Polymorphic dinucleotide microsatellites for the Mediterranean angler species (Lophiidae)

A microsatellite‐enriched genomic library was obtained from black‐bellied angler Lophius budegassa and six polymorphic dinucleotide markers were successfully optimized. These markers showed levels of polymorphism ranging from 0.363 to 0.662 and allele numbers ranging from three to seven. These markers were also found to successfully amplify in the closely related Lophius piscatorius (angler) and thus appear to be useful for genetic stock structure analysis in both species.     

Isolation of polymorphic DNA microsatellites in the common sole Solea vulgaris

A microsatellite‐enriched genomic library was obtained from the common sole, Solea vulgaris, and seven polymorphic dinucleotide markers were successfully optimized. These markers showed levels of expected heterozygosity ranging from 0.55 to 0.83 and allele number ranging from eight to 12. Three of these markers were also found to successfully amplify in the closely related Solea senegalensis and can be employed to define population genetic structure of the two Solea species and for inferring stock origins.     

Isolation and characterization of microsatellite loci in the finless porpoise (Neophocaena phocaenoides)

Eight dinucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Analysis of 30 individuals showed the number of alleles ranged from four to 21 with observed heterozygosity ranging from 0.300 to 0.833, and expected heterozygosity ranging from 0.437 to 0.932. Cross‐species amplification was tested in four other cetacean species. These microsatellite markers would be valuable tools for population genetic studies of finless porpoises and other cetacean species.     

Isolation and characterization of microsatellite loci in the threatened brook lamprey Lethenteron sp. N

A microsatellite‐enriched genomic library was obtained for the threatened brook lamprey, Lethenteron sp. N, and from it 16 dinucleotide markers were successfully isolated and characterized. These markers were found to have between 1 and 6 alleles with heterozygosity ranging from zero to 0.79. Cross‐species amplification was successful, with eight loci amplifying products in the counterpart cryptic species, Lethenteron sp. S, as well as 15 loci in Lethenteron japonicum. One out of 10 primer pairs previously reported also amplified products in all the three species.     

Isolation and characterization of 12 microsatellite loci for cross-species amplification in the cyprinid gudgeons Squalidus chankaensis and S. japonicus

Twelve dinucleotide markers were successfully isolated and characterized from a microsatellite‐enriched genomic library obtained for the gudgeon Squalidus chankaensis biwae. These markers were also available for the congeners S. c. tsuchigae and S. japonicus from Japan, which had five to 46 alleles and an expected heterozygosity ranging from zero to 0.946. Linkage equilibrium was observed at all loci, and most loci did not show significant deviation from Hardy–Weinberg equilibrium. The isolated microsatellite markers will be useful for genetic diversity studies of Squalidus populations.     

Isolation and characterization of microsatellite loci in the Bang's leaf‐nosed bat Hipposideros turpis

The Bang's leaf‐nose bat, Hipposideros turpis, is an endangered cave‐dwelling species inhabiting the southwesternmost islands of Japan. We isolated six dinucleotide microsatellite markers from the partial genomic library of the bat, and examined their allelic variation using a sample (N = 33) from the largest colony in Japan. All the loci showed a moderate allelic variation ranging from two to eight alleles, with the observed heterozygosities from 0.33 to 0.73, and conformed to Hardy–Weinberg expectations. The present microsatellite markers will be useful in assessing population genetic structure and gene flow among populations of this species.     

Novel polymorphic microsatellite markers for the common pandora (Pagellus erythrinus)

Details of six highly polymorphic dinucleotide and one highly polymorphic tetranucleotide microsatellite markers are provided for Pagellus erythrinus. These markers are highly polymorphic, with an expected heterozygosity ranging from 0.713 to 0.959 and allele numbers ranging from seven to 36. These microsatellite markers should help determine population genetic structure and fisheries stocks for management purposes.     

