian horses. By studying a group of both affected and control horses, researchers were able to potentially identify a 2-MB region on chromosome 14 as the location of this gene.
Background and Aim
- This study aims to utilize the newly completed horse genome data and the readily available equine SNP genotyping array to map disease genes.
- The gene responsible for dwarfism—a recessive trait observed in Friesian horses—was the target in this case.
- The researchers strove to locate the precise site of this gene using 10 dwarf horses and 10 regular-sized horses as control.
Methodology
- The team successfully genotyped 34,429 SNPs (Single-Nucleotide Polymorphisms), which are variations occurring at a single site in the DNA.
- These SNPs were then tested for association with dwarfism through chi-square tests, a statistical method used to detect if there’s a relationship between two categorical variables—in this case, SNP and dwarfism presence.
Findings
- The SNP most significantly associated with dwarfism in the study, known as BIEC2-239376, is located close to a gene previously implicated in human dwarfism.
- This could potentially suggest a similar genetic basis for the condition in both species.
- The SNP is located in a 2-MB region on chromosome 14.
Conclusions and Future Work
- Despite the significant findings, fine-mapping and resequencing analyses did not further aid in specifically locating the causative variant—likely due to this gene’s complexity and potential interactions with other genetic factors.
- As such, replication of these findings in independent sample sets will be necessary to confirm the results and further refine the location of this variant.
Cite This Article
APA
Orr N, Back W, Gu J, Leegwater P, Govindarajan P, Conroy J, Ducro B, Van Arendonk JA, MacHugh DE, Ennis S, Hill EW, Brama PA.
(2010).
Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses.
Anim Genet, 41 Suppl 2, 2-7.
https://doi.org/10.1111/j.1365-2052.2010.02091.x Publication
Researcher Affiliations
- Section of Veterinary Clinical Studies, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland.
MeSH Terms
- Animals
- Dwarfism / genetics
- Dwarfism / veterinary
- Genome-Wide Association Study
- Horse Diseases / genetics
- Horses
- Polymorphism, Single Nucleotide
Citations
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