Development and characterization of microsatellite markers for genetic analysis of Cyclina sinensis Gmelin, 1791

Cyclina sinensis is one of the most popular commercially cultivated clam species in China. In this study, sixteen novel polymorphic microsatellite loci were isolated and characterized from a wild population of C. sinensis from the Dalian coast of China. The number of alleles varied between three and seven, and the observed and expected heterozygosity at the population level ranged from 0.4333 to 1.0000 and 0.3689 to 0.8070, respectively. No single locus significantly deviated from Hardy?CWeinberg equilibrium (P?>?0.01). These informative microsatellite markers will be useful for future population assessments and genome mapping studies in this species.     

Development and characterization of polymorphic microsatellite markers of Fejervarya syhadrensis useful for genetic studies

We describe here ten new microsatellite markers of Fejervarya syhadrensis (long-legged cricket frog). These markers were developed from the short sequence repeat-enriched genomic library and further validated using 34 frog samples collected from different parts of India. All markers were found to be polymorphic revealing 6?C30 alleles in the tested samples, with the observed heterozygosity and PIC values varying from 0.067?C0.882 to 0.573?C0.944, respectively. These markers also showed cross-species/cross-genera transferability to varying extent when tested on four related species of Fejervarya and two species of related genera Hoplobatrachus tigerninus and Euphlyctis cyanophlyctis. Importantly, four markers Fej_ccmb_01, Fej_ccmb_04, Fej_ccmb_06, and Fej_ccmb_07 showed 100?% transferability both across species and genera. Thus, this first report of ten new microsatellite markers is expected to greatly facilitate population genetic studies aimed to understand biogeography of Fejervarya, and/or the effect of various anthropogenic factors on amphibian decline.     

Development and characterization of thirty-three microsatellite markers for the Patagonian sprat,Sprattus fuegensis (Jenyns, 1842), using paired-end Illumina shotgun sequencing

We isolated and characterized a total of 33 microsatellite loci from the Patagonian sprat Sprattus fuegensis, a recent exploited marine resource with a conservation status unknowing. Loci were screened in 24 individuals from the inshore waters of the Aysén Fjord, Chile. The number of alleles per locus ranged from 7 to 24, observed heterozygosity ranged from 0.217 to 0.875, and the probability of identity values ranged from 0.006 to 0.133. These new loci will provide tools for examining population genetic structure, estimating effective population size and provide information to fisheries management and conservation.     

Development and characterization of 19 microsatellite markers for Collichthys lucidus

Nineteen microsatellite DNA markers of Collichthys lucidus were developed. The number of alleles for each locus ranged from three to 11. A total of 104 alleles were identified in 30 individuals collected from Zhejiang, China. The observed and expected heterozygosity per locus ranged from 0.2857 to 1.000 and from 0.5539 to 0.8774, respectively. Significant deviation from Hardy–Weinberg equilibrium at four microsatellite loci was detected after Bonferroni correction (P < 0.0026). These novel loci will be helpful for understanding the background of C. lucidus at genetic level.     

Development and characterization of 12 microsatellite markers for Johnius belengerii

Twelve microsatellite DNA markers were developed for Johnius belengerii by 5′ anchored PCR technique. A total of 64 alleles were identified in 30 individuals and the number of alleles per locus ranged from three to eight, with an average of 5.3. The observed and expected heterozygosity per locus ranged from 0.5000 to 0.9643 and from 0.5158 to 0.8413, respectively. Significant deviation from Hardy–Weinberg equilibrium was detected at three microsatellite loci after Bonferroni correction (P < 0.0042). No significant linkage disequilibrium was found between all pairs of 12 loci. These novel loci will be helpful for better understanding of genetic background of J. belengerii.     

Development and characterization of twelve microsatellite markers for miiuy croaker

Twelve microsatellite DNA markers were reported for miiuy croaker in this paper, of which nine were developed by 5’anchored PCR technique, and three were detected in three genes (CC, cathepsin D and CCL4) of miiuy croaker. A total of 63 alleles were identified in 30 individuals and the number of alleles per locus ranged from three to eight, with an average of 5.3. The observed and expected heterozygosity per locus ranged from 0.4667 to 1.0000 and from 0.4910 to 0.7755, respectively. Significant deviation from Hardy–Weinberg equilibrium was detected at two microsatellite loci after Bonferroni correction (P < 0.0042). No significant linkage disequilibrium was found between all pairs of twelve loci. These loci will be helpful for better understanding of genetic background of miiuy croaker.     

