title: High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.
abstract: BACKGROUND
  Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility.
  
  
  RESULTS
  We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species.
  
  
  CONCLUSIONS
  When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK. d.a.dawson@sheffield.ac.uk
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Dawson
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Ball
authors.forename: Lewis G
authors.initials: LG
authors.lastname: Spurgin
authors.forename: David
authors.initials: D
authors.lastname: Martín-Gálvez
authors.forename: Ian R K
authors.initials: IR
authors.lastname: Stewart
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Horsburgh
authors.forename: Jonathan
authors.initials: J
authors.lastname: Potter
authors.forename: Mercedes
authors.initials: M
authors.lastname: Molina-Morales
authors.forename: Anthony W J
authors.initials: AW
authors.lastname: Bicknell
authors.forename: Stephanie A J
authors.initials: SA
authors.lastname: Preston
authors.forename: Robert
authors.initials: R
authors.lastname: Ekblom
authors.forename: Jon
authors.initials: J
authors.lastname: Slate
authors.forename: Terry
authors.initials: T
authors.lastname: Burke
mesh_terms: D000483:Alleles; D000818:Animals; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D017931:DNA Primers / Q000737:chemistry / Q000378:metabolism; D046369:Finches / Q000235:genetics*; D056426:Genetic Loci; D016678:Genome; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers