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 and characterization of 23 microsatellite loci in the veined rapa whelk (Rapana venosa)

Rapana venosa is a commercially important mollusk species, but has been suffering from severe population decline due to over-exploitation and habitat destruction in China. The first set of 23 polymorphic microsatellite loci was isolated and characterized for population studies. The number of alleles per locus ranged from 3 to 17, and the observed and expected heterozygosities varied from 0.167 to 1.000 and from 0.455 to 0.924, respectively. These microsatellite loci will be useful tools for fisheries management and conservation programme for this species.     

Isolation and characterization of 12 microsatellite loci in the Chinese crocodile lizard (Shinisaurus crocodilurus)

The Chinese crocodile lizard (Shinisaurus crocodilurus) is listed as one of the most endangered species in the world. There are only nine isolated populations of crocodile lizards distributed in China and one population distributed in Vietnam. 12 polymorphic microsatellite loci were isolated and characterized from a DNA library. To characterize each loci, 40 crocodile lizards individual from Guangdong province, China were genotyped. These loci showed allele numbers ranging from 11 to 20. The ranges of observed and expected heterozygosity were 0.8500?C0.9750 and 0.8372?C0.9347, respectively. All loci followed Hardy?CWeinberg equilibrium (HWE) after Bonferroni correction. No evidence of significant linkage disequilibrium was found among any loci. Thus, we expect these markers will be useful for conservation genetic study of the Chinese crocodile lizard.     

Isolation and characterization of microsatellite loci in the Chinese water snake Enhydris chinensis (Colubridae)

The Chinese water snake Enhydris chinensis is an ovoviviparous colubrid snake distributed in China and Vietnam. It is commonly used in the production of Chinese snake oil, which is known for treating ailments such as fever, joint pain, and headache. It is listed as a vulnerable species according to the China red data book of endangered animals. Specific molecular markers such as mitochondrial DNA and microsatellite loci are helpful for us to get a better understanding of population structure and evolutionary history of the snake and take effective conservation action for this species. Here, we characterize eight polymorphic microsatellite loci isolated from E. chinensis genomic libraries. Forty-seven individuals were collected from Ji’an population in Jiangxi, China. These markers revealed a high degree of genetic diversity (3–10 alleles per locus) and heterozygosity (H _O ranged from 0.532 to 0.957, and H _E ranged from 0.565 to 0.806). No locus exhibited significant deviations from Hardy–Weinberg equilibrium. There was no evidence of linkage disequilibrium among pairs of loci. The results of this paper will be useful for future study of population structure and genetic diversity of E. chinensis.     

Isolation and characterization of 10 polymorphic microsatellite loci from the Chinese ratsnake (Zaocys dhumnades)

The Chinese ratsnake (Zaocys dhumnades) is widely distributed in China, including Taiwan, northwards to Henan, Shanxi and Gansu. The snake has been overexploited by local people for food and traditional Chinese medicine, and is listed as least concerned species according to the China Red Data Book of Endangered Animals. In this study, 10 polymorphic microsatellite markers were isolated and characterized from Z. dhumnades genomic libraries. The mean number of alleles per locus was 15.3 (ranged from 6 to 23), with expected (H _E) and observed (H _O) heterozygosity ranging from 0.550 to 0.914 and from 0.519 to 0.778, respectively. Significant deviation form Hardy–Weinberg equilibrium was not detected at all loci. There was no evidence of linkage disequilibrium among pairs of loci. These microsatellite markers will be valuable tools for further studies on the population structure, genetic variation, and evolutionary history of Z. dhumnades.     

Isolation and characterization of microsatellite loci in the Ussuri mamushi (Gloydius ussuriensis)

The Ussuri mamushi (Gloydius ussuriensis) is especially adapted to low temperature environments in the high latitude area and it is classified as least concern according to the China Red Data Book of Endangered Animals. In this study, ten microsatellite loci were isolated from G. ussuriensis. These markers revealed a high degree of genetic diversity (4–13 alleles per locus) and heterozygosity (H _O ranged from 0.205 to 0.848, and H _E ranged from 0.317 to 0.874). No locus exhibited significant deviations from Hardy–Weinberg equilibrium. There was no evidence of linkage disequilibrium among pairs of loci. These microsatellite markers will facilitate studies that address conservation of the species, such as gene flow, population structure and evolutionary history.     

Isolation and characterization of microsatellite loci in blesbok (Damaliscus pygargus phillipsi)

Eight microsatellite markers were developed via pyrosequencing for the blesbok (Damaliscus pygargus phillipsi). These microsatellite loci and microsatellite loci from two cross species markers displayed two to four alleles with an expected heterozygosity range between 0.2899 and 0.6268 and an observed heterozygosity between 0.2083 and 0.6667. The high level of polymorphisms observed in the microsatellite markers indicates that they can be used to strongly improve our knowledge of the genetic structure and relatedness of these animals.     

Isolation and characterization of 11 microsatellite loci in Schizothorax wangchiachii (Fang)

72 microsatellite loci were isolated from a (GATA)₈ enriched genomic library of Schizothorax wangchiachii (Fang), an endemic fish species in the upper reaches of the Yangtze River. A population of 32 wild captured individuals of this species was tested by these 72 primer pairs developed, 11 pairs of which exhibited polymorphic. The number of observed alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.344 to 0.875 and from 0.289 to 0.875, respectively. No significant linkage disequilibrium was detected among the loci. One loci showed significant deviation from Hardy–Weinberg equilibrium and none was detected in linkage equilibrium. These microsatellite loci described for S. wangchiachii will be useful for future study on population structure, breeding, and conservation studies.     

Isolation and characterization of 15 microsatellite loci in Acrossocheilus labiatus Regan (Cyprinidae)

Acrossocheilus labiatus Regan occurs in the clear mountain streams in the east of Asia. Eighteen microsatellite loci were isolated from A. labiatus and fifteen loci were polymorphic observed in 30 samples tested. The number of alleles per locus ranged from 2 to 10. The polymorphism information content varied from 0.090 to 0.825. The observed and expected heterozygosities ranged from 0.069 to 0.900 and from 0.067 to 0.844, respectively. Although significant deviations from Hardy?CWeinberg equilibrium were detected for three loci (HC-G11-1, HC-C3-3 and HC-G8-1, P?<?0.01), no significant deviations were detected for other twelve loci (P?>?0.05). These microsatellite loci will be useful for the further study of population genetic analysis and subsequently provide important genetic data for the conservation and recovery of the A. labiatus resources.     

Isolation and characterization of microsatellite loci from blue-footed boobies (Sula nebouxii)

Blue-footed boobies (Sula nebouxii) are socially monogamous, colonial seabirds exhibiting intra-specific nest parasitism and extra-pair copulations. Prior DNA fingerprinting assays failed to detect extra-pair offspring in the nests of congeners, and the rate of intra-specific nest parasitism has not been estimated using molecular techniques. We describe the development and characterization of 11 microsatellite DNA loci, tested using 31 individuals collected on Isla Isabel, Nayarit, México. The number of alleles per locus ranged from three to 22, averaging seven; total exclusionary power of the microsatellite panel was 0.99; no loci deviated from Hardy-Weinberg equilibrium; and we did not detect linkage disequilibrium following Bonferroni correction. This microsatellite panel will facilitate future studies of nest parasitism and extra-pair paternity in blue-footed boobies.     

Isolation and characterization of species-specific microsatellite loci in red-billed oxpeckers (Buphagus erythrorhynchus)

Ten microsatellite markers were developed via pyrosequencing for the red-billed oxpecker (Buphagus erythrorhynchus). These microsatellite loci displayed 3?C15 alleles with expected heterozygosity values ranging between 0.580 and 0.907 and observed heterozygosity between 0.509 and 0.870. The high level of polymorphisms observed in the microsatellite markers supports future investigations to improve our knowledge of the genetic structure and relatedness of these birds. This is the first development of species specific markers for the red-billed oxpecker.     

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 species-specific microsatellite loci in African penguin (Spheniscus demersus)

Eight microsatellite markers were developed via pyrosequencing of a microsatellite-enriched library for the African Penguin (Spheniscus demersus). These microsatellite loci displayed 2–6 alleles with expected heterozygosity values ranging between 0.316 and 0.782 and observed heterozygosity between 0.381 and 0.84. These loci may be suitable for assessing patterns of genetic variability in African penguin. This is the first development of species-specific markers for the African penguin.     

Isolation and characterization of 12 polymorphic microsatellite loci in Illicium verum (Schisandraceae)

Twelve polymorphic microsatellite loci were isolated and characterized for Illicium verum, a member of the basal angiosperms. The observed number of alleles per locus ranged from two to nine. The observed and expected heterozygosity varied from 0.10 to 1.00 and 0.097 to 0.85, respectively. Twelve loci were screened in cross-amplification tests for three other Illicium species, in which all loci were successfully amplified. These newly developed microsatellite markers could provide a useful tool for the ongoing efforts in studying the population genetic variation of I. verum, which will facilitate formulation of appropriate strategies for conservation and sustainable utilization of star anise and its congeneric species.     