Development of microsatellite markers for genetic analysis in the large scale loach Paramisgurnus dabryanus

The large scale loach (Paramisgurnus dabryanus) is endemic to China and is one of the most abundant edible fish in East Asia. The species is invasive in Japan, competing and hybridizing with the native Misgurnus anguillicaudatus. In this study, microsatellites were developed for the first time in this species using biotinylated probes for hybridization and library screening. Twelve polymorphic microsatellite loci were isolated and characterized in farmed fish. The number of alleles varied between two and five, and the observed and expected heterozygosity ranged from 0.32 to 1.00 and 0.51 to 0.75, respectively. Three loci (Pda14-102, Pda15-139, Pda18-104) deviated significantly from Hardy–Weinberg equilibrium values (P < 0.01). These microsatellite markers could prove useful for genetic identification and population management of P. dabryanus in the future.     

Development and characterization of microsatellite markers for the seagrass Halodule wrightii

Halodule wrightii is a seagrass widely distributed in tropical areas, particularly in the western Atlantic. We have developed eight microsatellite markers from H. wrightii for use in genetic studies. The number of alleles ranged from 2 to 12 and the observed and expected heterozygosity ranged from 0.080 to 0.88, and from 0.077 to 0.86, respectively. No locus pair showed significant linkage disequilibrium or deviation from Hardy?CWeinberg proportions after Bonferroni correction (P?<?0.05). These markers should prove useful for elucidating genetic structure, phylogenetic relationships, and ecological processes in this foundational coastal species.     

Development and characterization of 23 polymorphic microsatellite markers for Sympetrum frequens

Twenty-three polymorphic microsatellite markers for Sympetrum frequens were developed and characterized. The number of distinct alleles per locus in 32 individuals ranged from 2 to 23. The observed heterozygosity ranged from 0.031 to 0.938, while the expected heterozygosity varied from 0.031 to 0.922. No loci deviated significantly from Hardy?CWeinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite markers are expected to contribute to future investigations of genetic variation and structure in S. frequens populations.     

Development and characterization of 17 microsatellite markers for Chinese soft-shelled turtle,Pelodiscus sinensis

A set of 17 polymorphic microsatellite markers were isolated and characterized for the Chinese soft-shelled turtle (Pelodiscus sinensis) using a next generation sequencing approach. The number of alleles per locus ranged from 2 to 11. The observed, expected heterozygosities and polymorphic information content per locus varied from 0.103 to 0.750, 0.222 to 0.883 and 0.158 to 0.788, respectively. Significant linkage disequilibrium and deviations from the Hardy–Weinberg disequilibrium between two pairs of loci were found. These loci will be beneficial for the population genetic structure investigation and marker assisted breeding for P. sinensis.     

Development and characterization of microsatellite markers for the Pacific Oyster Crassostrea gigas

Thirty-three polymorphic microsatellite DNA markers were developed and characterized for the Pacific Oyster Crassostrea gigas, a widespread oyster species with great economic and ecological importance, by the end-sequencing of an in-house fosmid library. The polymorphism of each locus was analyzed by screening 30 Pacific oysters from a natural population. The size of repeat motif ranged from 2 to 6 and the number of alleles per locus ranged from 3 to 9. The observed and expected heterozygosity ranged from 0.080 to 0.880 and from 0.174 to 0.876, respectively. These microsatellite markers will contribute to the increasing genetic studies in C. gigas.     

Development and characterization of genomic microsatellite markers in Rhododendron arboreum

Population genetics characteristics are the fundamentals of conservation and management practices. Rhododendron arboreum, a key biodiversity component inhabiting Indian Himalayas, suffers from overexploitation and global warming. Using biotin–streptavidin hybridization technique, 41 microsatellite markers were designed from an enriched DNA library to provide a genetic background and an insight into the population structure of the species. With a range of 2–14 alleles amplified from 38 loci, the populations were reported with observed and expected heterozygosity of 0.167–0.933 and 0.422–0.917 respectively. Some of the loci showed significant deviations from Hardy–Weinberg equilibrium and overall no linkage disequilibrium was detected. These markers will support genetic diversity and further genotyping studies in R. arboreum.     

Development and characterization of microsatellite markers for giant sequoia,Sequoiadendron giganteum (Cupressaceae)

We describe eleven polymorphic microsatellite markers for giant sequoia [Sequoiadendron giganteum (Lindl.) J. Buchh.], the world’s largest tree. Size-selected genomic DNA was enriched for short sequence repeats (SSR) and the resulting SSR library was analyzed on a Roche 454 platform. DNA samples from seedlings grown in a common garden (n = 359), representing a gene pool from twenty-three groves, were examined for SSR polymorphisms. The total observed alleles per locus ranged from three to twenty-five. Samples from the cabin creek grove (n = 21) exhibit observed heterozygosities ranging from 0.19 to 1.0, with one loci displaying significant deviation from Hardy–Weinberg equilibrium. Within this grove, no loci showed significant linkage disequilibrium. These microsatellite markers are important for assessing and conserving genetic diversity in this rare conifer.     

