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Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags
I Coulibaly1, K Gharbi, R G Danzmann
1Animal and Veterinary Sciences Division, West Virginia University, PO Box 6108, Morgantown, WV 26506, USA.
Animal Genetics
|July 20, 2005
Summary
Researchers developed 428 microsatellite markers for rainbow trout (Oncorhynchus mykiss) to create high-density linkage maps. Microsatellite markers from expressed sequence tags (ESTs) showed higher polymorphism information content (PIC) and cross-species amplification than anonymous markers.
Area of Science:
- Aquatic Genomics
- Molecular Ecology
- Fisheries Science
Background:
- High-density linkage maps are crucial for identifying genes controlling important traits in species like rainbow trout (Oncorhynchus mykiss).
- Development of numerous, evenly spaced, polymorphic genetic markers across the genome is essential for constructing these maps.
- Microsatellite markers are valuable genetic tools for mapping and population genetics studies.
Purpose of the Study:
- To compare the utility of expressed sequence tag (EST)-derived microsatellite markers versus anonymous genomic DNA-derived microsatellite markers for rainbow trout.
- To characterize marker properties including polymorphism information content (PIC), allele number, repeat number, genome duplication, and cross-species amplification.
- To develop a substantial set of microsatellite markers for future mapping and population genetic analyses in rainbow trout.
Main Methods:
- Developed and characterized a subset of 70 microsatellite markers (37 from ESTs, 33 from repeat-enriched genomic libraries).
- Assessed polymorphism information content (PIC), number of alleles, and repeat characteristics for each marker type.
- Investigated locus duplication within the genome and evaluated cross-species amplification potential in other salmonids.
Main Results:
- EST-derived dinucleotide microsatellites exhibited higher PIC (72.7%) compared to anonymous markers (54.0%).
- Anonymous microsatellites showed higher dinucleotide repeat numbers (27.4) than EST-derived markers (18.1).
- EST microsatellites demonstrated a higher rate of cross-species amplification; genomic microsatellites were more effective for discriminating among salmonid species.
Conclusions:
- Both EST-derived and anonymous microsatellite markers are useful, with distinct advantages for different applications.
- Approximately half of each marker type were duplicated within the rainbow trout genome.
- A total of 428 microsatellite markers were successfully developed for mapping and population genetics in rainbow trout.