Abstract
BackgroundMicrosatellite 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.ResultsSixty-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.ConclusionGenomic 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.
Highlights
Microsatellite markers are popular genetic markers frequently used in forensic biology
Mapping Sixty-eight Charadriiformes microsatellite sequences were assigned to a location on the chicken genome based on sequence homology
Excluding the markers that had been isolated in the target species, we found on average that 7 of 24 markers per species were polymorphic when tested in four unrelated individuals from a single population (Figure 4)
Summary
Microsatellite markers are popular genetic markers frequently used in forensic biology. 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. 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. BMC Genomics 2008, 9:502 http://www.biomedcentral.com/1471-2164/9/502 ble for the variability in microsatellites are considered to be replication-slippage and recombination [3]. Both processes change the length of the microsatellite by altering the number of repeats of the microsatellite. It was found that microsatellites with tri- or hexanucleotide motifs are more frequent in coding than in non-coding regions, possibly because mutations of these microsatellites in coding regions are less likely to result in deleterious frameshift mutations [1,2]
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