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.     

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.     

Characterization of eight polymorphic microsatellite markers in the tarnished plant bug,Lygus lineolaris (Palisot de Beauvois)

A partial genomic library of the tarnished plant bug, Lygus lineolaris, enriched for microsatellite sequences was screened to identify marker loci. Eight polymorphic loci suitable for population genetic studies were identified by screening 192 field‐collected insects. The observed number of alleles ranged from four to 21 with an average of 12.25 (SE ± 1.94) while the effective number of alleles ranged from 1.23 to 11.05 with an average of 4.49 (SE ± 1.15). No linkage disequilibria or significant deviations from Hardy–Weinberg expectations were detected at any of the loci. Seven of the eight L. lineolaris microsatellite loci were transferable to Lygus hesperus.     

Isolation and characterization of microsatellite markers in Koompassia malaccensis (Leguminosae), an important tropical timber species

This paper reports the isolation and characterization of 24 polymorphic microsatellite markers in an important tropical timber species, Koompassia malaccensis (Leguminosae). The primers were designed from a genomic library enriched for dinucleotide (CT) repeats and screened on 24 samples from a natural population. The number of alleles detected per locus ranged from two to 13 while the observed heterozygosity ranged from 0.042 to 1.000. Significant departure from Hardy–Weinberg equilibrium (P < 0.05) was detected in two loci. These microsatellite markers were tested across 13 timber species of the same family. The amplification success appeared to be associated with taxonomy classification at the genus but not subfamily levels.     

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 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.     

Characterization of microsatellite loci in the western tarnished plant bug,Lygus hesperus Knight (Hemiptera: Miridae)

A microsatellite‐enriched partial genomic DNA library of Lygus hesperus was generated and screened by sequencing. Ten polymorphic microsatellite marker loci were characterized by genotyping 92 insect samples. The observed number of alleles ranged from three to seven with an average of 4.5 (SE ± 0.45), while the effective number of alleles ranged from 1.21 to 3.02 with an average of 2.14 (SE ± 0.20). Significant deviations from Hardy–Weinberg expectations were detected at three loci. Significant linkage disequilibrium was also detected between the loci LhMS2‐54 and LhMS3‐32. Seven of the L. hesperus markers could be transferred to Lygus lineolaris.     

Isolation and characterization of microsatellite loci in Hexagrammos otakii based on 2b-RAD method

In this study, we isolated 20 novel microsatellites loci associated with the growth of Hexagrammos otakii (Fat greenling) by using 2b-RAD sequencing method. The characteristics of 20 microsatellite loci were amplified in 105 H. otakii individuals which came from four different groups and tested by Capillary electrophoresis. The number of allele of the 20 microsatellite loci ranged from 8 to 26 with an average of 19.95. PIC value ranged from 0.1659 to 0.9227 with an average of 0.7555. Observed and expected heterozygosity varied from 0.0667 to 0.8571 and from 0.1710 to 0.9314, respectively. Highly polymorphic characteristics were observed in each microsatellite loci of the study except HO6. Further research showed that 10 microsatellite loci had transferability in Hexagrammos agrammus. In this study, high polymorphism and genetic diversity using the 15 polymorphic microsatellite loci suggest that they are suitable for investigating the fine-scale population structure, genetic relationship and further evaluating the artificial reproduction strategy of H. otakii.     

Isolation and characterization of polymorphic microsatellite markers in Anthyllis vulneraria

To study the reproductive system of the putative autogamous species Anthyllis vulneraria in Belgian calcareous grasslands, eight polymorphic microsatellite loci were developed using the sequence‐tagged microsatellite profiling technique and 35 plants were typed for all loci. No linkage disequilibrium was found between any pair of loci. Over the loci, the number of alleles ranged from two to five. Observed and expected heterozygosities ranged from 0.053 to 0.688 and from 0.053 to 0.631, respectively. The estimated F_IS values (F_IS = 0.031 and 0.122) are not in accordance with a predominantly selfing reproductive system.     

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 characterization of 12 microsatellite loci from cutlassfish (Trichiurus haumela)

The cutlassfish (Trichiurus haumela) is an important commercial fish species. In the present study, we report 12 polymorphic microsatellite DNA markers for cutlassfish. The number of alleles per locus ranged from 2 to 9 in a sample of 26 individuals. Observed and expected heterozygosities per locus varied from 0.2727 to 0.9583 and from 0.4059 to 0.7926, respectively. Two loci (Trha25 and Trha27) showed significant departure from Hardy–Weinberg equilibrium after sequential Bonferroni correction (P < 0.0042). No significant linkage disequilibrium between pairs of loci was found. These microsatellite markers provide powerful tools for investigating genetic population structure, population history and conservation management of cutlassfish. Jin-Zhen Bi and Chang-Wei Shao contributed equally to this work.     

