Polymorphic microsatellite markers isolated from partially enriched genomic library of Chitala chitala

A total eight polymorphic microsatellite loci were obtained from genomic library of Indian feather back, Chitala chitala (order Osteoglossiformes, family Notopteridae) and the 46 samples were analysed to determine genetic variation. The mean number of alleles per locus ranged from 4.50 to 5.25, and expected heterozygosity ranged from 0.124 to 0.852. Deviation from Hardy–Weinberg equilibrium expectations (P < 0.002) was observed at loci Cch2, Cch9 (Bhaghirathi) and Cch9 (Brahmaputra). The identified microsatellite loci were found promising for population genetics studies of C. chitala and related species Notopterus notopterus (family Notopteridae).     

Isolation and characterization of microsatellite markers for the heavily exploited rockfish Sebastes schlegeli, and cross-species amplification in four related Sebastes spp.

Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity.     

Isolation of microsatellite loci in the freshwater goby,Rhinogobius sp. (Gobiidae)

The Rhinogobius species complex (Pisces: Gobiidae) includes great variation in colour, morphology and ecological form. In particular, R. sp. OR (Orange type) exhibits some of the greatest colour variation among the species complex, although the genetic relationships among the variations in this fish remain unclear. Thirteen microsatellite loci were identified from R. sp. OR, and all loci were polymorphic with two to 17 alleles per locus. Observed heterozygosity ranged from 0.1 to 0.9, while the expected heterozygosity ranged from 0.19 to 0.96. Multiplex polymerase chain reaction reaction (PCR) were optimized. All loci except Rhi‐5 conform to Hardy–Weinberg equilibrium (P > 0.05).     

A panel of polymorphic EST-derived microsatellite loci for the small yellow croaker (Larimichthys polyactis)

Small yellow croaker (Larimichthys polyactis) is an important economic species of marine fishery. We developed and evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Pseudosciaena crocea, Paralichthys olivaceus and Psetta maxima. Characteristics of nine EST–SSR loci were investigated using 46 L. polyactis individuals. The number of alleles per locus ranged from 2 to 6. The observed heterozygosity ranged from 0.0652 to 0.7391, while the expected heterozygosity ranged from 0.0638 to 0.7754. Seven loci departed from Hardy–Weinberg equilibrium (P < 0.01) significantly. These loci and markers will be useful for population genetics and systemic evolution among species of small yellow croaker.     

Isolation and characterization of microsatellite loci in the highland papaya Vasconcellea × heilbornii V. Badillo (Caricaceae)

Nine polymorphic microsatellite loci were identified in the tropical plant Vasconcellea ×heilbornii and used to estimate allelic diversity in two populations of southern Ecuador. Allelic richness ranged from two to five alleles, observed heterozygosity ranged from 0.150 to 0.947 and expected heterozygosity ranged from 0.186 to 0.701. Most of these markers also amplified microsatellite loci in two other Vasconcellea species (Vasconcellea stipulata and Vasconcellea cundinamarcensis). Hence, these markers will be useful for population genetic analysis and the evaluation of genetic diversity and gene flow in these species.     

Eight SSR loci from Oyster Crassostrea gigas EST database and cross-species amplification in C. plicatula

Oyster (Crassostrea plicatula) is widely distributed in coastal areas of China. We developed and evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Crassostrea gigas and to amplify EST-SSR in C. plicatula. Characteristics of eight EST-SSR loci were investigated using 37 wild-type C. plicatula individuals. The number of alleles per locus ranged from four to six. The observed heterozygosity (H _O) ranged from 0.1892 to 0.7027 (0.3919 on average) and the expected heterozygosity (H _E) ranged from 0.6068 to 0.7656 (0.7039 on average) (P < 0.05). The average observed heterozygosity was much lower than the average expected heterozygosity. All loci except C15 departed from Hardy-Weinberg equilibrium (P < 0.05) significantly. Contribution of the eight EST-SSR primers presented here will provide necessary and powerful molecular tools for management and conservation studies on the species of oysters in the future.     

Development of EST-SSRs in scallop (Patinopecten yessoensis) from sequence database

Patinopecten yessoensis is a kind of cold water shellfish, and is an important economic species in China. In our study, we developed and evaluated simple sequence repeat (SSR) markers of P. yessoensis. Characteristics of 11 EST-SSR loci were investigated using 40 P. yessoensis individuals. The number of alleles per locus ranged from two to five. The observed heterozygosity ranged from 0.1026 to 0.9487, while the expected heterozygosity ranged from 0.1865 to 0.7433. All loci except P4 departed from Hardy–Weinberg equilibrium (P < 0.05) significantly. There was no LD observed between all pairs of EST-SSRs loci. These loci and markers will be useful for population genetics and systemic evolution of scallop.     

