Development of 34 new microsatellite markers for the endangered Chinese sucker (Myxocyprinus asiaticus) using 454 sequencing

Chinese sucker (Myxocyprinus asiaticus) is an endangered fish species in China which is only distributed in Yangtze River basin. Here we isolated and characterized 34 polymorphic tri and tetra-nucleotide microsatellite loci in the genome of M. asiaticus using 454 sequencing. Of the 73 loci screened, 47 were amplified successfully and 34 were polymorphic. The genetic diversity in M. asiaticus Wanzhou population was moderate with the number of alleles per locus ranged from 2 to 8 (mean 3.97), and the observed and expected heterozygosities ranged from 0.08 to 1.000 (mean 0.50) and from 0.12 to 0.83 (mean 0.55), respectively. These polymorphic microsatellite markers should be useful for further studies of population structure, parentage analysis, and conservation management for this species.     

Isolation of polymorphic microsatellite loci from an endangered freshwater species Chinese sucker, <Emphasis Type="Italic">Myxocyprinus asiaticus</Emphasis>

Chinese sucker (Myxocyprinus asiaticus) is an endangered freshwater fish species endemic to the Yangtze River in China. In this work, we described the isolation and characterization of 14 new polymorphic microsatellite loci from (CA) _n and (GA) _n microsatellite enriched libraries of the M. asiaticus. The number of alleles per locus ranged from 6 to 14 with the observed (H _O) and expected (H _E) heterozygosities ranging from 0.120 to 1.000 and from 0.767 to 0.952, respectively. Five loci displayed significant departures from Hardy–Weinberg expectations. These polymorphic microsatellite loci will be useful molecular tools for understanding population genetic structure and conservation of M. asiaticus.     

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.     

Isolation and characterization of nineteen novel polymorphic microsatellite loci for the northern snakehead Channa argus

Channa argus is one of the most important economic fish species in China. However, there is limited genetic information on its population structure and genetic diversity. Nineteen novel polymorphic microsatellite loci were isolated and characterized in 42 individuals from one natural population collected from the Poyang Lake in Jiangxi Province. The number of alleles per locus ranged from 5 to 18 with an average of 11.16. The observed and expected heterozygosities ranged from 0.214 to 1.000 and from 0.630 to 0.923, respectively. The average polymorphic information content value was 0.814. Among these polymorphic microsatellites, eleven loci conformed to Hardy–Weinberg equilibrium. These microsatellite loci are currently being used to assess the genetic diversity and population structure of C. argus and will contribute to the effective conservation and rational utilization of genetic resources of this species.     

Isolation and characterization of polymorphic microsatellite loci from yellow catfish (Pelteobagrus fulvidraco)

Eleven polymorphic microsatellite loci from yellow catfish (Pelteobagrus fulvidraco) have been isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. These loci were characterized by genotyping 40 individuals. The observed number of alleles ranged from 4 to 11 with an average of 6.2 of each loci. The expected and observed heterozygosities ranged from 0.125 to 0.925 and from 0.648 to 0.877, respectively. Among these polymorphic microsatellite loci, eight-ones conformed to Hardy–Weinberg Equilibrium. All microsatellites were in linkage equilibrium. These microsatellite markers would be useful for investigating the genetic diversity and population structure of yellow catfish.     

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.     

New fourteen highly polymorphic STR markers developed and characterized from edible dormouse (Glis glis)

Fourteen new polymorphic di- and di-tetra complex microsatellite loci were isolated and characterized from the edible dormouse (Glis glis). The markers were tested on 427 individuals representing populations from Croatia and Poland. All loci were polymorphic, with the number of alleles per locus ranged from 4 to 31, with a mean of 10. Observed and expected heterozygosities ranged from 0.208–0.957 to 0.228–0.907, respectively. No evidence of linkage disequilibrium between loci has been found. These highly polymorphic markers could provide a powerful tool for detailed genetic studies of this endangered species.     

