Polymorphic microsatellite loci and PCR multiplexing in the common vole,Microtus arvalis

We isolated and characterized 14 dinucleotide microsatellite loci in the common vole Microtus arvalis (Palas). Two multiplex panels both comprising seven loci were developed. Application to a set of 21 individuals allowed clear and easy characterization of allele sizes except for two loci which were then withdrawn from further analyses. The number of alleles ranged from four to 19 per locus with the observed heterozygosity ranging from 0.55 to 0.95. These sets of microsatellite loci provide high throughput capacity for population genetic studies at a minimum cost.     

Isolation and characterization of polymorphic microsatellite loci in the lance‐tailed manakin (Chiroxiphia lanceolata)

Eight microsatellite loci were isolated from the lance‐tailed manakin (Chiroxiphia lanceolata), a polygynous lek‐breeding bird from Central America. Five of these loci were polymorphic (two to seven alleles per locus), with observed levels of heterozygosity ranging from 0.100 to 0.860 (n = 50 individuals). These variable loci provide a valuable tool for assessing patterns of parentage and relatedness within lance‐tailed manakin social groups.     

Development and characterization of polymorphic microsatellites from Prunus avium‘Napoleon’

Primers were developed for 21 microsatellite loci isolated by enrichment from Prunus avium‘Napoleon’. Twelve loci contained uninterrupted dinucleotide repeats and nine were more complex. Nineteen primer pairs (EMPA001–019) showed single locus polymorphisms in a cultivar survey of 14 sweet cherries, with two to seven alleles per locus. Three primer pairs in combination (EMPA014, 015 and 018) discriminated all cultivars. Two primer pairs for loci monomorphic in P. avium were included: EMPA020 revealed segregation in an interspecific progeny and EMPA021 revealed polymorphism in P. dulcis. Twelve primer pairs reliably amplified products in three peach cultivars of which seven revealed polymorphisms.     

Characterization of seven polymorphic microsatellite loci in the Common Loon (Gavia immer)

We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from 10 locations in North America, including breeding, migration stopover, and wintering areas. Between two and seven alleles were observed to segregate at the seven microsatellite loci, with observed heterozygosities ranging from 0.048 to 0.695.     

Characterization of microsatellite loci isolated in trumpeter swan (Cygnus buccinator)

Primers for 16 microsatellite loci were developed for the trumpeter swan (Cygnus buccinator), a species recovering from a recent population bottleneck. In a screen of 158 individuals, the 16 loci were found to have levels of variability ranging from two to seven alleles. No loci were found to be linked, although two loci repeatedly revealed significant departures from Hardy–Weinberg equilibrium. Amplification in the closely related tundra swan (Cygnus columbianus) was successful for all except one locus. These microsatellite loci will be applicable for population genetic analyses and ultimately aid in management efforts.     

Characterization of one trinucleotide and six dinucleotide microsatellite markers in bicolor damselfish, <Emphasis Type="Italic">Stegastes partitus</Emphasis>, a common coral reef fish

Fourteen primer pairs were designed from 47 sequences containing microsatellites isolated from a genomic library enriched for (GACA)₄ in Stegastes partitus. Seven of these were shown to be polymorphic and provided clean amplification products. These seven loci were further characterized using 38 individuals, yielding a range in number of alleles from 5 to 31 and observed and expected heterozygosity values ranging from 0.45–0.89 and 0.66–0.96 respectively. Six of seven loci conformed to Hardy-Weinberg equilibrium. Successful amplification was also achieved in other Pomacentridae.     

Isolation and characterization of microsatellites in Chinese soft‐shelled turtle,Pelodiscus sinensis

Fifteen polymorphic microsatellite loci were developed for the Chinese soft‐shelled turtle (Pelodiscus sinensis) from the (GT)_n microsatellite‐enriched genomic library, using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol. The polymorphism of all 15 loci ranged from two to seven alleles with observed heterozygosities ranging from 0.03 to 0.98 (mean 0.43) in one population of 40 individuals. These novel loci will be helpful for understanding the population structure at genetic level and marker‐assisted breeding of this vulnerable species.     

