Characterization of polymorphic microsatellite markers in the water rat (Hydromys chrysogaster)

The water rat (Hydromys chrysogaster) is well adapted to a semiaquatic life and is endemic to dispersed regions of Australia and New Guinea. To analyse the genetic diversity of water rat populations, polymorphic microsatellite markers were developed. A partial genomic library was screened for microsatellite sequences. Following isolation of the microsatellite sequences, primers were designed to amplify seven loci and of these loci, five were polymorphic. The sample tested for polymorphisms came from areas across Australia and New Guinea. Between three and 13 alleles were detected for each locus. In addition the primers amplified two loci in Mus musculus and Rattus rattus.     

Development and characterization of microsatellite markers for the endangered northern riffleshell mussel Epioblasma torulosa rangiana (Bivalvia: Unionidae)

Primers for six polymorphic microsatellite loci were developed for the endangered northern riffleshell Epioblasma torulosa rangiana from the Sydenham River, Ontario, Canada. These loci along with an additional nine microsatellite loci, developed from other unionoid species, available in the literature, were tested and characterized on individuals from two populations in the Allegheny River; one population in French Creek, PA, USA, and one population from the Sydenham River. Allelic diversity ranged from two to 28 alleles per locus and averaged 13.7 per locus. These primers are being used in a rangewide study on the conservation genetics of remaining extant populations of the northern riffleshell.     

Cross‐species comparison of microsatellite loci in the Culex pipiens complex and beyond

In the past, we have developed microsatellite loci from the two most common members of the Culex pipiens complex, Culex quinquefasciatus and Culex pipiens. Here we describe seven additional loci and present an extensive survey of a panel of 20 loci across most of the species and subspecies in the complex as well as in morphologically related species. Because we observed a high degree of polymorphism in the flanking regions, we designed new primers and surveyed multiple populations. We present alternate primers and discuss the cross‐species usefulness of these Culex microsatellite loci in a phylogenetic context.     

Isolation and characterization of the first polymorphic microsatellite markers for Schistosoma haematobium and their application in multiplex reactions of larval stages

The ability of microsatellite loci to reveal genetic diversity within the trematode Schistosoma haematobium is demonstrated for the first time. Nine novel polymorphic microsatellite markers were isolated and their viability assessed on 36 S. haematobium adult worm individuals from three geographical populations. Allelic diversity and gene diversity ranged from two to seven and from 0.29 to 0.76, respectively, suggesting high variability between individuals and between unrelated populations. Three primers also amplified Schistosoma mansoni and two Schistosoma japonicum. The results suggest these primers are useful for population genetic analyses of S. haematobium.     

Microsatellite markers isolated from barn swallows (Hirundo rustica)

Fifteen polymorphic microsatellite DNA loci were isolated from barn swallow (Hirundo rustica) and optimized for future studies of radiation‐induced mutations in populations from Ukraine. The loci were screened for variability among 25 individuals from two populations. The primers amplified loci with relatively high numbers of alleles ranging from five to 32 alleles per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.458 to 0.960. None of the loci showed deviations from Hardy–Weinberg equilibrium in either population.     

Microsatellite markers isolated from saltgrass (Distichlis spicata)

Twelve polymorphic microsatellite DNA loci were isolated from saltgrass (Distichlis spicata) and optimized for future studies of its breeding system. The loci were screened for variability among 24 individuals from two populations. The primers amplified loci with numbers of alleles ranging from four to 14 per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.227 to 0.958.     

Isolation and characterization of microsatellite DNA loci in Aquilegia sp.

We obtained a microsatellite‐enriched genomic library isolated from the tissue of a single columbine (Aquilegia sp.) plant taken from a southwestern USA natural population. The primers developed for these microsatellite loci performed consistently in polymerase chain reactions and yielded multiallelic genotypes with relatively high observed heterozygosities. We describe polymerase chain reaction primers and conditions to amplify 16 unique, codominant di‐, tri‐ and tetra‐nucleotide microsatellite DNA loci so that other population biology researchers using columbine natural populations as a model system may benefit.     

Isolation of nine microsatellite loci in Dolichogenidea homoeosomae (Hymenoptera) a parasitoid of the sunflower moth Homoeosoma electellum (Lepidoptera)

Nine microsatellite loci were isolated from the insect Dolichogenidea homoeosomae (Hymenoptera: Braconidae), an important parasitoid of the sunflower moth Homosoeosoma electellum (Lepidoptera: Pyralidae), and assayed for polymorphism. All nine loci were polymorphic within the five populations tested, with two to 14 alleles per locus. Expected and observed heterozygosities ranged from 0.39 to 0.90 and 0.25 to 0.72 respectively. These are the first microsatellite primers developed for D. homeosomae and will be useful for studies of population dynamics and connectivity.     