Characterization of new microsatellite loci for the ring‐tailed lemur (Lemur catta)

In this report we describe the development and characterization of six dinucleotide microsatellite loci for the ring‐tailed lemur (Lemur catta). The new markers were isolated from the genomic DNA of L. catta and all loci were found to be polymorphic when evaluated by genotyping a minimum of 34 individuals. Mendelian inheritance of each locus was verified using four families of captive ring‐tailed lemurs. The loci presented will facilitate the genetic survey of free‐ranging L. catta, enabling study of their social organization and mating patterns.     

Isolation and characterization of microsatellite markers in pangolins (Mammalia,Pholidota, Manis spp.)

Thirty‐four polymorphic dinucleotide microsatellite loci were developed in the Malayan pangolin Manis javanica. Of the 34 markers, 32 and 18 were also amplified, respectively, in the Chinese pangolin (Manis pentadactyla) and the African tree pangolin (Manis tricuspis). Analysis of 24 Malayan, 12 Chinese and 2 African tree pangolins showed high levels of variability (heterozygosity ranging from 0.321 to 0.708). These are the first available microsatellite markers in Pholidota and will be an invaluable tool for evolutionary and conservation genetic studies in pangolins.     

Identification of microsatellite markers in a neotropical seasonally dry forest tree,Astronium urundeuva (Anacardiaceae)

Nine dinucleotide microsatellites were developed in Astronium urundeuva (Anacardiaceae), a typical tree of the seasonally‐dry tropical forests of South America and characterized on three populations from Paraguay and Argentina. Seven microsatellites were found polymorphic in within population gene diversities ranging from 0.32 to 0.91, and an observed number of alleles varying between four and 20. Despite their relatively low number of alleles, these markers proved valuable tools in detecting genetic structure between three populations in Paraguay and North Argentina.     

Nine new microsatellite loci for the orange roughy (Hoplostethus atlanticus)

We isolated nine new dinucleotide microsatellites for the deep-sea fish Hoplostethus atlanticus. These loci are generally highly polymorphic, with allele number ranging from 3 to 31 and observed heterozygosity ranging from 0.067 to 0.933. In conjuction with previously published loci, these markers will be useful for fine-scale analysis of population structure in this commercially important and threatened species.     

Development of simple sequence repeat markers for the plant pathogenic rust fungus,Puccinia graminis

Twenty‐four dinucleotide simple sequence repeat markers were developed for the phytopathogenic fungus, Puccinia graminis. The identified loci were polymorphic, with allelic diversity ranging from two to 11 alleles. Observed and expected levels of heterozygosity ranged from 0.000 to 0.960 and from 0.113 to 0.846, respectively. Fourteen of the loci deviated significantly from Hardy–Weinberg equilibrium. Null alleles were observed for 10 of the 24 loci with a frequency of 4–16%. A preliminary screen of other Puccinia cereal rust fungi (P. coronata, P. striiformis and P. triticina) indicated that these primer pairs are specific to P. graminis.     

Development of microsatellite markers for mango (Mangifera indica L.)

Microsatellite markers for mango (Mangifera indica L.) were developed using a genomic library enriched for (GA)_n and (GT)_n dinucleotide repeats. A subset of 41 positive clones was sequenced and primers were designed. Twenty‐eight primer pairs produced polymorphic amplification products for a diversity sample including 15 mango cultivars and two accessions from the related species Mangifera laurina and Mangifera applanata. Nineteen simple sequence repeat (SSR) loci with clear scorable patterns were chosen to study diversity in the mango germplasm bank of Guadalupe (FWI). The number of alleles ranged from three to 13 with observed levels of heterozygosity ranging from 0.059 to 0.857.     

