Characterization of novel microsatellite loci in the great leaf-nosed bat, Hipposideros armiger and cross-amplification in other related species

Eight microsatellite loci were isolated from an enriched genomic library of the great leaf-nosed bat, Hipposideros armiger. The polymorphism of these loci was tested on a population of 48 individuals from Anhui Province, China. All loci revealed the polymorphism ranging from three to 12 alleles. The observed heterozygosity values were from 0.213 to 0.875 and expected heterozygosity from 0.232 to 0.820. No significant linkage disequilibrium was detected. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. In addition, successful cross-amplification also suggested that these microsatellite markers will facilitate research on the population genetics and gene flow of H. armiger and other related species.     

Isolation and characterization of 16 microsatellite loci in an endangered fish Ussuri cisco, <Emphasis Type="Italic">Coregonus usssruensis</Emphasis>

Sixteen polymorphic microsatellite loci were isolated from an enriched genomic library of Ussuri cisco, Coregonus usssruensi. The polymorphism of these loci was tested on a population of 30 individuals captured from Heilongjiang River. The number of observed alleles per locus ranged from 3 to 18. The expected and observed heterozygosity values ranged from 0.126 to 0.919 and 0.133 to 0.833, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. No significant linkage disequilibrium was detected. These polymorphic markers will be used to assess population structure in Ussuri cisco.     

Isolation of 15 polymorphic microsatellite loci in Acacia hybrid (Acacia mangium×Acacia auriculiformis)

This study reports the isolation of 15 microsatellites in Acacia hybrid (Acacia mangium×Acacia auriculiformis) based on the 5′ anchored polymerase chain reaction technique. Polymorphism of these loci was evaluated in a sample of 24 hybrid individuals. The level of polymorphism ranged from two to eight alleles with an observed heterozygosity ranging from 0.083 to 0.875. These loci were also characterized in both the parental species. The number of alleles ranged from two to six for both A. mangium and A. auriculiformis with the observed heterozygosity values ranging from 0.167 to 0.625 and 0.042 to 0.458 respectively. Five of these loci demonstrated Mendelian inheritance in a segregating F₁ population; four presented a distorted ratio and the remaining six did not segregate in progenies as they were homozygous in both parents.     

Characterization of <Emphasis Type="Italic">TPMT</Emphasis> minisatellite locus in five ethnic groups of India

A total of 206 random, healthy individuals belonging to five distinct ethnic groups (Ezhavas, Arayas, Nairs, Vishwakarmas and Muslims) were analyzed for 18 bp VNTR repeat polymorphism present in the 5í flanking region of the Thiopurine Methyl Transferase gene (TPMT). In the present study, the population data of TPMT minisatellite was compared with the population data of other loci and the utility of minisatellite was evaluated in population studies. Human tandem repeat alleles of the TPMT minisatellite locus were characterized for the length polymorphism. The expected and observed heterozygosity did not show any significant difference. All five populations were in Hardy-Weinberg equilibrium. High polymorphism information iontent (PIC) (≥0.658) and power of discrimination (PD) (ranging from 0.775–0.860) value of this VNTR showed that this marker is informative. The combined power of discrimination of TPMT minisatellite along with other two loci studied earlier in our lab was 0.9964. The paternity exclusion power (PE) of TPMT VNTR ranged from 0.203 to 0.533 and the combined power of paternity exclusion (with two other loci D8S315 and D2S1328) was ≥0.8285. All these parameters (heterozygosity, PD, PIC, PE) of TPMT minisatellite locus showed that this marker is informative and can be used for DNA typing and population studies besides being used in clinical investigation in checking thiopurine drug sensitivity of individuals. The text was submitted by the autor in English.     

Isolation and characterization of polymorphic microsatellites in the tropical plant‐ant Cataulacus mckeyi (Formicidae: Myrmicinae)

Eleven microsatellite loci were isolated from the plant‐ant Cataulacus mckeyi (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 16, and heterozygosity from 0 to 0.929 per population sample. Cross‐species amplification of these loci was also tested in four other species of the ant genus Cataulacus.     

Evaluating a Putative Bottleneck in a Population of Bowhead Whales from Patterns of Microsatellite Diversity and Genetic Disequilibria

A size-selected Balaena mysticetus genomic library was screened for clones containing simple sequence repeat, or microsatellite, loci. A total of 11 novel loci was identified. These loci were combined with a set of 9 published loci, for a total of 20 markers, and were scored across a sample of 108 bowhead whales from the Bering–Chukchi–Beaufort Seas population of bowhead whales. Genetic variability was measured in terms of polymorphism information content values and unbiased heterozygosity. From the latter, estimates of long-term effective population size were obtained. In addition, gametic phase disequilibrium among loci was investigated. Moderate to high levels of polymorphism were found overall, and the long-term effective size estimates were large relative to total population size. Tests of heterozygosity excess (Cornuet and Luikart 1996) and allele frequency distribution (Luikart et al. 1998) indicated that the possibility of a recent genetic bottleneck in the Bering–Chukchi–Beaufort Seas population of bowhead whales is highly unlikely. However, the fact that five loci displayed a statistically significant heterozygote deficiency remains to be explained. Received: 3 November 1998 / Accepted: 28 April 1999     

Characterization of polymorphic microsatellites in the castration parasite plant‐ant Allomerus octoarticulatus cf. demerarae (Formicidae: Myrmicinae)

Fifteen microsatellite loci were isolated from the Peruvian tropical plant‐ant Allomerus octoarticulatus cf. demerarae (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 21, and heterozygosity from 0 to 1 per population sample. Cross‐species amplification of these loci was also tested in one other species of the ant genus Allomerus (Allomerus decemarticulatus), displaying similar life history.     