Characterization of nine microsatellite loci in the sea star Astropecten aranciacus and cross-species amplification for related taxa

So far, only few microsatellite markers have been developed and extensively tested for echinoderms. To study the population genetic structure of the sea star Astropecten aranciacus, we developed primers for nine polymorphic microsatellite loci and tested them on two populations from Faro in Portugal (N = 25) and from La Herradura in Spain (N = 20). Within populations, allele numbers varied from four to 20, while expected and observed heterozygosities ranged from 0.593 to 0.936 and from 0.222 to 0.900, respectively. Additional cross‐species amplifications were polymorphic at some loci, indicating their potential usefulness for related taxa.     

Primers from the orders Osteoglossiform and Siluriform detect polymorphic microsatellite loci in sun-catfish, Horabagrus brachysoma (Teleostei: Bagridae)

Horabagrus brachysoma (sun‐catfish, Bagridae, Siluriformes) is a valuable ornamental and food fish. The stock structure of H. brachysoma, necessary to conserve its declining natural populations, is not known. Twenty‐five primers developed for four fish species belonging to the orders Siluriform (3) and Osteoglossiform (1) were tested and eight primers amplified microsatellite loci in H. brachysoma. The results demonstrate that cross‐priming between fish species belonging to different families and even to different orders can yield microsatellite loci. Five of eight primers each amplified two loci. However, the loci that had repeat motifs after sequencing were considered only for genotyping. Finally, eight loci were polymorphic with hree to seven alleles. Individual fish genotype data (n = 42; 21 each in two rivers) at each locus was analysed. Significant genetic heterogeneity was detected at six loci. The identified loci exhibited potential for use in population genetics application in H. brachysoma.     

Development of microsatellite DNA loci from the wood stork (Aves,Ciconiidae, Mycteria americana)

We isolated 11 polymorphic microsatellite loci for wood stork (Mycteria americana). Polymerase chain reaction (PCR) primers and conditions are described for the amplification of five dinucleotide, one trinucleotide and five tetranucleotide microsatellite loci. The PCR primers were tested on two wood stork populations, Fazenda Ipiranga, Mato Grosso, Brazil (n = 11) and Tamiami West, Everglades, Florida, USA (n = 20). The primers yielded two to four alleles per locus, an observed heterozygosity of 0.0–0.727 and a polymorphic information content of 0.048–0.604. The low level of polymorphism for these markers is consistent with previous studies of this species.     

Isolation and characterization of novel polymorphic nuclear microsatellite markers from Ophrys fusca (Orchidaceae) and cross-species amplification

The present study reports the isolation and characterization of eight new polymorphic microsatellite loci from the sexually deceptive orchid Ophrys fusca. Microsatellites were isolated from two partially enriched genomic libraries using FIASCO (Fast Isolation by AFLP of Sequences COntaining repeats). Seventy-three loci were screened for primer design and primer pairs corresponding to eight different loci were selected for microsatellite characterization of two Portuguese populations. Total number of alleles per locus ranged from 10 to 32. All loci showed a high level of observed heterozygosity (H₀) ranging from 0.33 to 1 and were possible to amplify in 16 other species of Ophrys using the same primers. H. C. Cotrim and F. A. Monteiro have contributed equally to this work.     

Development and characterization of microsatellite loci in the endangered oyster mussel Epioblasma capsaeformis (Bivalvia: Unionidae)

Primers for 10 polymorphic microsatellite loci were developed and characterized for the endangered oyster mussel Epioblasma capsaeformis from the Clinch River, Tennessee. Microsatellite loci also were tested in four other populations or species. Amplification was successful for most loci in these closely related endangered species or populations; therefore, a high level of flanking sequence similarity was inferred for this group of species and populations. Allelic diversity ranged from nine to 20 alleles/locus, and averaged 13.6/locus. This study demonstrated the feasibility of using polymerase chain reaction (PCR) primers to amplify microsatellite loci across freshwater mussel species to conduct population genetics studies.     

