Isolation and characterization of polymorphic microsatellite loci from elongate loach (Leptobotia elongate), a threatened fish species endemic to the Yangtze River

Elongate loach (Leptobotia elongate) is a threatened fish species endemic to the Yangtze River in China. A first set of 22 polymorphism microsatellite loci isolated from this species was characterized. The number of alleles, observed and expected heterozygosity ranged from 2 to 12, from 0.2667 to 1.000 and from 0.2391 to 0.9011, respectively. Seven loci significantly deviated from Hardy?CWeinberg equilibrium after Bonferroni correction. The polymorphism information content ranged from 0.204 to 0.857. Ten loci were highly informative, 11 were moderately informative, and one was slightly informative. These polymorphic microsatellite markers will be useful for genetic monitoring of natural populations and management of breeding stocks in hatcheries.     

Development and characterization of microsatellite loci in Lamprotula leai, with cross-amplification in Hyriopsis cumingii

Eighteen microsatellite loci were isolated and characterized in Lamprotula leai. The number of alleles observed for each locus ranged from 3 to 13. The values of observed heterozygosity and expected heterozygosity ranged from 0.2083 to 0.8944 and from 0.4305 to 0.8961, respectively. Fifteen loci conformed to Hardy–Weinberg equilibrium and no linkage disequilibrium was found. A cross-amplification test showed ten out of eighteen loci were successfully amplified in three hyriopsis cumingii populations. These informative microsatellite markers will be useful to assess genetic diversity for this species.     

Isolation and characterization of novel microsatellite markers in Codonopsis tangshen (Campanulaceae)

In this study, sixteen novel microsatellite loci primers were developed for codonopsis tangshen, a traditional endemic medicinal plant species in the central-western China. The polymorphism of each locus was assessed through 62 individuals from two natural populations. Number of alleles per locus ranged from 5 to 13. The observed heterozygosity (H _O) ranged between 0.396 and 0.823, and the expected heterozygosity (H _E) was between 0.528 and 0.931. There was no significant linkage disequilibrium was detected between pairs of loci. The markers presented in the study are sufficiently polymorphic and quite informative to investigate the genetic diversity and population structure of C. tangshen.     

A first set of polymorphic microsatellite loci isolated from Rhinogobio cylindricus

Rhinogobio cylindricus is an endemic freshwater fish species with relevant commercial importance in the Yangtze River, China. Nineteen polymorphic microsatellite loci were developed by fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. The number of alleles, observed and expected heterozygosity ranged from 2 to 6, from 0.3333 to 1.000 and from 0.2943 to 0.7695, respectively. Ten loci were highly informative, nine were moderately informative. Six loci significantly deviated from Hardy?CWeinberg equilibrium after Bonferroni correction. Two groups of couple loci exhibited significant linkage disequilibrium. These polymorphic microsatellite loci will provide useful genetic tools for population study and conservation genetics of R. cylindricus.     

Characterization of ten microsatellite loci for the dark pomfret, Pampus cinereus (Stromateidae, Perciformes)

Ten polymorphic microsatellite loci were isolated in the dark pomfret (Pampus cinereus), an important commercial foodfish species. The mean number of observed alleles per locus was 21 (range 13–33). Observed and expected heterozygosity values ranged from 0.73 to 0.98 and from 0.83 to 0.97 respectively. Two loci showed significant departure from Hardy–Weinberg equilibrium and significant linkage disequilibrium was found between P15-2 and P230. These highly informative microsatellite markers should be useful for population genetic analyses of P. cinereus and other pomfret species.     

Isolation and characterization of twelve novel polymorphic microsatellite loci in the Branchiostoma belcheri Gray (Amphioxus)

Branchiostoma belcheri Gray is an endangered species. A set of twelve novel polymorphic microsatellite loci was developed in B. belcheri Gray. The polymorphism of these loci was tested on a population of thirty individuals from Xiamen, China. The number of alleles ranged from 3 to 7. The polymorphism information content ranged from 0.309 to 0.778. The levels of expected and observed heterozygosities varied from 0.2449 to 0.7825, and from 0.1786 to 0.8571, respectively. Three loci (WCY4-22, WCY4-39, WCY5-17) deviated from Hardy–Weinberg equilibrium. These microsatellite loci would contribute to population genetic studies and conservation of B. belcheri Gray.     