Microsatellite DNA markers for the pea aphid Acyrthosiphon pisum

Microsatellite loci were isolated from enriched partial genomic libraries of Acyrthosiphon loti and Acyrthosiphon pisum. Twenty of those loci were characterized in A. pisum. Fifteen of those loci were polymorphic. Genetic diversity varied across loci, allele repeat number ranging from two to 15, and observed heterozygosity from 0.1 and 0.96. An additional eight microsatellite loci originally isolated from other aphids but cross‐priming with A. pisum showed polymorphism as well. Allele size ranged from three to 9 and observed heterozygosity from 0.43 to 0.84. Overall, we present 23 microsatellite loci that can be used to reveal polymorphism in pea aphids.     

Characterization of microsatellite markers for the tanoak tree,Lithocarpus densiflorus

We describe the development of 19 primers for amplification of microsatellite loci for tanoak, Lithocarpus densiflorus (Hook. & Arn.). A population from Soquel State Demonstration Forest, Santa Cruz County, California (n = 20), and eight individuals from four additional coastal populations and one interior (Sierra Nevada) population were used to investigate polymorphism. The total number of alleles per locus ranged from two to 10. Observed heterozygosity in the Soquel population ranged from 0.05 to 0.70, with two loci being fixed.     

Isolation and characterization of polymorphic microsatellite loci in a traditional Chinese medicinal plant, Schisandra sphenanthera

Schisandra sphenanthera (Schisandraceae) is a traditional Chinese medicinal plant. In this study, nine polymorphic microsatellite loci were developed and characterized for the species. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 36 individuals sampled from a natural population. The observed number of alleles ranged from 2 to 10 with an average of 5.2. Expected and observed heterozygosity ranged from 0.30 to 0.82 and 0.33 to 0.97, respectively. These microsatellites have been directly applied to both population and conservation genetic studies of S. sphenanthera.     

Biochemical genetic variation between four populations of Labeobarbus polylepis from three river systems in South Africa

The genetic variation within four Labeobarbus polylepis populations from both river and dam environments in the Limpopo, Incomati and Phongolo River systems was studied. Gene products of 22 enzyme-coding loci were resolved using horizontal starch gel electrophoresis. Fourteen (64%) of the 22 loci were monoallelic in all populations. Levels of polymorphism (P_0.95) ranged between 9.1% and 22.7%. The heterozygosity varied from 0.028 for the Westoe Dam population (Phongolo River system) to 0.093 in the Spekboom River population (Limpopo River system). The genetic distance, F_ST and N_EM values, as well as pair-wise contingency χ² analyses indicate a lack of gene flow between populations, as expected for isolated fish. Evidence of foreign genetic material in one population was also observed.     

Studies on enzymatic polymorphism in rye (Secale cereale L.) cultivars

An electrophoretic study of seed peroxidases of eight rye (Secale cereale L.) cultivars was carried out in order to estimate the polymorphism and the variability degree of this highly variable enzymatic system. Analysis of the Cathodal Peroxidase System (CPX) were performed using polyacrylamide gel electrophoresis. Thirteen loci were recorded in embryo plus scutellum and endosperm. The percentage of polymorphic loci ranged from 53.84% to 92.30% when the 99% polymorphism criterion was used; these high values were possibly due to the studied system. The average heterozygosity values ranged from 0.179 to 0.378; these values fell into the expected for open-pollinated species. Genetic distance values fitted well with those expected for conspocific plants with a little of diversification.     

PCR primers for polymorphic microsatellite loci in the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicidae)

Fourteen microsatellite loci were isolated and their level of polymorphism characterized in two populations of the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from two to 15, and heterozygosity from 0.050 to 0.925. Cross‐species amplification of these loci was also tested in four plant‐ant species belonging to three other genera, Aphomomyrmex, Cladomyrma (both Formicinae) and Cataulacus (Myrmicinae).     

Isolation and characterization of microsatellite loci in Eurycorymbus cavaleriei,a dioecious endemic tree species in China

Eleven dinucleotide microsatellites were developed and characterized for Eurycorymbus cavaleriei, a dioecious, rare and endemic tree species in China. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 30 trees from two natural populations. The observed heterozygosity (H_O) ranged from 0.379 to 0.931, with an average of 0.625. These markers provide powerful tools for the ongoing population and conservation genetics studies of E. cavaleriei.     

Analysis of durum wheat germplasm adapted to different climatic conditions

A study of the extent and patterns of microsatellite diversity in 234 genotypes from Ethiopian durum wheat (Triticum turgidum) landraces was conducted to identify areas of diversity that could be used as a source of new germplasm for developing high yielding and stable varieties. Landraces belonging to nine populations, from three Ethiopian regions [Tigray (T), Gonder (G) and Shewa (S)] with different climates, were analysed by using 28 simple sequence repeat (SSR) markers. The level of polymorphism was high and quite consistent among populations underlining the great diversity existing. The highest level of diversity was found within populations, about 75.9%, while about 5.3% was attributed to differences between regions. The level of expected heterozygosity was on an average, rather high, ranging from 39% to 56%, whereas the observed heterozygosity was, on an average, limited to 14%. An average of about five alleles per locus was detected in each population. Nevertheless, alleles were not equally present in populations as confirmed by the high level of expected heterozygosity. The polymorphism information content (PIC) for the markers assessed showed a wide range of values from 0.14 to 0.92. The likelihood relationships among the nine Ethiopian populations indicated that the material collected in the Gonder region (a wet climate) was genetically more diverse than the materials from Shewa and Tigray (dryer climates). The high number of loci in linkage disequilibrium (LD), up to 23, has demonstrated that the loci were associated irrespective of their physical location. This holds true even if the loci are located on different chromosome arms. Genetic diversity values between populations was very different and was used to produce a dendrogram showing population relationships.     

Development of microsatellite marker loci for European hazelnut (<Emphasis Type="Italic">Corylus avellana</Emphasis> L.) from ISSR fragments

Polymorphic microsatellite markers were developed for European hazelnut (Corylus avellana L.) from the sequences of inter-simple sequence repeat (ISSR) fragments and flanking regions. Twenty-five ISSR primers were used to generate fragments for cloning. Of the 520 unique sequences obtained, 41 contained long internal repeats (≥20 bp) with flanking sequences sufficient for primer design. From these, we developed 23 new polymorphic microsatellite loci. The flanking sequences were obtained for fragment ends by chromosome walking, and an additional 47 polymorphic markers were developed. Two additional polymorphic markers were developed from a GA-enriched library. The 72 new marker loci were characterized using 50 diverse hazelnut accessions. For the internal repeat loci, the number of alleles per locus ranged from 2 to 16, with a mean of 7.52. Mean values for expected heterozygosity (H_e), observed heterozygosity (H_o), and polymorphism information content (PIC) were 0.62, 0.59, and 0.58, respectively. The estimated frequency of null alleles (r) was ≥0.05 at six of the 23 loci. For the 47 marker loci developed from fragment ends, the number of alleles per locus ranged from 2 to 16, with a mean of 7.30. Mean values for H_e, H_o, and PIC were 0.62, 0.47, and 0.58, respectively. The estimated frequency of null alleles (r) was ≥0.10 at 18 of the 47 loci. Of the 70 loci developed from ISSR and flanking sequences, 50 segregated in our mapping population and were assigned to linkage groups.     

Characterization of polymorphic microsatellite loci in the aphid species Macrosiphum euphorbiae (Hemiptera: Aphididae)

Fourteen microsatellite loci were isolated and characterized in the potato aphid, Macrosiphum euphorbiae Thomas, by screening a genomic library with the oligonucleotide probes (GA)₁₀ (GT)₁₀ and (GATA)₄. Allelic diversity was estimated in samples collected from potato fields in Tunisia. Ten loci displayed polymorphism that ranged from two to four alleles per locus and the observed heterozygosity ranged from zero to one. These markers could be used to study the population genetic structure of this polyphagous aphid species.     

Isolation and characterization of polymorphic microsatellites in a Yangtze River fish,brass gudgeon (Coreius heterodon Bleeker)

The brass gudgeon (Coreius heterodon) is a fish of economic importance in the Yangtze River. From a (GATA)_n‐enriched genomic library, 25 microsatellites were developed by employing the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Nine loci exhibited polymorphism with two to 12 alleles (mean 3.9 alleles/locus) in a test population, and observed heterozygosity ranged from 0.1111 to 0.9630 (mean 0.4426). Three of the nine loci showed polymorphism in a congeneric species, the largemouth bronze gudgeon Coreius guichenoti. These loci should provide sufficient level of genetic diversity to evaluate the fine‐scale population structure of C. heterodon.     

Development of 12 novel microsatellite loci in a traditional Chinese medicinal plant, Epimedium brevicornum and cross-amplification in other related taxa

A total of 12 polymorphic microsatellite loci were developed and characterized for a Chinese medicinal plant, Epimedium brevicornum (Berberidaceae). A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 38 individuals from one natural population. The observed number of alleles ranged from 2–14. The ranges of observed and expected heterozygosity were 0.00–0.83 and 0.15–0.88, respectively. In addition, successful cross-species amplification of this set of microsatellite markers in other four medicinal Epimedium species suggested that they would provide a useful tool for the genetic and conservation studies of Epimedium species.