Isolation and characterization of 13 microsatellite loci in Rhinolophus pusillus (least horseshoe bat) with cross-amplification in five related species

We used the enriched genomic library method to isolate and characterize dinucleotide microsatellite loci in the least horseshoe bat, Rhinolophus pusillus. Seventeen loci were obtained and tested on 31 individuals sampled from Guangxi Province in southern China. Thirteen of these markers were polymorphic with expected heterozygosity ranging from 0.821 to 0.909. A total of 164 alleles were detected and the number of alleles per locus ranged from 9 to 16 (mean 12.6). These polymorphic markers will be used to assess population structure in R. pusillus. In addition, successful cross-amplification in five congeneric bat species suggests most of these markers will also be useful for studying related species.     

Isolation of polymorphic microsatellite markers from Hymeniacidon sinapium (Porifera: Demospongiae: Halichondrida)

Eight dinucleotide microsatellite markers were developed on Hymeniacidon sinapium (Porifera: Demospongiae), common littoral sponge around Japan, to investigate population genetic structure. Two to 10 alleles were identified in an analysis of 24 individuals of H. sinapium, with observed heterozygosity ranging from 0.04 to 0.83. All loci did not deviate from the Hardy–Weinberg expectations; however, significant linkage disequilibrium between Sinp126 and Sinp142 was found.     

The highly polymorphic microsatellite markers for the greater long‐tailed hamster (Tscherskia triton)

We isolated 25 dinucleotide microsatellite loci from the greater long‐tailed hamster (Tscherskia triton) populations in North China. We developed the amplification conditions of polymerase chain reaction for producing high‐resolution genetic markers for each locus. We found 10 microsatellite loci were highly polymorphic in 90 individual hamsters from three areas of North China, and the number of alleles in each locus varied from three to 11. These markers are potential tools for studying the genetic variation of the natural populations of this species.     

Screening of ESTs from Mytilus for the detection of SSR markers in Mytilus californianus

A set of expressed sequence tag‐simple sequence repeat (EST‐SSR) markers for the genus Mytilus was developed through bioinformatic mining of the GenBank public database. A total of 33 782 EST sequences from GenBank were downloaded and screened for di‐, tri‐ and tetranucleotide, with 1274 EST containing SSR markers. Nine microsatellite markers were characterized in Mytilus californianus with a number of alleles per locus ranging from two to six, and total observed and expected heterozygosities ranging from 0.490 to 0.730 and from 0.510 to 0.860 respectively. Cross‐species amplification was achieved in several other species, confirming the usefulness of these markers in Mytilus genetics.     

Sixteen new polymorphic microsatellite markers isolated for red‐legged partridge (Alectoris rufa) and related species

We developed and tested 16 new polymorphic microsatellite markers for the red‐legged partridge (Alectoris rufa): four dinucleotide, two trinucleotide, eight tetranucleotide and two pentanucleotide repeat loci. The number of alleles per locus ranged from two to 21, observed heterozygosity was from 0.03 to 1.00 and expected heterozygosity was comprised between 0.18 and 0.91. Cross‐specific amplification in others members of the Phasianidae family highlighted the potential usefulness of these molecular markers for the study of related species.     

Isolation and characterization of microsatellite markers for the seagrass Cymodocea nodosa

In order to study the spatial patterns of genetic diversity of a clonal marine angiosperm, the seagrass Cymodocea nodosa, microsatellite markers were obtained by screening a genomic library enriched for the (CT) dinucleotide motif. Of 38 primer pairs defined, 15 amplified polymorphic microsatellites and are described. These loci identified a number of alleles ranging from two to seven, and showed expected heterozygosity ranging from 0.35 to 0.76, when a group of 40 individuals from Cadiz Bay in Spain was analysed. Additionally, we describe here the multiplexing conditions for 12 of these loci.     

Isolation and characterization of polymorphic microsatellite markers in Eurasian vulture Gyps fulvus

To obtain polymorphic molecular markers for population genetic and conservation studies in the Eurasian vulture Gyps fulvus populations, we screened a size‐selected partial genomic library enriched for microsatellites with dinucleotide motifs. A total of five polymorphic markers were obtained. The number of alleles ranged from two to nine and the observed and expected heterozygosity were very similar. These markers will be very useful for studying population structure and to evaluate conservation programmes.