Characterization of ten polymorphic microsatellite markers for the protected Spanish moon moth <Emphasis Type="Italic">Graellsia isabelae</Emphasis> (Lepidoptera: Saturniidae)

Ten polymorphic microsatellite loci were developed for Graellsia isabelae. Polymorphism was assessed for 20 individuals from a Spanish population (Els-Ports-de-Beseit, Catalonia) and 39 more individuals from one population in the French Alps and six other Spanish localities. Overall, the number of alleles per locus ranged from 5 to 24. Els-Ports-de-Beseit showed an average number of alleles per locus of 9.80 (SD = 4.32), observed heterozygosity was 0.71 (SD = 0.226), and expected heterozygosity was 0.788 (SD = 0.146). Genotypic frequencies conformed to Hardy–Weinberg equilibrium at the Catalonian population, and no evidence for linkage disequilibrium was observed. Multilocus genotypes resulting from this set of markers will be useful to determine genetic diversity and differentiation within and among populations of this highly protected moth. Several loci amplified and resulted polymorphic in two related species: two loci in Actias neidhoeferi, and three loci in A. luna.     

Isolation and characterization of eight microsatellite loci for the Neotropical freshwater catfish Pimelodella chagresi (Teleostei: Pimelodidae)

We report eight (CA)_10?35 unlinked microsatellite loci from the Neotropical freshwater catfish, Pimelodella chagresi (Siluriformes: Pimelodidae). These loci were characterized with 23 individuals collected in Panama. Number of alleles per locus varied from 7 to 23 (mean = 12.9) and observed heterozygosity ranged from 0.522 to 0.909 (mean = 0.732). These loci will be used to investigate the existence of cryptic species within the P. chagresi clade, and to study fine‐scale population structure.     

Isolation and characterisation of polymorphic microsatellite markers for the endangered ferreous limpet <Emphasis Type="Italic">Patella ferruginea</Emphasis> (Gastropoda,Patellidae)

The limpet Patella ferruginea is one of the most endangered marine invertebrates on western Mediterranean rocky shores. We have isolated and characterised 11 polymorphic microsatellites markers to provide new tools to investigate genetic structure and gather information necessary for the proper management of this severely threatened species. The number of alleles per locus ranged from 2 to 16 (mean; Na = 8.37) with an average observed heterozygosity of 0.64 (He = 0.66). The levels of polymorphism uncovered at these loci suggest that they should be useful for population genetic studies, parentage analysis and assessment of connectivity among protected areas. None of the pairwaise comparisons among loci showed significant linkage disequilibrium after sequential Bonferroni correction. All but one locus (Pf-31IF1) conformed to HW equilibrium. Further investigation revealed that departures at Pf-31IF1 were not caused by null alleles. Results from cross-species amplifications suggest that some of these loci may also be useful for Patella tenuis (two loci) P. ulyssiponensis (one locus) and P. piperata (three loci).     

Isolation and characterization of microsatellite DNA markers from mangrove crab,Scylla paramamosain

The first five variable microsatellite DNA loci for mangrove crab, Scylla paramanosain, were developed. Allelic variation and other characteristics at these loci were examined in this species captured at the Urado Bay, Japan. The number of alleles per locus ranged from 24 to 44. The expected heterozygosity across loci ranged from 0.900 to 0.999 and probability of identity (P_I) ranged from 2.8 × 10^?3 to 1.7 × 10^?2. Therefore, these microsatellite markers could be useful for estimating effect of stock enhancement release and population genetic structure of mangrove crab.     

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.     

Characterization of microsatellite markers for the mangrove tree Avicennia germinans L. (Avicenniaceae)

We describe 10 primers for amplification of microsatellite loci for the mangrove, Avicennia germinans. Eight loci were isolated from a DNA sample from the Pacific coast of Baja California, Mexico and two loci were isolated from a DNA sample from the Atlantic coast of Bermuda. Polymorphism was investigated in a population from the Mexican Pacific coast (n = 15) and in four samples scattered throughout the range of the species. Total number of alleles for the species ranged from two to 10. Observed heterozygosity in the Mexican Pacific coast population ranged from 0.27 to 0.60, with two loci having fixed alleles.     