Development of polymorphic microsatellite loci isolated from the Ancherythoculter nigrocauda

Twelve polymorphic microsatellite markers from Ancherythoculter nigrocauda were developed using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. These loci were characterized by genotyping 48 individuals. The observed number of alleles per locus ranged from 4 to 14 with an average of 9.4. The expected and observed heterozygosities ranged from 0.185 to 0.907 and from 0.083 to 0.952, respectively. Among these polymorphic microsatellite loci, four of the loci (HWB01, HWB04, HWB12 and HWB16) significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). All of the microsatellite loci were in linkage equilibrium. These microsatellite markers would be useful for investigating the genetic diversity and population structure of A. nigrocauda.     

Sixteen polymorphic microsatellite markers for the mud snail, <Emphasis Type="Italic">Bullacta exarata</Emphasis> (Philippi, 1848)

Sixteen polymorphic microsatellite markers were developed from a partial genomic library enriched using AG and AC repeats in mud snail (Bullacta exarata). Polymorphism of these loci was screened using 48 adult individuals of B. exarata. The number of alleles per locus ranged from 2 to 13. The observed and expected heterozygosities ranged from 0.5106 to 0.8125 and from 0.4868 to 0.9208, respectively. One locus departed significantly from Hardy–Weinberg equilibrium after Bonferroni correction. No linkage disequilibrium was found between any pair of loci. These polymorphic microsatellite markers are expected to provide valuable genetic information in population structure and genetic diversity, which will certainly facilitate management strategies of the mud snail.     

Development and characterization of novel microsatellite markers in yellowcheck (Elopichthys bambusa)

Out of 55 microsatellites isolated by an enriched genomic library from yellowcheck (Elopichthys bambusa), eighteen polymorphic loci were characterized in a wild population from the Zhangdu Lake of the Yangtze River. The number of alleles per locus ranged from 2 to 14, the observed and expected heterozygosity ranged from 0.019 to 0.346 and 0.019 to 0.529, respectively. Eight loci deviated from Hardy–Weinberg Equilibrium (HWE) after Bonferroni correction, and ten loci were in HWE. Lower rate of polymorphic loci and heterozygosity may suggest a relative low level genetic diversity in the studied population. These novel microsatellite markers would facilitate molecular population genetic studies for yellowcheck.     

Development and characterization of EST-derived microsatellite makers for swimming crab, Portunus trituberculatus

In this study, sixteen polymorphic microsatellite makers were developed and characterized from expressed sequence tag sequence of the swimming crab, Portunus trituberculatus. The analysis of polymorphic was performed by using 30 specimens from the coastal waters of Xiangshan, Zhejiang province, China. The number of alleles at each locus ranged from 4 to 14 with an average of seven alleles per locus. The ranges of observed and expected heterozygosity were from 0.517–1.000 to 0.508–0.736, respectively. The polymorphism information content ranged from 0.375 to 0.710. Four loci were found deviate significantly from Hardy–Weinberg equilibrium. These microsatellite loci will be helpful for the genetic evaluation of P. trituberculatus enhancement.     

Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace (Tribolodon hakonensis)

Twenty one polymorphic microsatellite loci for the Japanese dace (Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.     

Development of microsatellite markers for Leptobotia rubrilaris, a threatened fish species in the Yangtze River

Leptobotia rubrilaris is a threatened fish species of the Yangtze River in China. A first set of sixteen polymorphism microsatellite loci isolated from this species was characterized. The number of alleles, observed and expected heterozygosity ranged from 2 to 8, 0.1667 to 1.000 and 0.1587 to 0.8342, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. The polymorphism information content ranged from 0.148 to 0.791. Ten loci were highly informative, four were moderately informative, and two was slightly informative. These polymorphic microsatellite markers will be useful to study genetic diversity and genetic structure of L. rubrilaris for conservation and management.     