Development and characterization of microsatellite markers for parentage analyses of the coral reef damselfish (<Emphasis Type="Italic">Pomacentrus amboinensis</Emphasis>: Pomacentridae)

Five new polymorphic microsatellite loci were developed for the coral reef damselfish Pomacentrus amboinensis. Twenty-four individuals from two Great Barrier Reef populations were genotyped at the five loci, with numbers of alleles per locus ranging from 6–23 and observed heterozygosity between 0.42–0.92. In addition, the cross-species testing of six primers developed for Stegastes partitus revealed one primer (SpGATA40) that was also polymorphic for P. amboinensis. Due to high levels of polymorphism (≥14 alleles) in at least four of the six loci and a high proportion of tetranucleotide repeats, these microsatellite markers should be useful for parentage assignment as well as other investigations of individual relatedness.     

Characterization of microsatellite markers from capybaras,Hydrochoerus hydrochaeris (Rodentia: Hydrochoeridae)

Fourteen microsatellite loci were isolated from capybaras (Hydrochoerus hydrochaeris), which are large, diurnal social rodents that occur in the wet savannas of South America. Five of these loci were monomorphic. The remaining nine loci were polymorphic (two to seven alleles per locus), with observed levels of heterozygosity ranging from 0.063 to 0.800 (n = 17 animals). The latter loci provide a valuable tool for assessing patterns of parentage and kinship within capybara social groups.     

Novel microsatellite loci for the study of the black‐capped vireo (Vireo atricapillus)

We identified 14 novel polymorphic microsatellite loci in the black‐capped vireo (Vireo atricapillus). We also attempted to amplify and genotype these loci in other Vireo species, including the white‐eyed vireo (Vireo griseus), red‐eyed vireo (Vireo olivaceus), and blue‐headed vireo (Vireo solitarius). In 33 genotyped black‐capped vireos from two locations, total alleles ranged from six to 20, with observed heterozygosity ranging from 0.58 to 0.91 and expected heterozygosity from 0.65 to 0.93. Two loci had detectable levels of null alleles. Many of the loci were able to be amplified in the related Vireo species.     

Development of EST‐SSRs from the Alpine Lady‐fern,Athyrium distentifolium

The utility of EST‐simple sequence repeats (EST‐SSRs) was evaluated in the fern Athyrium distentifolium. From 1152 frond cDNA clones, 165 microsatellites, including di‐, tri‐, tetra and penta‐nucleotide repeat motifs, were identified. Primer design was possible for 74 of the SSRs; subsequent screening of 10 loci on 186 individuals from six natural populations revealed between two and seven alleles per locus and expected heterozygosity (H_E) estimates ranging from 0.027 to 0.809. Eight of these loci were further examined for cross‐species and cross‐generic amplification in other Woodsiaceae species, and polymorphic products were detected. EST‐derived SSRs provide robust, informative and potentially transferable polymorphic markers suitable for biodiversity research.     

Microsatellite loci for the Australian field cricket Teleogryllus oceanicus and their cross‐utility in Teleogryllus commodus

Microsatellite loci were isolated from the Australian field cricket Teleogryllus oceanicus. Seven polymorphic loci were found with an observed number of alleles ranging from eight to 17 and observed heterozygosities between 0.26 and 0.94. One locus was found to be X‐linked. These seven loci were also tested for amplification and polymorphism in the congeneric species Teleogryllus commodus. The loci will be used for paternity studies in these species.     

Characterization of polymorphic microsatellite loci for the Tawny Pipit Anthus campestris and their utility in other steppe birds

New microsatellite loci for Tawny Pipit Anthus campestris were isolated from a genomic library. We were able to unambiguously score six loci: two were dinucleotide, one trinucleotide, two tetranucleotide and one pentanucleotide that turned out to be sex-linked. Four out of six loci were polymorphic with 7–23 alleles in our population and an observed heterozygosity ranging between 0.286 and 0.936. Cross-utility of these markers was tested in other 17 steppe-bird species of six families. In addition, 16 microsatellite loci developed for other species were tested for cross-species amplification in A. campestris. Eight microsatellite markers were successfully amplified; seven of them were polymorphic with 2–43 alleles and an observed heterozygosity of 0.040–0.863. Overall, 14 functional locus markers have been characterized for A. campestris that could be useful for future studies of paternity, genetic variability and population structure.     

Ten polymorphic microsatellite loci in Tibetan chicken, <Emphasis Type="Italic">Gallus gallus domesticus</Emphasis>

Through an improved enrichment protocol, a genomic library for (AC)₁₂ repeats was constructed and 34 microsatellite loci were isolated and characterized in an endangered animal, Tibetan chicken, Gallus gallus domesticus. In the 34 loci, ten loci showed a distinct allelic variation ranging from 4 to 14 alleles in 54 individuals tested. Polymorphism information content (PIC) ranged from 0.590 to 0.869 with an average of 0.713. Average observed and expected heterozygosities were 0.7988 (ranged from 0.310 to 1.000) and 0.7495 (ranged from 0.609 to 0.897), respectively. These ten microsatellites loci would be the valuable genetic markers for further investigation of Tibetan chicken.     

Polymorphic microsatellite loci for the Puerto Rican crested anole (<Emphasis Type="Italic">Anolis cristatellus</Emphasis>) and their amplification in related Puerto Rican species

We isolate six highly polymorphic microsatellite loci for the Puerto Rican crested anole (Anolis cristatellus) from a genomic library enriched for CA repeats. The number of alleles per locus ranged from 14 to 19, with levels of observed heterozygosity ranging from 0.60 to 0.73. Most of these loci were successfully cross-amplified in other members of the cristatellus species group (A. evermanni, A. gundlachi, A. krugi, A. stratulus), but levels of polymorphism were lower.     

Development of microsatellite markers in black locust (Robinia pseudoacacia) using a dual‐supression‐PCR technique

Black locust (Robinia pseudoacacia) is an economically and ecologically important tree species in the world. We isolated seven polymorphic microsatellite loci from R. pseudoacacia using a dual‐suppression‐PCR technique. These loci provided microsatellite markers with high polymorphism ranging from three to 12 alleles per locus and expected heterozygosity between 0.538 and 0.944. The markers are now available for more detailed investigation of population genetic structure and pollen and seed dispersal.     

Characterisation of 14 blue crane <Emphasis Type="Italic">Grus paradisea</Emphasis> (Gruidae,AVES) microsatellite loci for use in detecting illegal trade

Forty-two unique microsatellite loci were isolated from an unenriched and a tetranucleotide-enriched blue crane (Grus paradisea) genomic library. Fourteen polymorphic loci were characterised in 20 unrelated wild blue crane individuals from the Karoo region, South Africa, and displayed 4–27 alleles with observed heterozygosities ranging between 0.50 and 0.95. All 14 loci were also polymorphic in the grey-crowned crane (Balearica regulorum) and the wattled crane (Grus carunculatus). These markers are aimed at assisting the identification of illegal trade in the blue crane but have wider population and conservation applications for most, if not all, crane species.     

Isolation and characterization of sequence‐tagged microsatellite sites markers in chickpea (Cicer arietinum L.)

In this study we report the isolation of microsatellite sequences and their conversion to sequence‐tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Thirteen putative recombinants isolated from a chickpea genomic library were sequenced, and used to design 10 STMS primer pairs. These were utilized to analyse the genetic polymorphism in 15 C. arietinum varieties and two wild varieties, C. echinospermum and C. reticulatum. All the primer pairs amplified polymorphic loci ranging from four to seven alleles per locus. The observed heterozygosity ranged from 0 to 0.6667. Most of the STMS markers also amplified corresponding loci in the wild relatives suggesting conservation of these markers in the genus. Hence, these polymorphic markers will be useful for the evaluation of genetic diversity and molecular mapping in chickpea.     

Microsatellite loci for the field cricket,Gryllus bimaculatus and their cross‐utility in other species of Orthoptera

We have isolated 16 microsatellite loci in the field cricket, Gryllus bimaculatus. Nine loci were found to be polymorphic in G. bimaculatus and the number of alleles varied from seven to 14. All 16 loci were tested for amplification in nine other species. In the five species tested belonging to the same subfamily (Gryllinae), a minimum of nine loci amplified. These loci will be used to determine paternity as part of a study to investigate the genetic benefits of polyandry.     

Isolation and characterization of 43 microsatellite DNA markers for guppy (Poecilia reticulata)

Thirty‐nine polymorphic microsatellite DNA markers were isolated from the guppy (Poecilia reticulata) genomic library. All of the loci showed moderate allelic variation ranging from two to seven alleles, with observed heterozygosities from 0.000 to 0.938. The microsatellite DNA markers isolated will be available for use in analysis of quantitative trait loci in breeding programmes and for population genetic studies on experimental fish.