Polymorphic microsatellite markers for the ant Plagiolepis pygmaea

Detailed studies on kin structure, mating patterns and dispersal in social insects require highly polymorphic markers, of which the most commonly used today are DNA microsatellites. Here we characterize 10 polymorphic microsatellite markers for the ant Plagiolepis pygmaea. We also investigated the within‐genus applicability of the markers on P. xene, a social parasite of the source species. In addition, we tested amplification of the markers in three species of the genera Formica and Lasius. Eight of the markers also amplified in P. xene and were polymorphic. Seven markers amplified in at least one other formicine ant.     

Di‐ and tetranucleotide microsatellite markers for the Alpine newt (Triturus alpestris): characterization and cross‐priming in five congeners

We developed a set of di‐ and tetranucleotide microsatellite markers for the Alpine newt, Triturus alpestris. Polymorphism as detected in 39 individuals ranged from 3 to 32 alleles at a locus. Cross‐priming with samples of five other Triturus species showed extremely poor levels of cross‐species utility. Still, these markers are suitable for studies of inter‐ and intrapopulation genetic diversity in the focal species.     

ISSR as new markers for genetic characterization and evaluation of relationships among phytoplankton

In order to increase the molecular tools and markers needed for the identification of phytoplankton species, the inter simple sequence repeat (ISSR) fingerprinting was adapted to micro-algae and its use in genetic analysis was demonstrated. Twelve strains, 6 Alexandrium, 4 Pseudo-nitzschia, 1 Skeletonema and 1 Tetraselmis were analysed for the first time with ISSR amplifications. The patterns were highly polymorphic and very reproducible. The 6 primers gave 223 polymorphic markers that clearly and easily distinguished all 12 strains (mainly toxic ones) and gave 187 polymorphic markers among the Alexandrium and the Pseudo-nitzschia species. ISSR amplifications also indicated a large occurrence of simple sequence repeat (SSR) in phytoplankton genomes, especially in Pseudo-nitzschia, and show their usefulness to cluster intra and inter species. ISSR markers were found to be good markers for genetic characterization and diversity study and led to consider them as new tools for the survey of phytoplankton.     

Molecular and morphological evidence of hybridization between newts Triturus vulgaris and T. montandoni (Caudata: Salamandridae) in Slovakia

Natural hybridization and introgression is recorded between the newt species Triturus vulgaris and T. montandoni in Slovakia. To confirm a hybrid status of two putative hybrids, morphological and Randomly Amplified Polymorphic DNA (RAPD) markers specific for T. vulgaris and T. montandoni were used. The individuals found in Zbojská (Veporské vrchy Mts, Slovakia; analyzed morphologically and genetically) and Zubrohlava (Oravská kotlina basin, Slovakia; analyzed only morphologically) possessed markers of both species. Segregation of RAPD markers together with a model-based Bayesian analysis revealed that the specimen from Zbojská belonged to later generation hybrids.     

Development of microsatellite markers for the dwarf bamboo species Sasa cernua and Sasa kurilensis (Poaceae) in northern Japan

Ten polymorphic microsatellite markers were isolated from the dwarf bamboo species Sasa cernua and Sasa kurilensis. The applicability of these markers was confirmed by genotyping of open‐pollinated seeds and leaf samples from natural populations. Genotypes of seeds from each culm shared at least one allele from the maternal parent without contradiction. All 10 loci were polymorphic in S. cernua with 2–15 alleles (average H_E = 0.532). Eight loci were polymorphic in S. kurilensis with 2–10 alleles (average H_E = 0.532). These markers will be useful in detailing the extent of clonal and sexual reproduction in these species.     

Isolation and characterization of nine polymorphic microsatellite loci from the desert locust,Schistocerca gregaria

Because of the scarcity of polymorphic genetic markers, only a few genetic studies on the population structure of the desert locust, Schistocerca gregaria, have been carried out. We isolated and characterized nine polymorphic dinucleotide microsatellite loci. These markers were evaluated using individuals from Niger and Senegal. Seven of these microsatellite markers are also applicable to the nongregarious subspecies Schistocerca gregaria flaviventris. Cross‐species applicability was limited to one of the loci in the sister species S. americana and in the locust Locusta migratoria.     

Development of novel chloroplast microsatellite markers for Cucumis from sequence database

The development of chloroplast microsatellite (cpSSR) markers in Cucumis species and analysis of their polymorphism and transferability were reported. Fifteen microsatellite markers, represented by mononucleotide repeats, were developed from the complete sequence of Cucumis sativus chloroplast genome. Intraspecific variation was successfully detected in C. sativus and C. melo and revealed mean 1.6 and 1.9 alleles per cpSSR locus, respectively. With the exception of two exon region-located cpSSR markers being monomorphic, each of the others amplified polymorphic fragments in C. sativus or C. melo. A total of 34 polymorphic loci were detected with these cpSSR markers in the two species. Transferability of the newly developed cpSSR markers was checked on an additional set of 41 Cucurbitaceae accessions (belonging to 12 different species), and except for two markers with no amplification in Cucurbita maxima, the others could be transferable to all the accessions tested. Of the 15 cpSSR markers, 14 markers generated fragments with expected band sizes and 13 markers detected interspecific polymorphism among the accessions. Intraspecific polymorphism was also observed within four Cucurbitaceae species excluding C. sativus and C. melo.     

Microsatellite loci for euglossine bees (Hymenoptera: Apidae)

The Neotropical Euglossini (Hymenoptera: Apidae) are important pollinators of many flowering plants, particularly orchids. Lack of highly polymorphic genetic markers for euglossine species has limited the study of their social organization and inbreeding. We therefore developed microsatellite markers for two species, Eulaema nigrita (11 loci) and Euglossa cordata (nine loci), most of which were highly polymorphic in the source species and in a range of related euglossine bees.     

Reverse ascertainment bias in microsatellite allelic diversity in owls (Aves, Strigiformes)

A rich source of markers may be overlooked by screening for polymorphism in the source species only. We screened 129 microsatellite loci isolated from the powerful owl (Ninox strenua) against two closely related species; Ninox connivens and Ninox novaeseelandiae. From the screening effort 20 polymorphic markers were isolated, including six loci which were originally discarded as they were monomorphic in the source species. Further cross-species amplification of all 20 loci across species from two families, Strigidae and Tytonidae, revealed unusually high levels of polymorphism within closely related species, and limited success within phylogenetically distant species. Routine screening of multiple species during the marker development phase can yield a wider range of polymorphic markers which can subsequently enhance cross-species amplification attempts.     

Development and characterization of microsatellite markers for Prosopis chilensis and Prosopis flexuosa and cross‐species amplification

Prosopis chilensis and Prosopis flexuosa (Fabaceae) are closely related hardwood arboreal species that are widely distributed in the arid regions of Argentina. The development of highly polymorphic markers, such as microsatellites, is desirable for genetic studies of these species. Here, we present the development and characterization of six polymorphic microsatellite markers in P. chilensis and P. flexuosa. These markers showed a polymorphism information content between 0.14 and 0.85 and the number of alleles varied from two to 13 considering both species. All markers revealed a broad cross‐species affinity when tested in seven other Prosopis species. All primers amplified in at least five species.     

Development and characterization of polymorphic microsatellite DNA markers for Sasa senanensis (Poaceae: Bambuseae)

Sasa senanensis is a dwarf bamboo species distributed on the floors of cool temperate forests in Japan and adjacent regions. We isolated eight polymorphic microsatellite loci from this species. The number of alleles ranged from two to eight and the observed heterozygosity per locus from 0.13 to 0.74. Seven of the eight loci were also polymorphic in Sasa nipponica. Most of these markers were successfully amplified in other dwarf bamboo species. These markers will be useful for investigating clonal structure and population genetics in some dwarf bamboo species.     

Development and characterization of microsatellite markers for a monoecious Ficus species,Ficus insipida,and cross‐species amplification among different sections of Ficus

The animal‐mediated pollination and seed‐dispersal mutualisms of Ficus species give them key roles in tropical ecosystems, but may make them vulnerable to habitat fragmentation. The development of highly polymorphic markers is needed to analyse their genetic diversity and investigate the effects of fragmentation on gene flow. Of thirteen microsatellite loci isolated from Ficus insipida, a monoecious species in French Guiana, eleven were polymorphic (two to six alleles each). High levels of variation were found among loci; expected heterozygosities ranged from 0.151 to 0.715. All markers revealed a broad cross‐species affinity when tested in 23 other Ficus species.     

Microsatellite markers for European Daphnia

We present 32 polymorphic microsatellite markers for species of the European Daphnia longispina group: D. galeata, D. hyalina, D. rosea, D. cucullata and D. curvirostris. Microsatellite markers were either isolated from genomic libraries or optimized based on previously published sequence information of sister taxa. Cross‐species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra‐ and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.     

