Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Open Badges Methodology article

Enhanced cross-species utility of conserved microsatellite markers in shorebirds

Clemens Küpper12*, Terry Burke1, Tamás Székely2 and Deborah A Dawson1

Author Affiliations

1 NERC Molecular Genetics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2 TN, UK

2 Department of Biology and Biochemistry, University of Bath, Bath, BA2 7 AY, UK

For all author emails, please log on.

BMC Genomics 2008, 9:502  doi:10.1186/1471-2164-9-502

Published: 24 October 2008



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.


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.


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.