Isolation of polymorphic tetranucleotide microsatellite markers for the streak‐necked flycatcher Mionectes striaticollis

We have isolated 11 polymorphic microsatellite markers for the streak‐necked flycatcher Mionectes striaticollis from genomic libraries enriched for either (AACC)_n, (AAGG)_n or (AAAG)_n repetitive elements. The number of alleles ranged from four to 14 per locus with the observed heterozygosity ranging from 0.38 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.     

Isolation of polymorphic tetranucleotide microsatellite markers for the skink Mabuya affinis

We isolated 10 polymorphic microsatellite markers for the skink Mabuya affinis from genomic libraries enriched for (AAGG)_n and (AAAG)_n repetitive elements. The number of alleles ranged from eight to 13 per locus with the observed heterozygosity ranging from 0.60 to 0.92. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.     

Microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida)

A genomic cosmid library was used to develop seven highly polymorphic microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida). These are the first reported microsatellite markers derived from this species. The cloned and sequenced repeat motifs include a triplet repeat of (AAT)_n, two tetranucleotide repeats of (GATA)_n, a tetranucleotide repeat of (ATCC)_n, a compound repeat of (GA)_n(GATA)_n and the two pentanucleotide repeats (AGAAT)_n and (ATTTT)_n. The microsatellites described represent six presumably independent loci with the two pentanucleotide repeats having originated from a single cosmid. Primer pairs allow locus‐specific amplification of each marker from Mexican spotted owl genomic DNA.     

Isolation of polymorphic tetranucleotide microsatellite markers for the pygmy kingfisher Ceyx picta

We have isolated 13 polymorphic microsatellite markers for the pygmy kingfisher, Ceyx picta, from genomic libraries enriched for either (AAGG)_n or (AACC)_n repetitive elements. The number of alleles range from three to 15 per locus with an observed heterozygosity ranging from 0.46 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.     

SSR marker and ITS cleaved amplified polymorphic sequence analysis of soybean × Glycine tomentella intersubgeneric derived lines

Wild perennial Glycine species are an invaluable gene resource for the cultivated soybean [Glycine max (L.) Merr., 2n=40]. However, these wild species have been largely unexplored in soybean breeding programs because of their extremely low crossability with soybean and the need to employ in vitro embryo rescue methods to produce F₁ hybrids. The objective of this study was to develop molecular markers to identify gene introgression from G. tomentella, a wild perennial Glycine species, to soybean. A selection of 96 soybean simple sequence repeat (SSR) markers was evaluated for cross-specific amplification and polymorphism in G. tomentella. Thirty-two SSR markers (33%) revealed specific alleles for G. tomentella PI 483218 (2n=78). These SSR markers were further examined with an amphidiploid line (2n=118) and monosomic alien addition lines (MAALs), each with 2n=40 chromosomes from soybean and one from G. tomentella. The results show that the use of SSR markers is a rapid and reliable method to detect G. tomentella chromosomes in MAALs. We also developed a cleaved amplification polymorphism sequence (CAPS) marker according to the sequences of internal transcribed spacer (ITS) regions in soybean and G. tomentella. Four MAALs that carry the ITS (rDNA) locus from G. tomentella were identified. The SSR and ITS-CAPS markers will greatly facilitate the introgression and characterization of gene transfer from G. tomentella to soybean.Communicated by F.J. Muehlbauer     

Polymorphic microsatellite DNA markers for the grey fantail,Rhipidura albiscapa

We isolated and characterized five polymorphic microsatellite markers for the grey fantail Rhipidura albiscapa from genomic libraries enriched for (AC)_n and (GT)_n microsatellites. In 34 adult individuals, the number of alleles per locus ranged from eight to 17. Observed and expected heterozygosities ranged from 0.65 to 0.94 and 0.83 to 0.94, respectively. These markers will be useful for analysing extra‐pair paternity in fantails.     

Isolation of polymorphic tetranucleotide microsatellite markers for the large‐billed scrubwren (Sericornis magnirostris)

We isolated 12 polymorphic microsatellite markers for the large‐billed scrubwren Sericornis magnirostris from genomic libraries enriched for (AAGG)_n and (AACC)_n repetitive elements and characterized them in 11 individuals. The number of alleles ranged from four to 15 per locus with the observed heterozygosity ranging from 0.14 to 0.91. These markers will be useful to address questions concerning population genetic structure and models of speciation.     

Isolation of polymorphic tetranucleotide microsatellite markers for the green‐eyed tree frog (Litoria genimaculata)

We have isolated 16 polymorphic microsatellite markers for the green‐eyed tree frog, Litoria genimaculata, from genomic libraries enriched for (AAGG)_n and (AAAG)_n repetitive elements. The number of alleles ranges from four to 14 per locus with the observed heterozygosity ranging from 0.36 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and speciation.     

Polymorphic microsatellite DNA markers for the white‐breasted thrasher,Ramphocinclus brachyurus

We isolated and characterized six polymorphic microsatellite markers for the white‐breasted thrasher from genomic libraries enriched for (AC)_n, (GT)_n, (CAAA)_n, (TTTC)_n, (GAC)_n, (CT)_n and (TTTG)_n microsatellites. The number of alleles per locus ranged from two to seven. Observed heterozygosity (H_O) ranged from 0.30 to 0.85.     

Isolation of polymorphic tetranucleotide microsatellite markers for the ornate nursery frog Cophixalus ornatus

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG)_n, (AACC)_n and (AAGG)_n repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation.     

Isolation of polymorphic tetranucleotide microsatellite markers for the black‐bellied seedcracker (Pyrenestes ostrinus)

We have isolated 10 polymorphic microsatellite markers for the black‐bellied seedcracker (Pyrenestes ostrinus) from genomic libraries enriched either for (AAGG)_n or (ATCT)_n repetitive elements and characterized them in 39 individuals. The number of alleles ranged from two to 27 per locus with the observed heterozygosity ranging from 0.38 to 0.94. These markers will be useful for analysis of questions concerning parentage and population genetic structure.     

Sixty simple sequence repeat markers for use in the Festuca–Lolium complex of grasses

So far only very few simple sequence repeat (SSR) markers developed from grass species have had their primer sequences published. To make more markers available to the scientific community, we isolated and sequenced 256 microsatellite‐containing clones from four genome libraries of a Lolium multiflorum×Festuca glaucescens F₁ hybrid following enrichment in (TC)_n, (TG)_n, or both repeats. In this work, we report the primer sequences of 60 SSRs including preliminary results of polymorphism for mapping.     

Development and characterization of eight polymorphic microsatellite markers for Daphnia atkinsoni (Crustacea: Ctenodaphnia)

A microsatellite‐enriched genomic library was developed for the water flea Daphnia atkinsoni Baird, 1859, a dominant species of intermittent wetlands in Europe. Eight polymorphic microsatellite markers were successfully optimized. Characterization of 77 individuals from Belgium and Spain showed moderate (in the former) to high (in the latter) levels of polymorphism with two to 11 alleles per locus and an observed heterozygosity ranging from 0 to 0.87. Some of these microsatellite markers were successfully amplified in three other Daphnia species (D. magna n = 4, D. similis n = 6; D. obtusa n = 6).     

The use of microsatellite DNA markers for soybean genotype identification

Conventional morphological and pigementation traits, as well as disease resistance, have been used to distinguish the uniqueness of new soybean cultivars for purposes of plant variety protection. With increasing numbers of cultivars and a finite number of conventional characters, it has become apparent that such traits will not suffice to establish uniqueness. The objective of this work was to provide an initial evaluation of microsatellite or simple-sequence-repeat (SSR) DNA markers to develop unique DNA profiles of soybean genotypes. Microsatellites are DNA sequences such as (AT) _n /(TA) _n and (ATT) _n /(TAA) _n that are composed of tandemly repeated 2–5-basepair DNA core sequences. The DNA sequences flanking microsatellites are generally conserved allowing the selection of polymerase chain reaction (PCR) primers that will amplify the intervening SSR. Variation in the number of tandem repeats, n, results in PCR product length differences. The SSR alleles present at three (AT) _n /(TA) _n and four (ATT) _n /(TAA) _n loci were determined in each of 96 diverse soybean genotypes. Between 11 and 26 alleles were found at each of the seven loci. Only two genotypes had identical SSR allelic profiles and these had very similar pedigrees. The gene diversity for the seven markers averaged 0.87 for all 96 genotypes and 0.74 for a subset of 26 North American cultivars. These are much higher than soybean gene diversity values obtained using RFLP markers, and are similar to the average values obtained for human microsatellite markers. SSR markers provide an excellent complement to the conventional markers that are currently used to characterize soybean genotypes.     

Characterization of highly variable (GA/CT) n microsatellites in the bur oak,Quercus macrocarpa

The objective of this study was to ascertain the usefulness of polymerase chain reaction (PCR)-based microsatellite analysis for studying pollination and parentage in a wind-pollinated temperate tree. A small insert genomic library of the bur oak (Quercus macrocarpa) was constructed and screened for the presence of (CA/GT) _n and (GA/CT) _n repeats. The proportion of positive clones yielded estimates of 3×10⁵ such dinucleotide repeats per genome, roughly comparable to abundances reported in other eukaryotic genomes. Thirteen positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) _n motif was more abundant than the (CA/GT) _n motif in these clones. The (GA/CT) _n repeats also showed longer average repeat length (mean n=16.2 versus 7.3), suggesting that they are better candidates for yielding polymorphic genetic markers in oak genomes. Indeed, a survey of adult bur oaks and offspring in a small stand in northern Illinois at 3 of these (GA/CT) _n microsatellite loci revealed Mendelian inheritance and extremely high levels of polymorphism, with the number of alleles at each locus ranging from 11–20 and heterozygosity ranging from 0.66 to 0.75. These results, indicating that (GA/CT) _n microsatellites are both abundant and highly polymorphic in the bur oak genome, suggest that such genetic markers have tremendous potential for applications for studies of parentage, pollination and dispersal in temperate trees.     

