Species-specific genetic markers for identification of early life-history stages of Cape hakes, Merluccius capensis and Merluccius paradoxus in the southern Benguela Current

The correct identification of fish egg and larval stages is crucial for inferring spawning areas and subsequent dispersal routes for marine fishes. The authors use species-specific mtDNA polymerase chain reaction to estimate proportions of Merluccius capensis and Merluccius paradoxus eggs and larvae and to elucidate early life stage distribution patterns in the southern Benguela system.     

Sixteen polymorphic microsatellites in bighead carp (Aristichthys nobilis) and cross-amplification in silver carp (Hypophthalmichthys molitrix)

A (GT)(n) enriched partial genomic library of bighead carp (Aristichthys nobilis) was constructed by employing the (fast isolation by AFLP of sequences containing repeats) FIASCO protocol. Sixteen loci exhibited polymorphism with two to seven alleles/locus (mean 3.263) in a test population and the observed heterozygosity ranging from 0.100 to 0.690 (mean 0.392). Eleven of the 16 bighead carp microsatellites were found to be also polymorphic in silver carp. These polymorphic loci should provide sufficient level of genetic diversity to evaluate population structure of bighead carp.     

Isolation and characterization of new polymorphic microsatellite loci in the mixotrophic orchid Limodorum abortivum L. Swartz (Orchidaceae)

Here, we report the isolation and characterization of 11 polymorphic microsatellites in Limodorum abortivum. Allele variability has been characterized in three populations from Southern Italy and France. The number of alleles ranged from one to six per locus with an average of 3.8 alleles per locus. Observed and expected heterozygosity values ranged from 0.000 to 1.000 and from 0.492 to 0.806, respectively, with striking differences among populations. These microsatellites should be valuable tools for studying fine-scale genetic structure of scattered Limodorum abortivum populations, patterns of relationship with closely related taxa and the evolutionary ecology of its mycorrhizal interactions.     

A new set of highly polymorphic microsatellites for the white and black anglerfish (Lophiidae)

A microsatellite‐enriched genomic library was obtained using individuals of the black anglerfish (Lophius budegassa) and eight polymorphic microsatellites were successfully optimized. The genetic analysis of 50 black anglerfish individuals captured in the Cantabrian coasts revealed high polymorphism with a mean of number of alleles per locus of N_a = 10.5 (5–28 alleles) and a mean expected heterozygosity of 0.740 (0.521–0.962). This microsatellite set was also functional with a sample from the white anglerfish (Lophius piscatorious) showing a high polymorphism.     

Polymorphic tetranucleotide microsatellites for Cope's giant salamander (Dicamptodon copei) and Pacific giant salamander (Dicamptodon tenebrosus)

We present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.     

A set of 21 polymorphic microsatellites in Alpine chamois (Rupicapra rupicapra)

A cross‐species amplification test of 39 bovid microsatellite markers was carried out on chamois (Rupicapra rupicapra), a species with a high economic and tourist value, for which a number of life‐history traits remain to be quantified. Of 39 primer pairs tested, 26 gave a specific amplification product and 21 were polymorphic. Locus‐specific allelic richness ranged from two to six. Our results suggest that these loci will be useful for investigating basic population genetics as well as life‐history traits, such as dispersal.     

Isolation and characterization of polymorphic microsatellite loci for the dace complex: Leuciscus leuciscus (Teleostei: Cyprinidae)

Ten novel polymorphic microsatellites were isolated from the dace complex (Leuciscus leuciscus), which is a European cyprinid species. Four multiplex polymerase chain reaction sets were optimized in order to genotype 26 polymorphic loci in all, including 16 previously published cyprinid-specific loci. The level of genetic diversity was assessed in 142 dace individuals. We also successfully applied 26 of the microsatellites to 10 related species. These primers thus will be useful to assess population structure of the dace and other cyprinid species, with application for conservation issues and phylogeographical approaches.     

Isolation of polymorphic microsatellites in the stemless thistle (Cirsium acaule) and their utility in other Cirsium species

The genus Cirsium includes species with both widespread and restricted geographical distributions, several of which are serious weeds. Nine polymorphic microsatellite loci were isolated from the stemless thistle Cirsium acaule. Eight were polymorphic in C. acaule, six in C. arvense and seven in C. heterophyllum. One locus monomorphic in C. acaule showed polymorphism in C. heterophyllum. The mean number of alleles per locus was 4.1 in C. acaule, 6.2 in C. arvense and 2.9 in C. heterophyllum. These nine loci were also amplified in C. eriophorum and C. vulgare, suggesting that these markers may be of use throughout the genus.     