Molecular characterisation of Trichoderma species using SRAP markers

Trichoderma are commonly used as bio control agents in various agro ecosystems. They are known to produce a variety of compounds that induce resistance responses in plants. Among different species of Trichoderma, T. harzianum, T. viride, T. koningii and T. hamatum are commercially used as bio control agents. In the present study, four commercially important species of Trichoderma isolated from coffee ecosystem were screened with sequence related amplified polymorphism (SRAP) markers. Among 48 SRAP primer pairs tested, 29 primers were polymorphic and generated 316 distinct scorable fragments. Out of 347 amplified fragments, 177 fragments were found polymorphic with an average of 6.10 fragments per primer combination. The average polymorphism information content (PIC) and resolving power (Rp) of the 29 polymorphic SRAP primer pair were 0.42 and 14.62, respectively. The UPGMA dendrogram clearly divided Trichoderma species into two broad clusters. The highest homology (83.0%) was observed between T. viride and T. Harzianum and the lowest homology (74.0%) was observed between T. Harzianum and T. konangii. Further, among 29 polymorphic SRAP markers screened, four primer pairs (ME1-EM3, ME1-EM20, ME1-EM22 and ME2-EM4) produced unique fragments specific to each species. These markers can be useful in easy and rapid identification of the species.     

Detection of section-specific random amplified polymorphic DNA (RAPD) markers in Lilium

Random amplified polymorphic DNA (RAPD) markers were utilized for the identification of Lilium species and inter-specific hybrids. The optimum annealing temperature of the polymerase chain reaction (PCR) for the RAPD assay in Lilium was 54 °C, which is relatively higher than the temperature used for other genera reported by previous researchers. Among 76 primers used to amplify genomic DNA by PCR, 18 primers (24%) generated polymorphic DNA fragments in Lilium species and hybrids. Cultivars were also identified by RAPD markers. Some amplified fragments were unique to species of each section and to hybrids derived from these species; that is, they were the section-specific DNA markers. Sections, Sinomartagon, Leucolirion b, Leucolirion a and Archelirion could be identified by 6 section-specific markers amplified with five primers. Seven inter-section hybrids showed the section-specific bands of both parental sections, indicating that these markers would be useful for identifying the parental sections of inter-section hybrids.     

Polymorphic microsatellite DNA markers in the ant Formica exsecta

Highly polymorphic genetic markers provide a useful tool for estimating important genetic parameters in studies of the evolution of sociality in insects. Here we report 14 polymorphic microsatellite markers developed in the ant Formica exsecta. The number of alleles found ranged between 3 and 18 per locus. These markers were developed for studying genetic population structure and mating structure in F. exsecta populations with varying social organizations (monogyne and polygyne types of societies). Cross‐species amplification indicated that some of the markers might be usable even in species belonging to different subfamilies.     

Isolation and cross‐species amplification of microsatellite loci from the fucoid seaweeds Fucus vesiculosus,F. serratus and Ascophyllum nodosum (Heterokontophyta,Fucaceae)

The Fucaceae is a family of brown seaweeds that dominate and frequently co‐occur on North Atlantic rocky shores. We developed nine polymorphic microsatellite markers for the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum using a combined, enriched library. Six of these loci were polymorphic in at least two species, showing from two to eight alleles with heterozygosities ranging from 0.41 to 0.85. Loci were also tested on F. spiralis, revealing five polymorphic microsatellite loci in this species.     

Large scale development of selectively amplified microsatellite polymorphic loci (SAMPL) markers in spruce (Picea)

The spruce (Picea) species are ecologically and economically important in Canada. Highly informative markers with high multiplex ratios are needed to assist spruce genomics, genetics, and breeding programs. Selectively amplified microsatellite polymorphic loci (SAMPL) markers are highly suitable for these programs. We have developed, optimized, and characterized a set of 10 new SAMPL primers in combination with 16 MseI primers and resolved a large number of polymorphic SAMPL markers in spruce. The SAMPL primers were designed from the compound microsatellite repeats found in Norway spruce (Picea abies) and white spruce (Picea glauca). A total of 6313 polymorphic SAMPL makers were produced by 160 SAMPL–MseI primers combinations in eight progeny of a spruce mapping population.     

Seven polymorphic microsatellite DNA loci from the red‐spotted newt (Notophthalmus viridescens)

We describe polymerase chain reaction (PCR) primers and amplification conditions for seven microsatellite DNA loci isolated from the red‐spotted newt (Notophthalmus viridescens). Primers were tested on 16 individuals from two populations on the Savannah River Site in Aiken County, South Carolina. We detected six to 10 alleles per locus and an overall observed heterozygosity range of 0.31–0.81. Despite low heterozygosity at two of the seven loci, the high polymorphic information contents (from 0.54 to 0.85) of these markers render them useful for future studies of the behavioural and population ecology of this common salamander.