Development and characterization of microsatellite markers for Lychnophora ericoides, an endangered Cerrado shrub species

Lychnophora ericoides is an endangered species, endemic to cerrado rupestre. Herein we report the development and characterization of 13 polymorphic microsatellite loci for the species, using enriched genomic library. Number of alleles per locus and expected heterozygosity ranged from 06 to 13 and 0.696 to 0.894, respectively. The high combined probability of genetic identity (2.69 × 10^?17) and probability of paternity exclusion (0.9999) showed that multilocus genotypes are likely to be unique and will allow detailed parentage studies in natural populations of L. ericoides.     

Development and characterization of twenty microsatellite markers for the endangered fish Luciobarbus capito

Luciobarbus capito is an endangered fish species found in the Aral Sea of Uzbekistan. Here, we report the characterization of 20 polymorphic microsatellite loci from a (CA)₁₆-enriched genomic library. Among 15 individuals, the number of alleles per locus ranged from 2 to 6, and the observed and expected heterozygosity ranged from 0.143 to 1.00 and from 0.138 to 0.600, respectively. Four loci significantly deviated from Hardy?CWeinberg equilibrium and linkage disequilibrium. Polymorphism information content ranged from 0.175 to 0.680. These polymorphic microsatellite loci will be useful for population genetics, conservation and other relevant studies of this species.     

Development of polymorphic microsatellite markers of the common toad, Duttaphrynus melanostictus useful for genetic studies

Asian common toad, Duttaphrynus melanostictus, is a widespread habitat generalist species of Indian-subcontinent and South-East Asia. Here we report, 14 new microsatellite markers (SSRs) for this toad, developed from a SSR-enriched genomic library, and validated using 44 unrelated samples of Asian toad and ~20 samples belonging to four congeners. Nine SSRs were highly polymorphic; amplified 6–22 alleles/marker with H _o and PIC ranging from 0.477 to 0.955 and 0.518 to 0.918, respectively, while one was found to be monomorphic. Of the remaining four SSRs, two (DMccmb02, DMccmb17) amplified only two apparently fixed alleles in all samples, while the other two (DMccmb22, DMccmb29) amplified 1–4alleles/sample; these four SSRs probably represent duplicated loci. Interestingly, all the 14 SSRs showed cross-species transferability to varying extent, with four SSRs showing 100 % transferability. It is hoped that these SSRs will greatly facilitate population genetic studies on the Asian toad species across their geographic distribution.     

Development and characterization of 24 microsatellite markers in a eublepharid gecko,Goniurosaurus kuroiwae

The Ryukyu ground geckos, which comprise Goniurosaurus kuroiwae (sensu stricto) and four close relatives in the Ryukyu Archipelago, face conservation threats, and are listed as endangered in the Red List of both IUCN and Japan. We developed 24 microsatellite markers in G. kuroiwae and cross-amplified for another species, G. orientalis. All 24 and 22 loci were successfully amplified and genotyped in G. kuroiwae and G. orientalis, respectively. The number of alleles per locus and expected heterozygosity at polymorphic loci ranged from 1 to 11 and 0.050–0.891, respectively, in G. kuroiwae, and ranged from 1 to 15 and 0.050–0.932, respectively, in G. orientalis.     

Isolation and characterization of microsatellite markers for Sipunculus nudus

Conservation Genetics Resources - Sipunculus nudus is an economically important marine fish species in China. In this study, a (GT)13-microsatellite-enriched library was constructed and 18 novel...     

Development and characterization of microsatellite markers in Astronotus crassipinis (Heckel, 1840)

Astronotus crassipinis is an important freshwater fish in the Amazon basin. Little is known about their population structure and genetic diversity. They live in Amazon varzea lakes and are territorial fish practicing mouth brood. Studies involving populations of A. crassipinis are of great importance for the conservation and management of this species. Therefore, thirteen microsatellite markers were developed for this species and characterized in 30 accessions from lakes Preto and Ananá in Solimões river and lake Piranha, located in the system Negro–Solimões. The observed and expected heterozygosities ranged from 0.00 to 0.72 and 0.25 to 0.58, respectively. Alleles per locus varied from two to six, with an average of three. Three loci departed significantly from Hardy–Weinberg Equilibrium (P < 0.05) after Bonferroni correction. The value of Fis (f) ranged from ?0.666 to 0.909 (average on ?0.133). This new set of microsatellites will contribute towards studies of genetic diversity and conservation of A. crassipinis.     

Isolation and characterization of microsatellite markers for blue marlin, Makaira nigricans

In the Unites States, blue marlin, Makaira nigricans, is managed as separate Atlantic and Indo-Pacific stocks. To facilitate the discrimination of the two stocks for enforcement purposes, we developed 10 new microsatellite markers and screened collections of 20 individuals each from Ghana and Hawai’i. Observed heterozygosities (H_O) ranged from 0.700 to 1.000 among loci at the two collections. The number of alleles per locus ranged from 14 to 24, there were no significant deviations from the expectations of Hardy–Weinberg equilibrium, and there was no evidence of linkage disequilibrium among the loci. These new markers will provide more power to assign marketed blue marlin products to ocean origin.