Development and cross‐species amplification of 18 microsatellite markers in the Sumatran tiger (Panthera tigris sumatrae)

Eighteen polymorphic microsatellite loci from the highly endangered Sumatran tiger (Panthera tigris sumatrae) were isolated and characterized. Upon polymerase chain reaction amplification, 16 of these markers produced a single, sharp band in all three tiger and 10 non‐tiger felid species examined. Of the two remaining loci, 6HDZ057 and 6HDZ635 failed to amplify genomic DNA from puma (Felis concolor) and cheetah (Acinonyx jubatus), respectively. The amplification of these markers across four genera is an indication of their usefulness for population genetics studies and conservation work in a wide range of felid species.     

Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross‐amplification in other cyprinid species

Captive populations of silver carp (Hypophthalmichthys molitrix), a major aquaculture species in Asia, would undoubtedly benefit from genetic monitoring and improvement programs. We report the isolation and preliminary characterization of 16 microsatellite loci derived from both conventional and microsatellite‐enriched libraries. Inheritance studies confirmed the allelic nature of observed polymorphisms at all loci, while identifying null alleles at two loci. These loci, having varying degrees of polymorphism, should provide useful markers for applied genetic studies. A high degree of cross‐amplification among 10 other cyprinid species suggests that these loci may have more widespread utility.     

Five new microsatellite loci for Oliver flounder (Paralichthys olivaceus) from an expressed sequence tag (EST) library and cross‐species amplification

Five microsatellite loci have been isolated and characterized from a cDNA library of Oliver flounder, Paralichthys olivaceus. All loci were found to be polymorphic and had between four and 10 alleles. Observed and expected heterozygosities varied from 0.70 to 0.90 and from 0.52 to 0.80, respectively. Five additional fish species assessed for cross‐species amplification revealed between zero and three positive amplifications and between zero and two polymorphic loci per species.     

A panel of polymorphic microsatellites in the threatened Apennine chamois (Rupicapra pyrenaica ornata)

The Apennine chamois (Rupicapra pyrenaica ornata) is a highly endangered mountain ungulate. About 800 individuals still survive in central Apennines, Italy. Current conservation projects involve genetic identification of single animals, paternity tests, and assessment of relatedness. A suite of 60 microsatellite primer pairs from domestic bovids and cervids revealed polymorphisms for 10 loci, providing evidence for a low level of genetic variability, which might be a consequence of severe population bottlenecks and prolonged permanence at low numbers.     

Development of novel polymerase chain reaction (PCR) based microsatellite markers in Armillaria gallica by cross‐species amplification and species‐specific cloning

Cross‐species PCR amplification of Armillaria mellea group taxa with previously reported A. ostoyae microsatellite markers, indicative of flanking sequence conservation, was exploited for the species‐specific isolation of simple sequence repeat (SSR) motifs from A. gallica. Six SSR motifs were sequence characterized from cloned PCR fragments generated with primers previously developed from A. ostoyae. Five novel primer pairs, designed from motif flanking regions, allowed for improved, efficient amplification in this species. One original A. ostoyae primer pair was used directly. Polymorphims were observed at wide geographical levels only. Relative cross‐species amplification intensities generally supported the currently accepted molecular phylogeny of this group.     

Polymorphic microsatellites in largemouth bronze gudgeon (Coreius guichenoti) developed from repeat‐enriched libraries and cross‐species amplifications

Largemouth bronze gudgeon (Coreius guichenoti) is a medium‐sized fish endemic from the upper Yangtze River of China and its survival is threatened by the construction of the Three Gorges Dam. This study reports 20 new polymorphic microsatellites from a repeat‐enriched genomic library with a mean number allele of 5.2, and observed and expected heterozygosities ranging from 0.035 to 1, and from 0.13 to 0.917, respectively. In a cross‐species amplification test, nine of the 37 tested loci were found to be also polymorphic in a congeneric species, brass gudgeon (C. heterodon). In addition, other four loci from common carp (Cyprinus carpio) were also polymorphic in C. guichenoti. Out of these 24 polymorphic microsatellites, only three loci significantly deviated from Hardy–Weinberg equilibrium in the sampled population (P < 0.0025), and all pairwise tests for linkage disequilibrium among loci were nonsignificant after applying sequential Bonferroni correction (P > 0.0026). These novel microsatellites provide sufficient levels of polymorphism for studies on population genetics and conservation in C. guichenoti and its related species.     