Development of 134 novel polynucleotide-repeat microsatellite markers in silver carp (Hypophthalmichthys molitrix)

In this study, we developed 134 novel polymorphic polynucleotide-repeat microsatellite markers for silver carp (Hypophthalmichthys molitrix) and characterized 40 loci for polymorphism and genetic diversity in a test population. The number of alleles per locus ranged from 3 to 19 (mean 9.4), and the average observed and expected heterozygosities were 0.74–0.76, respectively. Thirty-five loci were highly informative (PIC > 0.5) in silver carp population. After Bonferroni adjustments, no pairs of loci showed evidence of significant linkage disequilibrium, and none of the loci significantly deviated from the Hardy-Weinberg equilibrium. All 134 silver carp microsatellite loci could be successfully amplified in bighead carp (Hypophthalmichthys nobilis) with 65 loci being polymorphic, indicating a high transferability of these microsatellites across species. This set of novel highly polymorphic polynucleotide—repeat microsatellites would be powerful tools for population and conservation genetics studies in silver carp and also in its closely-related bighead carp.     

Isolation and characterization of polymorphic microsatellite loci from the endangered Tarim schizothoracin (Schizothorax biddulphi Günther)

Tarim schizothoracin (Schizothorax biddulphi Günther) is an extremely endangered freshwater fish in China. In this paper, 15 polymorphic microsatellite loci were characterized in this species. The number of alleles ranged from 4 to 14, the observed heterozygosities (H _O) were from 0.7609 to 1.0000, and the expected heterozygosities (H _E) ranged from 0.7273 to 0.9194. The polymorphism information content was from 0.6684 to 0.9020. Only two loci deviated significantly from the Hardy?CWeinberg equilibrium, and none of the loci combinations showed significant linkage disequilibrium. These microsatellite loci are useful in investigating the genetic variability in Tarim schizothoracin.     

Isolation and characterization of microsatellite loci for Menziesia goyozanensis, an endangered shrub species endemic to Mt. Goyo in northern Japan

Menziesia goyozanensis, a Japanese kind of fool’s huckleberry, is a shrub species endemic only to Mt. Goyo in northern Japan. This species is listed as ‘critically endangered’ in the Red Data Book of wild plants in Japan, and only a single population has yet been discovered. We isolated and characterized 16 microsatellite loci for this species. The number of alleles ranged from 2 to 25. The range of expected heterozygosities was 0.292–0.917. Five of the 16 microsatellites were not conformed to Hardy–Weinberg equilibrium, probably due to the restricted population size, genetic drifting and the presence of null alleles. These 16 microsatellite loci gave a combined non-exclusion probability of <1.65E–15 in the sampled population. In Menziesia pentandra, which is closely related species to M. goyozanensis, the number of alleles detected and the expected heterozygosities of twelve loci ranged from 3 to 19 and 0.536 to 0.966, respectively. These informative microsatellite markers will be useful in studies of population genetic structure for these species.     

Development of microsatellite markers for Shorea platyclados (Dipterocarpaceae)

Nine polymorphic microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae) using CT-enriched library method. The polymorphism of the microsatellite loci was analyzed by screening 98 samples from a natural population. The number of alleles per locus ranged from 4 to 12, with an average of 8.22 per locus, and the observed heterozygosity ranged from 0.204 to 0.888 (average 0.562). These microsatellite loci will be useful for population genetic studies on S. platyclados and adding genetic information for hill dipterocarps.     

Development and characterization of 12 polymorphic microsatellite loci in Octopus minor (Sasaki, 1920)

To investigate the genetic structure of Octopus minor, 12 microsatellite DNA markers were developed firstly and polymorphism of each locus was assessed in a wild O. minor population. The number of alleles per locus ranged from 2 to 11, and the observed and expected heterozygosities varied from 0.200 to 1.000 and from 0.235 to 0.869, respectively. These microsatellite loci will be a useful tool in the study of population genetic structure of this species in future.     

Development and characterization of sixteen microsatellite primers in Abies chensiensis and A. fargesii (Pinaceae)

Abies chensiensis is a vulnerable species and has been included in the checklist of State Protection Category II in China. Sixteen microsatellite loci were developed in A. chensiensis and Abies fargesii (Pinaceae) to facilitate studies of population genetic structure and genetic diversity. All of these loci showed polymorphism, and the number of alleles per locus ranged from 1 to 21 from two wild populations. The observed and expected heterozygosities ranged from 0.172 to 1.000 and from 0.250 to 0.935, respectively. These markers will be useful in the research on the population genetic structure and genetic diversity of A. chensiensis, A. fargesi and other Abies species.     

