Kupper, C., Burke, T., Szekely, T. et al. (1 more author) (2008) Enhanced cross-species utility of conserved microsatellite markers in shorebirds. BMC Genomics, 9. 502. ISSN 1471-2164
Abstract
Background Microsatellite markers are popular genetic markers frequently used in forensic biology. Despite their popularity, the characterisation of polymorphic microsatellite loci and development of suitable markers takes considerable effort. Newly-available genomic databases make it feasible to identify conserved genetic markers. We examined the utility and characteristics of conserved microsatellite markers in Charadriiformes (plovers, sandpipers, gulls and auks). This order harbours many species with diverse breeding systems, life histories and extraordinary migration biology whose genetics warrant investigation. However, research has been largely restrained by the limited availability of genetic markers. To examine the utility of conserved microsatellite loci as genetic markers we collated a database of Charadriiformes microsatellites, searched for homologues in the chicken genome and tested conserved markers for amplification and polymorphism in a range of charadriiform species.
Results Sixty-eight (42%) of 161 charadriiform microsatellite loci were assigned to a single location in the chicken genome based on their E-value. Fifty-five primers designed from conserved microsatellite loci with an E-value of E-10 or lower amplified across a wider range of charadriiform species than a control group of primers from ten anonymous microsatellite loci. Twenty-three of 24 examined conserved markers were polymorphic, each in on average 3 of 12 species tested.
Conclusion Genomic sequence databases are useful tools to identify conserved genetic markers including those located in non-coding regions. By maximising primer sequence similarity between source species and database species, markers can be further improved and provide additional markers to study the molecular ecology of populations of non-model organisms.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2008 Küpper et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | GREAT REED WARBLERS; POLYMORPHIC MICROSATELLITES; SEQUENCE ALIGNMENT; PASSERINE BIRD; LOCI; EVOLUTION; CHICKEN; DNA; AMPLIFICATION; MUTATIONS |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 10 Jun 2015 10:55 |
Last Modified: | 11 Aug 2015 19:54 |
Published Version: | http://dx.doi.org/10.1186/1471-2164-9-502 |
Status: | Published |
Publisher: | BioMed Central |
Refereed: | Yes |
Identification Number: | 10.1186/1471-2164-9-502 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:86828 |