Isolation of microsatellite loci from spotted gum (Corymbia variegata), and cross‐species amplification in Corymbia and Eucalyptus

Corymbia variegata (spotted gum) is an important commercial hardwood timber species in Australia. Fourteen polymorphic microsatellite loci were isolated from C. variegata, with 3–5 alleles amplified in three individuals examined. Cross‐species amplification in Corymbia was successful for all primer pairs, while 10 loci (71%) were successfully transferred to at least one species in the closely related genus Eucalyptus.     

Isolation and characterization of polymorphic microsatellite loci in Wuchang bream (Megalobrama amblycephala)

Wuchang bream (Megalobrama amblycephala) is an economically important fish in China. From a (GT)₁₃‐enriched genomic library, 20 microsatellites were developed. Nine of these 20 loci were polymorphic in a test population with allele numbers ranging from two to four, and the observed and expected heterozygosities ranging from 0.2609 to 0.7826 and from 0.3739 to 0.7546, respectively. In the cross‐species amplifications, six of these nine loci were also polymorphic in white amur bream (Parabramis pekinensis). These polymorphic microsatellite loci are potentially useful for population genetics of Wuchang bream and its closely related species.     

Ten new microsatellite loci for the yellowhammer (Emberiza citrinella) and their cross‐species applicability among related taxa

We describe isolation and characterization of the first microsatellite loci specifically developed for a very common European passerine bird, the yellowhammer Emberiza citrinella. Nine out of our 10 loci are polymorphic within the species E. citrinella. Number of alleles ranged from two to 21 per locus and observed heterozygosity between 0.20 and 0.91. Four primer pairs also yielded reproducible results in other species of Emberizidae. These loci comprise a set of molecular markers for various applications, from moderately polymorphic loci suitable for population studies to highly polymorphic loci for pedigree analysis in Emberizidae.     

Fourteen microsatellite loci for the Chinese medicinal plant Epimedium sagittatum and cross-species application in other medicinal species

Epimedium sagittatum is a well-known medicinal plant as well as potential ground cover and ornamental plant. A total of 14 polymorphic microsatellite markers were developed for use in taxonomy, phylogenetics and conservation genetics. Markers were presented between two and eight alleles per locus. The observed heterozygosity (H(O) ) and expected heterozygosity (H(E) ) ranged from 0.03 to 0.81 and from 0.05 to 0.81, respectively. Cross-amplification among other four medicinal species revealed promising results in three to six polymorphic loci. These microsatellite loci contributed to the limited number of useful markers currently available for E. sagittatum.     

Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai)

Thirteen polymorphic microsatellite loci were developed in the Japanese pear (Pyrus pyrifolia Nakai) by using an enriched genomic library. The obtained microsatellite loci showed a high degree of polymorphism in the Japanese pear with 3–6 alleles per locus. The average values of observed and expected heterozygosities among these 13 loci were 0.69 and 0.71, respectively. Ten microsatellites could successfully amplify loci in the European pear (Pyrus communis L.), which were highly polymorphic as well.     

Isolation and characterization of polymorphic microsatellite loci in the freshwater fishes Telestes souffia and Telestes muticellus (Teleostei: Cyprinidae)

Ten novel polymorphic microsatellites (seven with perfect motifs) were isolated from vairone species (Telestes souffia and Telestes muticellus), which are endangered European cyprinid species. Together with 11 previously published cyprinid-specific loci, five multiplex sets were optimized, allowing the genotyping of 21 polymorphic loci. The level of genetic diversity was assessed in 97 individuals from the two species T. souffia and T. muticellus. We also successfully applied the 21 microsatellites to nine related species. These primers will thus be useful in assessing population structure of the vairone and other cyprinid species, with application for conservation issues and phylogeographical approaches.