Isolation and characterization of 15 microsatellite loci in an endemic Chinese cyprinid fish, Pseudogyrincheilus prochilus, and their cross-species amplification in two related species

Fifteen polymorphic microsatellite loci were developed for an endemic Chinese cyprinid fish, Pseudogyrincheilus prochilus. The number of observed alleles per locus ranged from 2 to 17. The observed and expected heterozygosities ranged from 0.067 to 1.000 and from 0.066 to 0.932, respectively. No significant linkage disequilibrium was detected among the loci. Two loci showed significant deviation from Hardy–Weinberg equilibrium, and one of them had evidence for null alleles. Fourteen primer pairs cross-amplified in Garra pingi pingi, and 13 primer pairs cross-amplified in Onychostoma sima. These microsatellite loci should prove highly informative for future studies of genetic diversity conservation.     

Development of ten microsatellite DNA markers in a hexaploid fish, Schizothorax prenanti (Tchang)

Ten dinucleotide microsatellite DNA markers were developed for a polyploidy fish, Schizothorax prenanti. Twenty-four individuals from two populations of this species were genotyped using these markers. All ten loci displayed a high level of polymorphism with the number of alleles per locus ranged from 9 to 19. Additionally, Nei’s genetic diversity ranged from 0.81 to 0.92. These markers provide an excellent toolkit to study population genetic structure and other biological characteristics of this commercially important species.     

Isolation and characterization of microsatellite markers for Glytothorax zanaensis

Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of Glyptothorax zanaensis. The polymorphism of these loci was tested on a population of 78 individuals captured from Nujiang River. The number of observed alleles per locus ranged from 3 to 8. The expected and observed heterozygosity values ranged from 0.578 to 0.820 and 0.623 to 1.000, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. No significant linkage disequilibrium was detected. These microsatellite markers will be useful in studies of population genetic structure of G. zanaensis.     

Characterizations of microsatellite DNA markers for Acacia tortilis

Nuclear microsatellite markers were developed for Acacia tortilis to study patterns of population genetic structure across the species’ distribution. Twelve dinucleotide repeat loci were developed and tested on 20 individuals sampled from four populations. The number of alleles per locus ranged from 5 to 15, expected heterozygosities from 0.701 to 0.873 and the polymorphism information content (PIC) ranged from 0.675 to 0.861.     

Isolation and characterization of ten microsatellite loci of endangered Anderson’s crocodile newt, Echinotriton andersoni

Due to an originally small distribution range and recent habitat loss, Anderson??s crocodile newt (Echinotriton andersoni) has been steadily declining in number. For effective conservation of this species, a greater amount of genetic information is needed. Here, we isolated ten microsatellite loci of E. andersoni using three different methods, and polymorphism of these 10 loci were evaluated for 27 individuals collected from three islands. The total number of alleles per locus ranged from 3 to 22, and the expected heterozygosity ranged from 0 to 0.876. Taken together, our findings suggest that these novel loci will be applicable for conservation genetic studies across varying scales.     

Isolation and characterization of microsatellite markers from the Chinese endemic species,Beal’s-eyed turtle (Sacalia bealei)

Beal’s-eyed turtle (Sacalia bealei) is an endangered species with important medicinal values and effective measures should be taken to protect this species. Development of molecular markers that could be used in population genetic assessment is necessary for the conservation of endangered species. In this investigation, we isolated 14 microsatellite DNA markers from an enriched library. The number of alleles at each locus was between 7 and 17. He and Ho ranged from 0.7958 to 0.9324 and 0.6333 to 0.9697 respectively. The PIC value ranged from 0.757 to 0.913, indicated all the loci are high polymorphism. No significant linkage disequilibrium was detected and only one locus deviated from Hardy–Weinberg equilibrium. These loci could provide useful information for the genetic analyses of S. bealei populations.     

Development and characterization of 14 microsatellite loci from an enriched genomic library of Eucalyptus camaldulensis Dehnh

Eucalyptus camaldulensis Dehnh is an Australian tree species which occurs in various climatic and environmental conditions and show large genetic diversity. Twenty five microsatellite markers were developed from a CT₈–GT₈ enriched genomic library of E. camaldulensis. The number of alleles ranged from 4 to 13 (average of 8). The polymorphism information content (PIC) and the discriminating power (D) of each primer ranged from 0.37 to 0.88 (average of 0.72) and 0.48 to 0.99 (average of 0.84), respectively. The observed and expected heterozygosities ranged from 0.28 to 0.84 and 0.25 to 0.90, respectively. Four loci showed statistically significant from Hardy-Weinberg equilibrium after Bonferroni correction (P, (5%) < 0.0038). All polymorphic markers were tested for cross-amplification in 25 different Eucalyptus species. Those microsatellite loci will be useful to investigate questions of genetic diversity and structure, gene flow, mating system and ex situ genetic conservation of E. camaldulensis.