Isolation and characterization of Brachymystax lenok microsatellite loci and cross‐species amplification in Hucho spp. and Parahucho perryi

We isolated and characterized eight polymorphic microsatellite markers for Brachymystax lenok (Pallas, 1773) from genomic libraries enriched for (GATA)_n, (GACA)_n and (ATG)_n microsatellites. The number of alleles per locus ranged from two to 17. Heterozygosity ranged from 0.2 to 0.95. In addition, cross‐species amplification was successful for seven loci in Hucho hucho, eight in H. taimen and seven in Parahucho perryi.     

Isolation and characterization of 18 microsatellites in the Peking duck (Anas platyrhynchos) and their application in other waterfowl species

We have isolated and characterized 18 microsatellite loci in the Peking duck (Anas platyrhynchos). The average number of alleles per locus was 3.5, ranging from one to six in domestic Peking ducks (n = 40). All of the markers were polymorphic in a sample of five mallards (A. platyrhynchos; two to eight alleles). Seventeen of the 18 markers amplified in Muscovy ducks (Cairina moschata) with 11 being polymorphic in our sample (n = 14). Amplification of the markers in different species comprising the subfamilies Anatinae and Anserinae indicates their potential value for population genetic applications in a wide range of waterfowl species.     

Isolation of polymorphic tetranucleotide microsatellite markers for the bay pipefish Syngnathus leptorhynchus

We have isolated nine polymorphic microsatellite markers for the bay pipefish Syngnathus leptorhynchus from genomic libraries enriched for (AAGG)_n repetitive elements. The number of alleles ranged from two to 15 per locus with the observed heterozygosity ranging from 0.09 to 1.00. These markers will be useful for analyses of questions concerning population genetic structure.     

Characterization and molecular genetic mapping of microsatellite loci in pepper

Microsatellites or simple sequence repeats are highly variable DNA sequences that can be used as informative markers for the genetic analysis of plants and animals. For the development of microsatellite markers in Capsicum, microsatellites were isolated from two small-insert genomic libraries and the GenBank database. Using five types of oligonucleotides, (AT)₁₅, (GA)₁₅, (GT)₁₅, (ATT)₁₀ and (TTG)₁₀, as probes, positive clones were isolated from the genomic libraries, and sequenced. Out of 130 positive clones, 77 clones showed microsatellite motifs, out of which 40 reliable microsatellite markers were developed. (GA) _n and (GT) _n sequences were found to occur most frequently in the pepper genome, followed by (TTG) _n and (AT) _n . Additional 36 microsatellite primers were also developed from GenBank and other published data. To measure the information content of these markers, the polymorphism information contents (PICs) were calculated. Capsicum microsatellite markers from the genomic libraries have shown a high level of PIC value, 0.76, twice the value for markers from GenBank data. Forty six microsatellite loci were placed on the SNU-RFLP linkage map, which had been derived from the interspecific cross between Capsicum annuum TF68 and Capsicum chinense Habanero. The current SNU2 pepper map with 333 markers in 15 linkage groups contains 46 SSR and 287 RFLP markers covering 1,761.5 cM with an average distance of 5.3 cM between markers.Communicated by J. Dvorak     

Variation of Mini- and Microsatellite DNA Repeats in Parthenogenetic Lizard Darevskia armeniaca as Revealed by DNA Fingerprinting Analysis

Population and family samples of two morphological forms (mutant and normal with respect to dorsal color) of parthenogenetic lizard species Darevskia armeniaca were examined by means of DNA fingerprinting using M13 mini- and (GACA) _n and (TCC) _n microsatellite DNA markers. The morphological forms examined were characterized by clonally inherited, species-specific patterns of the DNA markers, which were different from the species-specific DNA fingerprints of the other parthenogenetic species of the genus Darevskia (D. dahli, D. unisexualis, and D. rostombekovi). The mean index of similarity (S) obtained for a sample of 36 individuals from three isolated populations using three types of DNA markers was 0.966. This was similar to those observed in D. dahli (0.962) (P > 0.05), but higher than that in D. unisexualis (0.950) (P < 0.05) and D. rostombekovi(0.875) (P < 0.01). Inheritance of M13 minisatellite and (TCC) _n microsatellite DNA markers in the F1 offspring of parthenogenetic lizards was examined. It was shown that variability and clonal diversity of the fingerprint phenotypes observed in the populations and families of D. armeniaca could be at least partly explained by RFLP mutations in microsatellite repeats.