Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.
Abstract: Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.
Publication Date: 2000-05-03 PubMed ID: 10791825
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- Journal Article
Summary
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This research focuses on the construction of a genomic library of equines enriched with DNA fragments containing (CAG)n repeats, useful for linkage mapping and parentage testing. The study resulted in the identification of 66 different microsatellites, potentially beneficial for chromosome comparison between equines and humans.
Construction of Enriched Equine Genomic Library
- The researchers priority was tackling the limited number of known equine microsatellites, crucial for equine parentage testing and construction of a linkage map.
- To overcome this limitation, they built an equine genomic library, filled with DNA fragments containing (CAG)n repeats.
Enrichment Method Used
- The enrichment method implemented was a blend of several steps: hybridization-capture of repeat regions using biotin-tagged oligonucleotides, a nucleotide substrate-biased polymerase reaction, and subsequent PCR amplification.
- This method was chosen due to its efficiency in cloning trinucleotide microsatellites that are less common.
Result of the Enrichment Process
- The (CAG)n repeat microsatellites were obtained at a ratio of one per 3-4 clones, representing a 10(4)-fold enrichment. This denotes a considerably efficient method that requires less time and cost for cloning.
Microsatellites Identified
- The study succeeded in identifying 66 different microsatellites containing (CAG)n repeats. The number of complete simple CAG repeats in the clones varied between 4-33, showing an average repeat length of 8.8 units.
- These microsatellites can function as sequence-tagged site (STS) markers.
Potential Utility in Comparative Genomics
- Some clones containing (CAG)n repeats revealed homology to human (CAG)n-containing genes which have been previously located.
- This suggests that these clones could serve as valuable tools for contrasting chromosomes between humans and equines.
Cite This Article
APA
Tozaki T, Inoue S, Mashima S, Ohta M, Miura N, Tomita M.
(2000).
Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.
Genome, 43(2), 354-365.
Publication
Researcher Affiliations
- Department of Physiological Chemistry, School of Pharmaceutical Sciences, Showa University, Tokyo, Japan. ttozaki@nyc.odn.ne.jp
MeSH Terms
- Animals
- Blotting, Southern
- Databases, Factual
- Gene Library
- Genetic Linkage
- Genome
- Genome, Human
- Horses / genetics
- Humans
- Sequence Analysis, DNA
- Trinucleotide Repeats
Citations
This article has been cited 2 times.- Yang Z, Zhao T, Ma Q, Liang L, Wang G. Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species. Front Plant Sci 2018;9:927.
- Hong JM, Chae SH, Oriero N, Larkin DM, Choi CB, Lee JY, Lewin HA, Bae JH, Choi I, Yeo JS. Identification and chromosomal localization of repeat sequences through BAC end sequence analysis in Korean cattle. J Genet 2005 Dec;84(3):329-35.
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