Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods.
Abstract: We performed efficient cloning and genotyping methods for isolation of a large number of polymorphic microsatellites. The methods contain the time-efficient cloning method of constructing microsatellite-enriched libraries and the economic genotyping method of fluorescent labeling of PCR products. Eighty novel equine microsatellites cloned were efficiently isolated from the enrichment library and analyzed for genotype polymorphism. Of these, 72 microsatellites were analyzed with a good resolution. The average heterozygosity of all loci was 0.52, and the number of alleles ranged from one to 9 with an average of 4.5 alleles. The other eight loci showed multiple bands of PCR products, suggesting the occurrence of microsatellites in a repetitive element, in which the number of microsatellite repeats varies among different members of the repetitive element. We found five homologous groups at flanking regions in comparison with the flanking regions of microsatellites from DNA databases. One of them showed homology to equine repetitive element-2. In the other four homologous groups, the two groups were named equine microsatellite-linked repetitive element-1 (eMLRE-1) and equine microsatellite-linked repetitive element-2 (eMLRE-2) as novel equine repetitive elements identified from equine genome. These data should help the analysis of equine DNA sequences and the design of equine genome markers.
Publication Date: 2001-03-22 PubMed ID: 11258798DOI: 10.1093/dnares/8.1.33Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research introduces efficient methods for isolating a large number of polymorphic microsatellites, tiny repeating sections of DNA, in horses. The research team cloned a high number of novel equine microsatellites and successfully analysed the genetic variation. Their findings may potentially assist in future genetic studies of horses and the creation of genetic markers for the equine genome.
Methods Employed
- Efficient cloning and genotyping methods were employed specifically to isolate a large number of polymorphic microsatellites.
- The approach involves time-efficient cloning, which is constructing microsatellite-enriched libraries and economical genotyping, which is fluorescent labelling of PCR (Polymerase Chain Reaction) products, used to amplify DNA sequences.
Results of the Study
- Eighty novel equine microsatellites were successfully isolated from the enrichment library and their genotype polymorphism was analysed.
- Out of these 80, 72 microsatellites showed good resolution.
- The average heterozygosity, or genetic diversity, of all loci was 0.52.
- The number of alleles or different forms of a gene ranged from one to 9 with an average of 4.5 alleles.
- Eight loci showed multiple PCR product bands, implying the presence of microsatellites in a repetitive DNA sequence element.
Discovery of Repetitive Elements
- Five homologous groups were discovered at flanking regions, when compared to the flanking regions of microsatellites from DNA databases.
- One group demonstrated homology to an existing equine repetitive element-2.
- The researchers named two out of the other four groups as equine microsatellite-linked repetitive element-1 (eMLRE-1) and equine microsatellite-linked repetitive element-2 (eMLRE-2).
- These two groups represent new equine repetitive elements identified from the equine genome.
Potential Implications of the Study
- The study’s data can potentially support the analysis of equine DNA sequences.
- It could also aid in the design of equine genome markers, which are DNA sequences that can act as landmarks for genetic mapping.
Cite This Article
APA
Tozaki T, Mashima S, Hirota K, Miura N, Choi-Miura NH, Tomita M.
(2001).
Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods.
DNA Res, 8(1), 33-45.
https://doi.org/10.1093/dnares/8.1.33 Publication
Researcher Affiliations
- Department of Physiological Chemistry, School of Pharmaceutical Sciences, Showa University, Shinagawa, Tokyo, Japan. ttozaki@nyc.odn.ne.jp
MeSH Terms
- Animals
- Base Sequence
- Cloning, Molecular / methods
- Genetic Linkage
- Genomic Library
- Genotype
- Horses / genetics
- Microsatellite Repeats / genetics
- Molecular Sequence Data
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA / economics
Citations
This article has been cited 6 times.- Jenkins CA, Kalmar L, Matiasek K, Mari L, Kyöstilä K, Lohi H, Schofield EC, Mellersh CS, De Risio L, Ricketts SL. Characterisation of canine KCNIP4: A novel gene for cerebellar ataxia identified by whole-genome sequencing two affected Norwegian Buhund dogs. PLoS Genet 2020 Jan;16(1):e1008527.
- Veltjen E, Asselman P, Hernández Rodríguez M, Palmarola Bejerano A, Testé Lozano E, González Torres LR, Goetghebeur P, Larridon I, Samain MS. Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers. Heredity (Edinb) 2019 Apr;122(4):485-500.
- Cook D, Brooks S, Bellone R, Bailey E. Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses. PLoS Genet 2008 Sep 19;4(9):e1000195.
- Tozaki T, Hirota K, Hasegawa T, Ishida N, Tobe T. Whole-genome linkage disequilibrium screening for complex traits in horses. Mol Genet Genomics 2007 Jun;277(6):663-72.
- Tozaki T, Choi-Miura NH, Taniyama M, Kurosawa M, Tomita M. SNP analysis of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) gene by a fluorescence-adapted SSCP method. BMC Med Genet 2002 Jul 29;3:6.
- Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI. Construction of an individual identification panel for horses using insertion and deletion markers. J Equine Sci 2023 Sep;34(3):83-92.
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