Isolation and characterization of twenty-eight polymorphic microsatellite markers in Odontobutis potamophila and cross-amplification in other Gobioidei

Odontobutis potamophila is widely distributed in river systems of southeast China. Twenty-eight microsatellite loci were isolated and characterized for this species. Number of alleles ranged from 2 to 19 per locus, and the observed and expected heterozygosity were 0.161–0.967 and 0.207–0.928, respectively. No evidence of linkage disequilibrium was detected. The significant departures from Hardy–Weinberg expectations at three loci suggested the presence of null alleles. These microsatellite loci will be useful for studying population genetic variation. Cross-amplification of these microsatellite loci indicated that many are polymorphic in four closely related species of Gobioidei.     

Isolation and characterization of ten microsatellite loci from the Patagonian notothenioid fish Eleginops maclovinus

Eleginops maclovinus, the Patagonian blennie, is a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters. Here, we report ten polymorphic microsatellite loci isolated from a dinucleotide-enriched E. maclovinus genomic library. Among 48 individuals, the number of alleles per locus ranged from eight to 41, and the observed and expected heterozygosity ranged from 0.688 to 0.938 and from 0.695 to 0.968, respectively. No locus significantly deviated from Hardy–Weinberg equilibrium, and no significant linkage disequilibrium between pairs of loci was found. These polymorphic microsatellite loci will be useful for investigating genetic population structure and connectivity among natural populations.     

Development and characterization of 17 polymorphic microsatellite loci in Octopus vulgaris Cuvier, 1797

17 polymorphic microsatellite loci were screened and characterized in Octopus vulgaris using a microsatellite enriched genomic library. The number of alleles per polymorphic microsatellite locus ranged from 3 to 17, and the observed and expected heterozygosities varied from 0.154 to 1.000 and from 0.214 to 0.925, respectively. These microsatellite loci will be useful for further studies on the population structure and genetic variation of this species.     

Isolation and characterization of 16 polymorphic microsatellite loci in the leopard coral grouper Plectropomus leopardus

Plectropomus leopardus is an important commercial fish in South-East Asia. To date, there is little genetic information available about its population structure. In this study, 16 polymorphic microsatellite loci were developed for this species and characterized in 182 wild individuals. The observed and expected heterozygosity ranged from 0.236 to 0.912 and from 0.649 to 0.866, respectively. No linkage disequilibrium was detected between loci, and four loci were found to significantly depart from Hardy–Weinberg equilibrium. These polymorphic microsatellite markers are valuable for relative studies of population genetics.     

Isolation and characterization of twenty microsatellite markers for the endangered fish Alburnus chalcoides

Twenty polymorphic microsatellite loci were isolated from an enriched genomic library of Alburnus chalcoides. The polymorphism of these loci was tested on a population of 15 individuals from the Aral Sea, Uzbekistan. The number of alleles per locus ranged from 2 to 3. The observed and expected heterozygosity ranged from 0.2077–0.6720 to 0.1662–0.6837, respectively. One locus (CCA147) deviated from the Hardy–Weinberg expectations (P < 0.05) after Bonferroni correction. The polymorphic information content (PIC) for allelic diversity ranged from 0.12 to 0.8067 with 9 of these 20 loci revealing moderately high information content (PIC > 0.50). These loci will provide insights into species genetic diversity, population structure, and conservation strategy design.     

Isolation and characterization of 10 microsatellite markers in Helice tientsinensis (Brachyura: Varunidae)

Ten microsatellite loci of Helice tientsinensis (Brachyura: Varunidae) were isolated and characterized. Those loci were proved polymorphic by 21 individuals from coastal wetland along West-Pacific. The number of observed alleles ranged from 5 to 17. Observed and expected heterozygosity was in the range of 0.324–0.907 and 0.461–0.926 separately. In addition, those markers were tested polymorphic and suitable for further assessing genetic diversity and population structure of Helice tientsinensis.     

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.