Isolation and characterization of microsatellites in yellow perch (Perca flavescens)

A total of 45 microsatellite loci from yellow perch, Perca flavescens, were isolated and characterized. Among the 45 microsatellite loci, 32 had more than two alleles. A wild population of P. flavescens (n = 48) was used to examine the allele range of the microsatellite loci. Mendelian inheritance of alleles was confirmed by examining the amplified products in pair‐mated families. The number of alleles for the 32 polymorphic loci varied from two to 16, and observed heterozygosity ranged between 0.024 (YP79) and 0.979 (YP60). Cross‐species polymorphic amplification in four other Percidae species was successful for 22 loci.     

Isolation and characterization of novel microsatellite loci for the short‐beaked common dolphin (Delphinus delphis) and cross‐amplification in other cetacean species

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short‐beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.     

Microsatellite loci developed for black-crowned night-heron (Nycticorax nycticorax) and their cross-amplifications in Ardeidae

The present study reports isolation and characterization of 11 polymorphic microsatellite markers for Nycticorax nycticorax. A total of 82 alleles were detected with an average of 7.5 alleles per locus. The observed heterozygosity (H _O) ranged from 0.25 to 1.00, and the expected heterozygosity (H _E) ranged from 0.51 to 0.88. Analyses revealed no evidence for Linkage disequilibrium between any two loci, and only one locus was significantly deviated from HWE with the estimation of exact P values by the Markov chain method (P < 0.001). The 11 loci were successfully amplified in 11 other Ardeidae species. These results demonstrate these markers can be used for the study of intra- and inter-specific genetic diversity.     

Isolation and characterization of 24 microsatellite loci in Paphiopedilum rothschildianum, an endangered slipper orchid

This paper describes the characterization of 24 polymorphic microsatellite loci in Paphiopedilum rothschildianum, an endangered slipper orchid endemic to Sabah, Malaysia. A total of 36 clones containing microsatellite repeat motifs yielded 41 dinucleotide, 20 tetranucleotide and 30 cryptic simple repeat sequences. Thirty microsatellite loci were randomly selected to characterize the population, of which 24 were found to be polymorphic. The expected heterozygosity ranged from 0.0813 to 0.7279 (mean 0.4533) and the observed heterozygosity ranged from 0 to 1 (mean 0.3800). The results indicated that there was limited migration between the three subpopulations and a significant degree of genetic differentiation (F_ST = 0.5098) between populations implying that gene flow has been disrupted as a result of habitat fragmentation. The molecular markers have a potential application in population management, CITES enforcement and the forensic detection of specimens in international trade.     

Isolation of highly polymorphic microsatellite markers from the intertidal barnacle Chthamalus montagui Southward

This study reports the isolation and characterization of seven highly polymorphic microsatellite loci in Chthamalus montagui (Crustacea, Cirripedia). The loci were isolated from a library constructed from genomic DNA enriched for CA repeats. The markers yielded three to 43 alleles per locus (mean 16.7) in samples averaging 49 individuals. Observed heterozygosity ranged from 0.08 to 0.58 (mean 0.39). These microsatellite loci will be valuable tools for population genetic studies of this species.     

Development and characterization of 10 novel polymorphic microsatellite loci in Homatula potanini (Günther, 1896)

Homatula potanini is a genus Paracobitis which belongs to the family Cobitidae, subfamily Nemacheilinae. We first isolated ten novel microsatellite DNA loci using the FIASCO protocol. The number of observed alleles per locus ranged from 5 to 14. The observed heterozygosity and expected heterozygosity ranged from 0.3750 to 0.9375 and 0.4028 to 0.8819 respectively. The polymorphic information content ranged from 0.3515 to 0.8556 (M = 0.6170). No significant linkage disequilibrium was detected among the loci. In the present study, we have identified 10 new markers for H.  potanini. These loci should provide sufficient levels in the evaluation of genetic diversity and designing effective conservation programs of H.  potanini.     

Twelve polymorphic expressed sequence tags‐derived markers for Plasmopara halstedii,the causal agent of sunflower downy mildew

Twelve expressed sequence tags‐derived markers were isolated from Plasmopara halstedii (Oomycetes), the causal agent of sunflower downy mildew. A total of 25 single nucleotide polymorphisms and five indels were detected by single‐strand conformation polymorphism analysis and developed for high‐throughput genotyping of 32 isolates. There was a high level of genetic diversity (H_E = 0.484). Observed heterozygosity ranged from 0 to 0.143 indicating that P. halstedii is probably a selfing species. These markers were also useful in detecting significant genetic variations among French populations (F_ST = 0.193) and between French and Russian populations (F_ST = 0.23). Cross‐amplification tests on three closely related species indicated that no loci amplified in other Oomycete species.