Eight new polymorphic microsatellite loci for genetic analyses in the endangered common hamster (Cricetus cricetus L.)

We developed primers for eight polymorphic microsatellite loci in the endangered common hamster (Cricetus cricetus L.). Population genetic parameters were analysed on the basis of 70 adult individuals captured from a single population. Allele numbers per locus ranged from eight to 17. Expected and observed heterozygosities per locus ranged from 0.67 to 0.91 and from 0.41 to 0.8, respectively.     

New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini

We isolated 15 microsatellite markers for the scalloped hammerhead shark, Sphyrna lewini. Loci were tested on 80 specimens of S. lewini from four Eastern Pacific samples. The number of alleles per locus ranged from 6 to 31 (mean = 14). Observed and expected levels of heterozygosity per locus ranged from 0.39 to 0.91 (mean = 0.70) and from 0.54 to 0.90 (mean = 0.76), respectively. No pairs of loci were in gametic disequilibrium after Bonferroni correction of α. One locus showed significantly lower heterozygosity than expected under Hardy–Weinberg proportions in two populations, possibly caused by null alleles.     

Isolation and characterization of variable microsatellite loci in Lilium philadelphicum (Liliaceae)

Here we describe the characterization of six polymorphic microsatellite loci for Lilium philadelphicum (Liliaceae). Polymorphism levels ranged from 7 to 30 alleles per locus with a mean number of 15 alleles per locus. Observed heterozygosity (H_O) ranged from 0.17 to 0.82 and did not deviate from Hardy–Weinberg expectations in the three western Montana populations included in the analysis. These loci are proving useful in studying gene flow between populations of this species distributed across its range in North America.     

Characterization of microsatellite DNA markers in a critically endangered species,Mekong giant catfish,Pangasianodon gigas

Microsatellite DNA markers for a critically endangered Mekong giant catfish (Pangasianodon gigas Roberts and Vidthayanon, 1991) were developed from fin clips collected from captive fish using (GT)₁₅ probe. The number of alleles per locus ranged from two to four. The expected heterozygosities ranged from 0.13 to 0.68. Also, these primers were successfully amplified in four closely related species, Pangasius bocourti, Pangasius conchophilus, Pangasius larnaudii and Pangasius sanitwongsei with the number of alleles per locus ranged from 1 to 13, 1 to 16, 1 to 12 and 1 to 4, respectively. These markers should prove to be very useful for the evaluation of genetic diversity for this species and other related Pangasius species.     

Isolation and characterization of polymorphic microsatellite loci in the gudgeon,Gobio gobio (Cyprinidae)

A total of seven polymorphic microsatellite loci from Gobio gobio were isolated and characterized. A preliminary population survey of 82 specimens from four populations, located in a downstream pollution gradient of cadmium and zinc, demonstrated the usefulness of these primers both in population genetic studies in general, as well as in evaluating the effects of anthropogenic pollution on genetic structure. Overall locus polymorphism ranged from two to 13 alleles. Observed heterozygosity per locus ranged from 0.39 to 0.73.     

Ten microsatellite loci for the strawberry poison frog (Oophaga pumilio)

We describe primers and PCR conditions to amplify nine new tetranucleotide loci and one new dinucleotide locus isolated from the strawberry poison frog (Oophaga pumilio). In 21 individuals from Costa Rica, the number of alleles ranged from 4 to 16, observed heterozygosities from 40 to 100%, and polymorphic information content ranged from 0.60 to 0.90 per locus. Evidence for linkage disequilibrium was found only between two loci, but this pattern was not found in other populations tested. All primer pairs cross-amplified in Oophaga vicentei from Panama.     

Characterization of 14 tetranucleotide microsatellite loci derived from Pacific herring

Spawning aggregations of Pacific herring (Clupea pallasi) often exhibit significant interannual variation in allele frequencies of neutral gene markers. We isolated 14 tetranucleotide microsatellites to examine hypothetical processes that may produce this unique genetic signal. We developed and tested primer pairs for each locus and then estimated locus variability in samples (n = 60) from two populations. The number of alleles per locus ranged from five to 49. The expected heterozygosity across loci and populations ranged from 0.20 to 0.96. These microsatellites will be useful for estimating genetic variation in herring on a fine geographical scale.     