Isolation and characterization of 14 microsatellite loci for Chinese catfish Silurus asotus

Silurus asotus is a high commercially valuable aquaculture fish in some regions of China. In this survey, the first set of 14 polymorphic microsatellite loci for S. asotus was developed and characterized. The number of alleles per locus ranged from 9 to 15 and the observed and expected heterozygosities ranged from 0.593 to 0.931 and from 0.833 to 0.926, respectively. Four loci were found deviated from HWE in the sampled population after Bonferroni correction. These microsatellite loci will be useful for revealing population structure, and conservation genetics of S. asotus.     

Development and characterization of 23 microsatellite loci for scaled quail (Callipepla squamata)

The scaled quail (Callipepla squamata) is a common but declining game bird found throughout large portions of the arid southwest region of the United States. Range-wide population declines have been linked to long term drought and land use changes and have led to a resurgance in research investigating various aspects of scaled quail ecology. In order to facilitate future research on scaled quail, we have developed and characterized 23 polymorphic microsatellite loci. Among 16 individuals from populations located throughout scaled quail range, the number of alleles per locus ranged from 3 to 14 with an average of 7. Polymorphic information content ranged from 0.210 to 0.899 with an average of 0.654, indicating that these loci have high applicability for future scaled quail genetic studies.     

Isolation and characterization of microsatellite loci in Jinshaia sinensis

In this study, we isolated and characterized thirteen polymorphic microsatellite markers for Jinshaia sinensis, a fish species endemic to the upper reaches of the Yangtze River in China. Each locus was screened in a population of 48 individuals. Number of alleles per locus ranged between five and nineteen. Observed heterozygosity ranged between 0.121 and 0.854, and expected heterozygosity between 0.722 and 0.928. No significant linkage disequilibrium was found between pairs of loci. However, three loci showed significant departures from Hardy-Weinberg equilibrium and four loci had evidence of null alleles. These markers presented here will be valuable tools to understand the genetic structure of J. sinensis populations in the Yangtze River.     

Isolation and characterization of polymorphic microsatellite loci from the golden mouse (Ochrotomys nuttalli)

Thirteen polymorphic microsatellite loci were developed for golden mouse using an enrichment protocol. The markers were tested on 37 golden mouse specimens collected from southern Illinois. Numbers of alleles ranged from 3 to 11 with observed heterozygosities ranging from 0.29 to 0.92. Three of the loci exhibit nominally significant excesses of homozygosity, but none were significant following a correction for multiple tests. None of the loci appear to be linked. Although golden mouse is not considered at risk in the core of its range, peripheral populations in several states are considered threatened or otherwise at risk due to low population densities. Because of the evolutionary distinctiveness of Ochrotomys, species-specific primers are needed to identify patterns of gene flow among core and peripheral populations.     

Isolation and characterization of microsatellite loci in the short-tailed pit viper Gloydius brevicaudus (Viperidae)

The short-tailed pit viper Gloydius brevicaudus is a medium-sized, viviparous, highly venomous snake that has an exclusively temperate distribution ranging from eastern China to Korea. The snake is listed as a vulnerable species according to the China Red Data Book of Endangered Animals. To develop effective conservation strategies for the snake, we need a better understanding of gene flow, population structure and evolutionary history of this species. One approach for achieving this goal is to use microsatellites. Here, we characterize 8 polymorphic microsatellite loci isolated from G. brevicaudus genomic libraries. Twelve individuals were collected from Xiaoshan population in Zhejiang, China. These markers revealed a high degree of genetic diversity (7–16 alleles per locus) and heterozygosity (H _O ranged from 0.667–1.000, and H _E ranged from 0.822 to 0.960). No locus exhibited significant deviations from Hardy–Weinberg equilibrium. There was no evidence of linkage disequilibrium among pairs of loci. These microsatellite markers will be useful for future studies focusing on paternity test, population structure and evolutionary history of G. brevicaudus.     

Isolation and characterization of nine polymorphic microsatellite loci in the northern crayfish (Orconectes virilis)

Nine novel polymorphic microsatellite loci were isolated from Orconectes virilis and characterized in 46 individuals from two major rivers in Alberta, Canada. Number of alleles per locus per site ranged from 1 to 5. Observed and expected heterozygosity per site ranged from 0.000 to 0.900 and 0.000 to 0.740, respectively. All nine microsatellite loci conformed to expectations of Hardy–Weinberg and linkage equilibrium. These markers will be useful in the study of movement patterns, genetic diversity, and population structure of native and invading O. virilis.