Isolation and characterization of microsatellite loci in the black rat snake (Elaphe obsoleta)

We obtained molecular markers useful for population level studies of the black rat snake (Elaphe obsoleta) by screening genomic DNA libraries enriched for dinucleotide, tetranucleotide, and pentanucleotide microsatellite repeats. Following sequencing of the positive clones, 11 pairs of primers were designed for polymorphic loci and their variability assessed in > 350 individuals from four populations in North America. The loci had between 9 and 40 alleles and observed heterozygosities ranged from 0.071 to 0.87. Some of these pairs of primers also successfully amplified DNA from two other snake species.     

Tetranucleotide microsatellite DNA loci from the dollar sunfish (Lepomis marginatus)

We describe polymerase chain reaction (PCR) primers and conditions to amplify one dinucleotide and eight tetranucleotide microsatellite DNA loci isolated from the dollar sunfish (Lepomis marginatus). The PCR primers were tested on 20 or more individuals from five populations. The dollar sunfish microsatellite primers developed yielded a high number of alleles (4 to 14 per locus), and high observed heterozygosities (0.500–0.857).     

Characterization of microsatellite loci in the Kaka,Nestor meridionalis

Eight microsatellite loci were characterized from the Kaka (Nestor meridionalis), a New Zealand parrot, using a polymerase chain reaction‐based isolation technique. Locus‐specific primers were used to genotype nine Kaka populations and tested on 25 other species of parrot. The number of alleles observed within Kaka ranged from one to 16 in the 12–126 individuals screened and two loci exhibited greater than 60% heterozygosity. Furthermore, these primers are likely to be useful in population‐level studies of two other New Zealand parrots.     

Isolation and Characterization of Microsatellite Loci for Striped Bass (Morone saxatilis)

Genetic variation has been difficult to detect in striped bass (Morone saxatilis). Therefore, we identified and characterized 13 microsatellite loci to provide additional genetic markers for striped bass. Microsatellites were identified by screening a striped bass genomic library or by using primers developed for European sea bass (Dicentrarchus labrax) microsatellite loci. We found that 6 of the 13 microsatellite loci were polymorphic in DNA samples obtained from wild populations of striped bass. The number of alleles per locus varied from 3 to 12, and the observed heterozygosities ranged from 0.55 to 0.78. These results indicate that microsatellite loci provide more alleles and higher heterozygosities than other genetic markers developed for striped bass. Received November 9, 1999; accepted February 11, 2000.     

Characterization of 12 microsatellite markers in Serranus cabrilla (Pisces: Serranidae)

The commercial comber Serranus cabrilla is widely distributed in the Atlanto‐Mediterranean region, inhabiting a great variety of habitats and depths. We developed primers for 12 polymorphic microsatellite loci to analyse the genetic structure between comber populations and between their colour morphs in order to establish correct fisheries management. Characterization of 25 individuals from Columbretes Islands (Spain) showed an average large number of alleles (9.5 ± 1.3) and observed heterozygosity (0.657 ± 0.06). Only two loci showed significant departure from Hardy–Weinberg equilibrium. We found no evidence of linkage disequilibrium between pairs of loci. We rejected for primer design one clone with a microsatellite within the transposable element TX_FR2.     

Development and characterization of microsatellite loci for lotus (Nelumbo nucifera)

This paper reports the development of microsatellite primers for Nelumbo nucifera Gaerten. By screening genomic libraries enriched with 10 kinds of probes, Seventeen polymorphic loci were isolated and primers were designed. Polymorphism of these 17 loci was assessed in 24 individuals. All the 17 loci are polymorphic and the number of alleles ranged from two to seven. Observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.9176 and from 0.2837 to 0.7917 respectively. These microsatellite loci should be useful for studying the genetic diversity of N. nucifera.     

Development and characterization of microsatellite markers for parentage analyses of the coral reef damselfish (<Emphasis Type="Italic">Pomacentrus amboinensis</Emphasis>: Pomacentridae)

Five new polymorphic microsatellite loci were developed for the coral reef damselfish Pomacentrus amboinensis. Twenty-four individuals from two Great Barrier Reef populations were genotyped at the five loci, with numbers of alleles per locus ranging from 6–23 and observed heterozygosity between 0.42–0.92. In addition, the cross-species testing of six primers developed for Stegastes partitus revealed one primer (SpGATA40) that was also polymorphic for P. amboinensis. Due to high levels of polymorphism (≥14 alleles) in at least four of the six loci and a high proportion of tetranucleotide repeats, these microsatellite markers should be useful for parentage assignment as well as other investigations of individual relatedness.