Combining microsatellite and pedigree data to estimate relationships among Skyros ponies.
Abstract: Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyros pony breed, which consists of less than 200 individuals, divided into 3 main herds or subpopulations. In this study, relationships between individuals were estimated using traditional estimators as well as the newly developed method. For this purpose, 99 Skyros ponies were genotyped at 16 microsatellite loci. It appeared that the limitation of the most common molecular-based estimators is the use of weights that assume relationships equal to 0. The results showed that, as a consequence of this limitation, negative relationship values can be obtained in small inbred populations, for example. By contrast, the combined estimator gave no negative values. Using principal component analysis, the combined estimator also enabled a better graphic differentiation between the 3 subpopulations defined previously. In conclusion, this new estimator can be a promising alternative to traditionally used estimators, especially in inbred populations, with both incomplete pedigree and molecular information.
Publication Date: 2009-05-13 PubMed ID: 19433910DOI: 10.1007/BF03195664Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research article presents a novel method for estimating relationship coefficients in endangered populations, specifically applied to the Skyros pony breed. The method combines both molecular and pedigree data to improve genetic management of the Ponies.
Objective and Purpose of the Study
- The study aimed to develop a new method to estimate relationship coefficients in populations where pedigree and molecular data are both incomplete.
- This was deemed critical in aiding the conservation efforts of the endangered Skyros pony breed, which has less than 200 individuals, divided into three main herds or subpopulations.
- Understanding genetic relationships between individuals in such endangered populations helps ensure the healthiest possible breeding and thus aids in conservation.
Methodology Used
- The study genotyped 99 Skyros ponies at 16 microsatellite loci, using both traditional estimators and the new method developed for this study.
- The new method combines traditional pedigree data (tracking lineages based on recorded family history) with molecular data derived from DNA analysis, or genotyping.
Key Findings
- The common molecular-based estimators have a limitation in their reliance on assumption of relationships equal to zero.
- This limitation leads to possible negative relationship values particularly in the case of small inbred populations.
- The new combined method developed in this study did not result in any negative values, thus eliminating this particular limitation.
- Using principal component analysis, the new estimator also enabled better graphical differentiation between the three Skyros pony subpopulations previously defined.
Conclusion and Implications
- The study concludes that this new combined estimator can be a promising alternative to traditionally used estimators, particularly in managing inbred populations with incomplete pedigree and molecular information.
- Implementing this method can significantly enhance the genetic management and subsequent conservation efforts towards endangered populations like the Skyros ponies.
Cite This Article
APA
Bomcke E, Gengler N.
(2009).
Combining microsatellite and pedigree data to estimate relationships among Skyros ponies.
J Appl Genet, 50(2), 133-143.
https://doi.org/10.1007/BF03195664 Publication
Researcher Affiliations
- Gembloux Agricultural University, Animal Science Unit, Passage des Déportés, Gembloux, Belgium. bomcke.e@fsagx.ac.be
MeSH Terms
- Animals
- Breeding
- Genetics, Population
- Horses / classification
- Horses / genetics
- Microsatellite Repeats / genetics
- Pedigree
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Citations
This article has been cited 3 times.- Senju N, Tozaki T, Kakoi H, Shinjo A, Matsuyama R, Almunia J, Takasu M. Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. J Vet Med Sci 2017 Feb 28;79(2):425-431.
- Senju N, Tozaki T, Kakoi H, Almunia J, Maeda M, Matsuyama R, Takasu M. Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA. J Vet Med Sci 2017 Jan 24;79(1):218-223.
- Bömcke E, Gengler N, Cothran EG. Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds. Genet Mol Biol 2011 Jan;34(1):68-76.
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