Polymorphic microsatellite loci isolated from the marine sponge Scopalina lophyropoda (Demospongiae: Halichondrida)

A total of seven microsatellites out of 88 isolated from a genomic library enriched for (CA)_n and (GA)_n repeats were characterized in the Mediterranean marine sponge Scopalina lophyropoda. The microsatellite motifs were large (34.81 ± 13.9 bp) and imperfect. The seven microsatellite loci were screened in 30 individuals collected from Blanes, northwestern Mediterranean. All of them were polymorphic (allele numbers and observed heterozygosities ranged from 3 to 6 and from 0.16 to 0.76, respectively). No significant linkage disequilibrium between pairs of loci and no departure from Hardy–Weinberg equilibrium were found. These markers are therefore promising for studies of the population structure of the species.     

Eleven novel microsatellite markers developed from the living fossil Ginkgo biloba (Ginkgoaceae)

Ginkgo biloba L. (Ginkgoaceae), a famous and widely cultivated plant, is often referred to as a living fossil. Here we isolated and characterized 11 polymorphic microsatellite loci from G. biloba using a modified biotin-capture method. These loci showed high levels of allelic diversity, alleles sizes ranged from 4 to 16 per locus with polymorphism information content ranging from 0.432 to 0.909 (average = 0.752). The observed and expected heterozygosities ranged from 0.208 to 0.708 (average = 0.484) and from 0.501 to 0.934 (average = 0.795), respectively. These microsatellite markers can be used as genetic markers for further studies on genetic diversity, genetic structure and the gene flow among populations of this species.     

Twenty‐four novel microsatellites for the endangered Chinese sturgeon (Acipenser sinensis Gray, 1835)

The Chinese sturgeon (Acipenser sinensis) is an endemic and critically endangered species in China. In this study, a total of 24 polymorphic microsatellite loci were isolated and characterized using Illumina sequencing for A. sinensis. The number of alleles (Na) per locus ranged from 2 to 6 (mean 4.04), mean expected heterozygosities (He), Shannon‐Wiener Diversity Indices (SW) and evenness (E) per locus ranged from 0.235 to 0.786 (mean 0.62), from 0.396 to 1.608 (mean 1.13), and from 0.060 to 0.213 (mean 0.13), respectively. Exact tests revealed that nine loci showed significant (P < 0.01) deviation from Hardy‐Weinberg equilibrium (HWE). Cross amplification was tested in congeneric species A. schrenskii, A. baerii, A. dabryanus and Huso dauricus. The new microsatellite markers described herein will be useful for further studies on genetic variation, parentage analysis, and conservation management.     

Characterization of six microsatellite loci in the Baltic blue mussel <Emphasis Type="Italic">Mytilus trossulus</Emphasis> and cross-species amplification in North Sea <Emphasis Type="Italic">Mytilus edulis</Emphasis>

The blue mussel Mytilus trossulus occurs in the Pacific and in the North Atlantic. We developed and characterized six microsatellite loci for Baltic M. trossulus. Seventeen microsatellite loci were screened, of which six were polymorphic. The number of alleles among 50 individuals ranged from 3 to 13 and the observed and expected heterozygosity were 0.09–0.46 and 0.34–0.86, respectively. The loci were also tested for cross amplification in M. edulis, in which four of the six microsatellite loci were successfully amplified.     

Ten new polymorphic microsatellite loci for North American river otters (Lontra canadensis) and their utility in related mustelids

We describe 10 novel North American river otter (Lontra canadensis) polymorphic microsatellite loci. Individuals from two river drainages in New York were sampled, and the number of alleles per locus ranged from two to 12 (Drainage 1) and two to 10 (Drainage 2). Observed heterozygosities ranged from 0.21 to 0.83 (Drainage 1) and 0.20 to 0.80 (Drainage 2). Preliminary screening revealed that loci amplified in five other mustelids [Martes pennanti (n = 6), Martes fiona (n = 8), Mustela frenata (n = 8), Mustela erminea (n = 8) and Mustela vison (n = 5)].     

New microsatellite markers for the snow crab Chionoecetes opilio (Brachyura: Majidae)

Nine novel microsatellite loci were isolated from Chionoecetes opilio by screening an enriched genomic library using nonradioactive polymerase chain reaction techniques, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. All loci were found to be polymorphic with an average of 9.7 alleles per locus (range 3–25). The observed and expected heterozygosities ranged from 0.80 to 0.98 and from 0.56 to 0.95, respectively. Five loci showed significant Hardy–Weinberg disequilibrium at the P < 0.05 level. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for genetic variation monitoring of C. opilio.     

Development of twelve polymorphic microsatellite loci in polyploid endangered Omphalogramma vincaeflora Franch. (Primulaceae)

A total of twelve polymorphic microsatellite loci were developed from polyploid endangered species, Omphalogramma vincaeflora (Primulaceae). These loci were screened for variability among 45 individuals from three populations in China. The primers amplified loci with allele number ranging from 3 to 9, with an average of 4.25 per locus. Polymorphism information content ranged from 0.23 to 0.86. Nei’s genetic diversity ranged from 0.34 to 0.86. These primers provide an opportunity to use polymorphic DNA markers to study the population genetic structure and its breeding system in this species.     

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).