Isolation and characterization of fourteen polymorphic microsatellite markers in the viperine snake Natrix maura

Nineteen polymorphic microsatellite loci were identified and developed for Natrix maura. Polymorphism was assessed for 120 individuals sampled across four sampling sites from the French Pyrenees Mountains. The number of alleles per locus ranged from 3 to 15, and expected heterozygosity per locus ranged from 0.227 to 0.863. We tested for deviation from Hardy–Weinberg equilibrium and linkage disequilibrium and assessed the presence of null alleles for all loci, resulting in a selection of 14 high‐quality polymorphic markers. These markers will be extremely useful in identifying fine‐scale genetic structures and providing insight into conservation management plans of this species.     

Microsatellite markers for Vaccinium from EST and genomic libraries

We present 30 microsatellite loci isolated from expressed sequence tag (EST) and genomic libraries in Vaccinium corymbosum L. Allele number per locus in 11 tetraploid and one diploid V. corymbosum accessions ranged from two to 15 (mean = 8.16) in 24 single‐locus simple sequence repeats (SSRs). Cross‐species amplification in a panel of 12 species representing nine sections ranged from 30 to 100% (mean = 83%).     

Characterization of 16 microsatellite loci for a common coral reef fish,the fierce shrimpgoby Ctenogobiops feroculus

We developed 16 pairs of primers for microsatellite loci of the fierce shrimpgoby, Ctenogobiops feroculus. Analysis of 35–40 gobies per locus from five islands in French Polynesia indicated that allele frequency varied from two to 30 per locus, while observed heterozygosity ranged between 0.05 and 0.98. These microsatellites should provide insight into patterns of dispersal and connectivity among populations of this common coral reef fish.     

Development and characterization of microsatellite markers in the fungus Antrodia cinnamomea from dbEST database

We developed and characterized 8 polymorphic microsatellite loci or simple sequence repeats from the expressed sequence tags database of the medicinal fungus, Antrodia cinnamomea. Variability was assessed in a panel of 23 strains collected from various regions of Taiwan. The number of alleles per polymorphic locus ranged from two to seven loci with an average of 4.375 alleles per locus. The observed and expected heterozygosity values ranged from 0.130 to 0.783 and from 0.122 to 0.809, respectively. No significant Hardy–Weinberg equilibrium was detected (P < 0.01) at all loci. The EST-SSR markers developed in the present study can be used for strain identification and population genetic studies in A. cinnamomea.     

Genetic diversity and population genetic structure of the Wood Turtle (Glyptemys insculpta) at Delaware Water Gap National Recreation Area, USA

Glyptemys insculpta is considered to be one of the most endangered freshwater turtles in North America. Here microsatellite markers were employed to investigate the genetic variation and population structure of G. insculpta at Delaware Water Gap National Recreation Area (USA). Seven microsatellites revealed high allelic variation with 13–30 alleles per locus. Observed and expected heterozygosities per locus ranged from 0.875–0.925 to 0.888–0.952, respectively. Pairwise estimates of population structure (θ) ranged from 0.000–0.013 to θ estimated over all loci and aggregations was not significantly different from zero. Gene flow (Nm) was high and ranged from 19 migrants per generation to infinity in pairwise comparisons. No significant relationship between geographic distance and genetic distance was detected. These data indicate that G. insculpta at DEWA represent a single, genetically diverse management unit for conservation.     

Ten novel tetranucleotide microsatellite DNA markers from Asiatic black bear, Ursus thibetanus

Ten polymorphic microsatellite markers were developed for the endangered Formosan black bear (Ursus thibetanus formosanus) from a partial genomic library enriched for GAAA repeat. Polymorphism of these loci was evaluated in 27 Formosan black bear specimens of unknown relationship. The number of alleles per locus ranged from 5 to 15 and the observed heterozygosity of each locus ranged from 0.556 to 0.889. These loci should provide useful molecular tools to study conservation genetics of the Formosan black bear and other Asiatic black bears.     

Isolation and characterization of microsatellite markers in Perilla frutescens Brit

We isolated and characterized 13 polymorphic microsatellite primers from Perilla frutescens Brit. var. frutescens by using a modified method that involves one‐way PCR amplification with single primer prior to enrichment with an ‘oligo hook’. The efficiency of this procedure for isolating unique microsatellite sequences was approximately 77%. The number of alleles per microsatellite locus ranged from three to 10 with an average of 6.5 alleles per locus while fragment size varied from 156 to 298 bp. The observed and expected heterozygosities ranged from 0.52 to 0.86 and 0.52 to 0.89, respectively. These newly isolated microsatellite markers are expected to provide valuable resources for different genetic studies currently underway in our Perilla genome research program.     

Development and characterization of twelve polymorphic microsatellite loci in the threatened Red Hills salamander, Phaeognathus hubrichti

We isolated and characterized 12 microsatellite loci from the endangered Red Hills salamander, Phaeognathus hubrichti. Loci were screened in 24 individuals of P. hubrichti. The number of alleles per locus ranged from 2 to 16, observed heterozygosity ranged from 0.130 to 0.750, and the probability of identity values ranged from 0.012 to 0.778. These new loci provide tools for examining the population genetics of this federally threatened salamander.     

Development of polymorphic microsatellite markers for the Steere's Liocichla (Liocichla steerii)

For the Steere's Liocichla (Liocichla steerii) we developed seven polymorphic microsatellite markers from a partial genomic library enriched for GATA, tetranucleotide repeats. Among the 27–28 individuals screened, allelic diversity ranged from six to 19 alleles per locus and the observed heterozygosity of each locus ranged from 0.250 to 0.889. All loci conformed to Hardy–Weinberg expectations except for two that appeared to be Z‐Iinked; such Z‐Iinked loci can be used in studies of male dispersal.     

Development and characterisation of microsatellite markers for <Emphasis Type="Italic">Cordia verbenacea</Emphasis> (Boraginaceae), an important medicinal species from the Brazilian coast

Cordia verbenacea DC (Boraginaceae) is a Brazilian coastal shrub species extensively utilized in the folk medicine and also by the pharmaceutical industry. Despite its enormous economic and pharmacological potential, little is known about its reproductive biology, genetic structure and genetic diversity of natural populations. Due to the rapid degradation of its natural habitat, this knowledge became imperative. We developed a set of eight highly polymorphic microsatellite markers for the study of genetic structure and diversity of C. verbenacea natural populations and germplasm collections. Six of them revealed a multibanded pattern typical of polyploid species. The total number of bands per locus ranged from 2 to 12 and the number of bands per locus per individual ranged from 1 to 8. The primer pairs presented here will be used to generate information to guide conservation programs and rational exploitation of C. verbenacea.     

Isolation and characterization of polymorphic microsatellite markers in the white‐winged chough (Corcorax melanorhamphos)

We have isolated and characterized seven polymorphic microsatellite loci in the white‐winged chough (Corcorax melanorhamphos), a highly social, cooperatively breeding bird of Australian eucalypt woodlands. In analyses of 100 samples from 16 family groups, the number of alleles per locus ranged from four to 18, and observed heterozygosity ranged between 0.46 and 0.93. One locus appears to be sex‐linked. The primers were also tested in apostlebirds (Struthidera cinerea), the only other species in the subfamily Corcoracinae. Five loci were successfully amplified and three were polymorphic.     

Isolation and characterization of polymorphic microsatellite markers for the endangered Korean freshwater fish Hemibarbus mylodon

Korean barbel, Hemibarbus mylodon, is an endangered freshwater species endemic to Korea. In order to undertake a conservation program for this species in Korea, it is essential to evaluate its genetic diversity and population structure. For this purpose, we developed 10 polymorphic microsatellite markers and examined their allelic variation using a total of 60 wild individuals collected from three different localities. The number of alleles per locus ranged from three to 26. The expected and observed heterozygosities per locus ranged from 0.19 to 0.94 and from 0.20 to 0.98, respectively. Significant departures from Hardy–Weinberg equilibrium expectations occurred in four loci. These markers will be useful for the assessment of genetic diversity for this species.     

Isolation and characterization of EST‐derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum

Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum.