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Sequence Repeat (sequence + repeat)
Kinds of Sequence Repeat Terms modified by Sequence Repeat Selected AbstractsGenetic Diversity of Populations of Monilinia fructicola (Fungi, Ascomycota, Helotiales) from ChinaTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2010JIN-YAN FAN ABSTRACT. The genetic variation among 128 isolates of Monilinia fructicola (Fungi, Ascomycota, Helotiales) from China was analyzed using Inter-Simple Sequence Repeat (ISSR) markers and compared with those of samples from California, USA and New Zealand. A total of 72 reproducible DNA fragments were scored, of which 87.5% (63/72) were polymorphic. The Nei's gene diversity and Shannon's diversity indices of three Chinese regional populations were very similar to that from California. However, several differences were observed among geographic populations of M. fructicola from both within China and between China and California. The analysis of molecular variance (AMOVA) of isolates from different geographic locations suggested that most of the observed genetic variation was found within populations. Results of this study are inconsistent with the hypothesis that the Chinese populations of M. fructicola were derived from a single or few recent migrants from other countries. Instead, our results suggest that M. fructicola has been in China long before its first official recording in 2003. [source] Characteristics of strawberry plants propagated by in vitro bioreactor culture and ex vitro propagation methodENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 3 2009Samir C. Debnath Abstract Reproducible protocol for regeneration of complete plantlets from ,Bounty' strawberry (Fragaria ananassa Duch.), using a combination of gelled medium and bioreactor system, has been standardized. Sepals, leaf discs, and petiole halves produced multiple buds and shoots when cultured on semi solid-gelled medium containing 4 ,M thidiazuron (TDZ) for 4 wk followed by transferring in liquid medium containing 2,,M TDZ in a bioreactor system and cultured for another 4 wk. TDZ induced shoot proliferation at 0.1,,M in the bioreactor system but inhibited shoot elongation. TDZ-induced shoots were elongated and rooted in vitro on gelled medium containing 2,,M zeatin. Such bioreactor-derived tissue culture (BC) plantlets obtained from sepal explants were grown ex vitro and compared with those propagated by tissue culture on gelled medium (GC) and by conventional runner cuttings (RC), for growth, morphology, anthocyanin content, and antioxidant activity after three growth seasons. The BC and GC plants produced more crowns, runners, leaves, and berries than the RC plants although berry weight per plant did not differ significantly. BC and GC plants produced berries with more anthocyanin contents and antioxidant activities than those produced by the RC plants. However, intersimple sequence repeat (ISSR) marker assay produced a homogenous amplification profile in the tissue culture and donor control plants confirming the clonal fidelity of micropropagated plants. In vitro culture on TDZ and zeatin-containing nutrient media apparently induced the juvenile branching characteristics that favored enhanced vegetative growth with more crown, runners, leaf, and berry production. [source] Population dynamics of the ectomycorrhizal fungal species Tricholoma populinum and Tricholoma scalpturatum associated with black poplar under differing environmental conditionsENVIRONMENTAL MICROBIOLOGY, Issue 5 2006Hervé Gryta Summary Fungi combine sexual reproduction and clonal propagation. The balance between these two reproductive modes affects establishment dynamics, and ultimately the evolutionary potential of populations. The pattern of colonization was studied in two species of ectomycorrhizal fungi: Tricholoma populinum and Tricholoma scalpturatum. The former is considered to be a host specialist whereas T. scalpturatum is a generalist taxon. Fruit bodies of both basidiomycete species were mapped and collected over several years from a black poplar (Populus nigra) stand, at two different sites. Multilocus genotypes (= genets) were identified based on the analysis of random amplified polymorphic DNA (RAPD) patterns, inter-simple sequence repeat (ISSR) patterns and restriction fragment length polymorphisms (RFLPs) in the ribosomal DNA intergenic spacer (rDNA IGS). The genetic analyses revealed differences in local population dynamics between the two species. Tricholoma scalpturatum tended to capture new space through sexual spores whereas T. populinum did this by clonal growth, suggesting trade-offs in allocation of resources at the genet level. Genet numbers and sizes strongly differ between the two study sites, perhaps as a result of abiotic disturbance on mycelial establishment and genet behaviour. [source] Hybridization between perennial ryegrass and Italian ryegrass in naturalized Japanese populationsGRASSLAND SCIENCE, Issue 2 2008Hiroyuki Tobina Abstract Introduced Lolium species, including perennial ryegrass (Lolium perenne) and Italian ryegrass (Lolium multiflorum), have been widely utilized in Japan for forage, turf and soil conservation. These ryegrasses have escaped from cultivated areas and become naturalized, and this has become a serious issue in recent years. Interspecific hybrids between perennial ryegrass and Italian ryegrass have often been found in naturalized populations. It has also been suggested that hybridization between plant species might serve as a stimulus for the evolution of invasiveness. We surveyed the genetic structure of naturalized ryegrass populations in Japan using genetic markers that distinguished perennial ryegrass and Italian ryegrass. Of the 55 naturalized populations surveyed, 41 exhibited morphological traits of Italian ryegrass. DNA analysis using simple sequence repeat and chloroplast DNA markers characterized 20 of these 41 populations as Italian ryegrass, with the remaining populations as interspecific hybrid derivatives. Approximately half of the naturalized ryegrasses populations in Japan were inferred to include interspecific hybrids. [source] Cross-species amplification of Lolium microsatellites in Poa sspGRASSLAND SCIENCE, Issue 3 2006Bryan Kindiger Abstract Cross-species amplification of 47 Lolium ssp. microsatellite primers were evaluated across eight Poa species or subspecies. Of the 47 evaluated Lolium simple sequence repeat (SSR) primer pairs examined, 18 generated one or more amplification products. Of these, only two resulted in the identification of Poa ssp. microsatellite motifs, of which only one was complementary to the microsatellite motif identified in Lolium. Though few Poa ssp. microsatellite regions were identified, several of the amplification products were polymorphic within and across the Poa ssp. and could be utilized as markers in Poa ssp. intergeneric hybrid studies. Results of the research suggest the use of Lolium microsatellite derived primers to identify complementary SSR regions in Poa is not an effective approach for the development of microsatellite markers in Poa. [source] SSR based linkage and mapping analysis of C, a yellow cocoon gene in the silkworm, Bombyx moriINSECT SCIENCE, Issue 5 2008Yun-Po Zhao Abstract The yellow color of the cocoon of the silkworm Bombyx mori is controlled by three genes, Y (Yellow haemolymph), I (Yellow inhibitor) and C (Outer-layer yellow cocoon), which are located on linkage groups 2, 9 and 12, respectively. Taking advantage of a lack of crossing over in females, reciprocal backcrossed F1 (BC1) progeny were used for linkage analysis and mapping of the C gene using silkworm strains C108 and KY, which spin white and yellow cocoons, respectively. DNA was extracted from individual pupae and analyzed for simple sequence repeat (SSR) markers. The C gene was found to be linked to seven SSR markers. All the yellow cocoon individuals from a female heterozygous backcross (BC1 F) showed a heterozygous profile for SSR markers on linkage group 12, whereas individuals with light yellow cocoons showed the homozygous profile of the strain C108. Using a reciprocal heterozygous male backcross (BC1 M), we constructed a linkage map of 36.4 cM with the C gene located at the distal end, and the closest SSR marker at a distance of 13.9 cM. [source] Microsatellite markers application on domesticated silkworm and wild silkwormINSECT SCIENCE, Issue 6 2005LIE ZHANG Abstract Twenty-seven sets of simple sequence repeat (SSR) primers were developed through hybridizing of (CA)n, (CT)n and (GT)n and sequencing the positive clones in libraries constructed by using p50 silkworm strain. Of those primer pairs, 26 sets of SSR primers amplified well in two regional wild silkworm strains. Ten domesticated silkworm strains and two regional wild silkworm strains were used for comparing the polymorphisms and for constructing a phylogenetic tree employing the UPGAM method. The result showed that the genetic distances within Japanese strains are closer than those of Chinese strains. And this result also implies that Japanese strains diverged from domesticated silkworm later than Chinese strains. According to the clustering result, the domesticated silkworm is firstly clustered in one class, but could be classified into two groups. Within a strain, the individual polymorphism of wild silkworm was significantly higher in abundance than those of domesticated silkworm. The S SR primers of domesticated silkworm could be used in genetic studies for wild silkworm. [source] The role of genotypic diversity in determining grassland community structure under constant environmental conditionsJOURNAL OF ECOLOGY, Issue 5 2007RAJ WHITLOCK Summary 1A recent experiment varied the genetic diversity of model grassland communities under standardized soil and management conditions and at constant initial species diversity. After 5 years' growth, genetically diverse communities retained more species diversity and became more similar in species composition than genetically impoverished communities. 2Here we present the results of further investigation within this experimental system. We proposed that two mechanisms , the first invoking genetically determined and constant differences in plant phenotypes and the second invoking genotype,environment interactions , could each underpin these results. This mechanistic framework was used as a tool to interpret our findings. 3We used inter-simple sequence repeat (ISSR) DNA markers to confirm which of the individuals of six study species initially included in the model communities were unique genotypes. We then used the molecular markers to assess the survival and abundance of each genotype at the end of the 5-year experimental period. 4The DNA marker data were used to create, for the first time, a genotype abundance hierarchy describing the structure of a community at the level of genotypes. This abundance hierarchy revealed wide variation in the abundance of genotypes within species, and large overlaps in the performance of the genotypes of different species. 5Each genotype achieved a consistent level of abundance within genetically diverse communities, which differed from that attained by other genotypes of the same species. The abundance hierarchy of genotypes within species also showed consistency across communities differing in their initial level of genetic diversity, such that species abundance in genetically impoverished communities could be predicted, in part, by genotypic identity. 6Three species (including two canopy-dominants) experienced shifts in their community-level genotype abundance hierarchies that were consistent with an increased influence of genotype,environment interactions in genetically impoverished communities. 7Our results indicate that under relatively constant environmental conditions the species abundance structure of plant communities can in part be predicted from the genotypic composition of their component populations. Genotype,environment interactions also appear to shape the structure of communities under such conditions, although further experiments are needed to clarify the magnitude and mechanism of these effects. [source] A Genetic Map Constructed Using a Doubled Haploid Population Derived from Two Elite Chinese Common Wheat VarietiesJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2008Kun-Pu Zhang Abstract Genetic mapping provides a powerful tool for the analysis of quantitative trait loci (QTLs) at the genomic level. Herein, we report a new genetic linkage map developed from an F1 -derived doubled haploid (DH) population of 168 lines, which was generated from the cross between two elite Chinese common wheat (Triticum aestivum L.) varieties, Huapei 3 and Yumai 57. The map contained 305 loci, represented by 283 simple sequence repeat (SSR) and 22 expressed sequence tag (EST)-SSR markers, which covered a total length of 2141.7 cM with an average distance of 7.02 cM between adjacent markers on the map. The chromosomal locations and map positions of 22 new SSR markers were determined, and were found to distribute on 14 linkage groups. Twenty SSR loci showed different chromosomal locations from those reported in other maps. Therefore, this map offers new information on the SSR markers of wheat. This genetic map provides new opportunities to detect and map QTLs controlling agronomically important traits. The unique features of this map are discussed. [source] Genetic Diversity and Association Analysis for Salinity Tolerance, Heading Date and Plant Height of Barley Germplasm Using Simple Sequence Repeat MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2008Lilia Eleuch Abstract The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers. Four of the 22 markers (Bmac316, scssr03907, HVM67 and Bmag770) were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H, bin 13) in two different environments with common significant alleles (175, 177), whereas the HVHOTR1 marker (2H, bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398. [source] Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland CottonJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 3 2006Wang-Zhen Guo Abstract Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a(TM-1 × Hai 7124) × TM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6. (Managing editor: Li-Hui Zhao) [source] CYANIDIA (CYANIDIALES) POPULATION DIVERSITY AND DYNAMICS IN AN ACID-SULFATE-CHLORIDE SPRING IN YELLOWSTONE NATIONAL PARK,JOURNAL OF PHYCOLOGY, Issue 1 2007Corinne R. Lehr The unicellular eukaryotic algae Cyanidium, Galdieria, and Cyanidioschyzon (herein referred to as "cyanidia") are the only photoautotrophs occurring in acidic (pH<4.0) geothermal environments at temperatures above 40°C. In Yellowstone National Park (YNP), we examined an annual event we refer to as "mat decline," where cyanidial mats undergo a seasonably defined color fading. Monthly sampling of chemical, physical, and biological features revealed that spring aqueous chemistry was essentially invariant over the 1-year sampling period. However, multiple regression analysis suggested that a significant proportion of algal most probable number (MPN) count variation could be explained by water temperature and UV,visible (VIS) light exposure. Irradiance manipulations (filtering) were then coupled with 14CO2 incorporation experiments to directly demonstrate UV inhibition of photosynthesis. Population dynamics were also evident in 18S rDNA PCR clone libraries, which were different in composition at MPN maxima and minima, and again evident in PCR-amplified chloroplast genomic short sequence repeat (SSR) analysis. PCR-cloned SSRs of the YNP isolates and mats were very similar to Cyanidioschyzon merolae Luca, Taddei et Varano, although distance analysis could distinguish the YNP cyanidia from the genome sequenced C. merolae that was isolated in Italy. Unexpectedly, while phylogenetic analysis of 18S rDNA sequences and SSR sequences derived from YNP cyanidial mats and pure cultures suggested these algae are most closely related to C. merolae (99.7% identity), cell morphology was consistent with the genera Galdieria and Cyanidium. [source] Use of RAPD and ISSR Markers in Detection of Genetic Variation and Population Structure among Fusarium oxysporum f. sp. ciceris Isolates on Chickpea in TurkeyJOURNAL OF PHYTOPATHOLOGY, Issue 3 2008H. Bayraktar Abstract Genetic variation among the isolates of Fusarium oxysporum f. sp. ciceris, the causal agent of chickpea wilt worldwide, was analysed using pathogenicity tests and molecular markers , random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) polymorphism. Hundred and eight isolates were obtained from diseased chickpea plants in 13 different provinces of Turkey, out of which 74 isolates were assessed using 30 arbitrary decamer primers and 20 ISSR primers. Unweighted pair-grouped method by arithmetic average cluster analysis of RAPD, ISSR and RAPD + ISSR datasets provided a substantially similar discrimination among Turkish isolates and divided into three major groups. Group 1, 2 and 3 consisted of 41, 18 and 15 isolates, respectively. These methods revealed a considerable genetic variation among Turkish isolates, but no correlation with regard to the clustering of isolates from different geographic regions. Analysis of molecular variance confirmed that most genetic variability resulted from the differences among isolates within regions. Our results also indicated that the low-genetic differentiation (FST) and high gene flow (Nm) among populations had a significant effect on the emergence and evolutionary development of F. oxysporum f. sp. ciceris. This is the first report on genetic diversity and population structure of F. oxysporum isolates on chickpea in Turkey. [source] Host-driven divergence in the parasitic plant Orobanche minor Sm. (Orobanchaceae)MOLECULAR ECOLOGY, Issue 19 2008C. J. THOROGOOD Abstract Many parasitic angiosperms have a broad host range and are therefore considered to be host generalists. Orobanche minor is a nonphotosynthetic root parasite that attacks a range of hosts from taxonomically disparate families. In the present study, we show that O. minor sensu lato may comprise distinct, genetically divergent races isolated by the different ecologies of their hosts. Using a three-pronged approach, we tested the hypothesis that intraspecific taxa O. minor var. minor and O. minor ssp. maritima parasitizing either clover (Trifolium pratense) or sea carrot (Daucus carota ssp. gummifer), respectively, are in allopatric isolation. Morphometric analysis revealed evidence of divergence but this was insufficient to define discrete, host-specific taxa. Intersimple sequence repeat (ISSR) marker-based data provided stronger evidence of divergence, suggesting that populations were isolated from gene flow. Phylogenetic analysis, using sequence-characterized amplified region (SCAR) markers derived from ISSR loci, provided strong evidence for divergence by clearly differentiating sea carrot-specific clades and mixed-host clades. Low levels of intrapopulation SCAR marker sequence variation and floral morphology suggest that populations on different hosts are probably selfing and inbreeding. Morphologically cryptic Orobanche taxa may therefore be isolated from gene flow by host ecology. Together, these data suggest that host specificity may be an important driver of allopatric speciation in parasitic plants. [source] Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvaticaMOLECULAR ECOLOGY, Issue 5 2007ALISTAIR S. JUMP Abstract Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30,40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100,150 AFLP loci and 150,200 individuals appear sufficient for adequately estimating SGS in our analysis, 150,200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species. [source] Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree speciesMOLECULAR ECOLOGY, Issue 2 2006OLIVIER J. HARDY Abstract The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift,dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies. [source] SHORT COMMUNICATION: Do farmers reduce genetic diversity when they domesticate tropical trees?MOLECULAR ECOLOGY, Issue 2 2005A case study from Amazonia Abstract Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. [source] Development of SSR primers using ISSR,PCR in Diospyros kaki Thunb.MOLECULAR ECOLOGY RESOURCES, Issue 3 2006D. L. GUO Abstract Nine polymorphic single sequence repeat (SSR) primers were developed in Japanese persimmon using inter-SSR (ISSR) suppression polymerase chain reaction (PCR). These primers were tested on 30 individuals from Japan and China. The number of alleles per locus ranged from five to 20. Expected (HE) and observed (HO) heterozygosities at each locus ranged from 0.42 to 0.77 and 0.27 to 0.59, respectively. The SSR primers developed herein could be applied to cultivar identification, estimation of genetic diversity and divergence in Diospyros spp. [source] Fifteen polymorphic simple sequence repeat markers from expressed sequence tags of Liriodendron tulipiferaMOLECULAR ECOLOGY RESOURCES, Issue 3 2006MENG XU Abstract We developed and evaluated simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) of Liriodendron tulipifera. Characteristics of 15 EST-SSR loci were investigated using 33 L. tulipifera individuals. The number of alleles per locus ranged from two to five. The expected and observed heterozygosities ranged from 0.216 to 0.751 and from 0.182 to 0.97, respectively. These loci were further tested for their cross-species transferability to Liriodendron Chinense. Because of their high level of polymorphism and transferability, our 15 single-locus EST-SSR markers will be valuable tools for research on mating system, population genetics and systemic evolution of Liriodendron. [source] Development of simple sequence repeat (SSR) markers and their use in identification of Dendrobium varietiesMOLECULAR ECOLOGY RESOURCES, Issue 3 2006G. H. YUE Abstract The aim of this study was to develop simple sequence repeat (SSR) markers for Dendrobium varieties/species, many of which have medicinal and horticultural values. Two genomic DNA libraries of Dendrobium Sonia enriched with GA repeats and CA repeats were constructed. Fourteen polymorphic SSR markers were identified when screened against 42 popular commercial Dendrobium hybrids. The average allele number was 12.0 ± 1.9 and the observed heterozyosity was averaged at 0.70. All 42 hybrids tested, except for two tissue culture mutants, were uniquely identified with the markers used. Sibling hybrids were closely clustered. Hybrids were also closer to parents. These SSR markers can be used for molecular ecology research, genetic mapping and marker-assisted breeding. They can also help protection for new Dendrobium varieties. [source] Characterization of microsatellite markers for rough fescue species (Festuca spp.)MOLECULAR ECOLOGY RESOURCES, Issue 3 2006YONG-BI FU Abstract One major challenge in genetic diversity analysis of minor grass species is the lack of informative molecular markers. A set of 210 simple sequence repeat (SSR) markers developed from wheat and barley were evaluated for their transferability to three rough fescue species [Festuca altaica Trinius, F. campestris (Rydb.) and F. hallii (Vassey) Piper]. Twelve SSR primer pairs displayed scorable polymorphism among and within the species. The number of alleles per primer pair ranged from three to 17 with an average of 8.3 for all the species and greatly varied for each species. About 82% of SSR variation resided within the species. Festuca hallii was genetically most distinct among the three species. [source] Development of DNA microsatellite markers in tropical yam (Dioscorea sp.)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006S. TOSTAIN Abstract We developed new simple sequence repeat (SSR) markers in different species of yam (Dioscorea sp.). A microsatellite-enriched bank was created from Dioscorea alata, Dioscorea abyssinica and Dioscorea praehensilis. Sixteen polymorphic loci were characterized. Several of these markers are transferable to species of other Dioscorea sections. [source] Development and characterization of microsatellite markers for the fungus Ceratocystis fimbriataMOLECULAR ECOLOGY RESOURCES, Issue 2 2004J. Steimel Abstract Ceratocystis fimbriata is a serious fungal pathogen on a wide range of plants, but many cryptic species within C. fimbriata are apparently host-specialized. Anchor polymerase chain reaction (PCR) and simple sequence repeat (SSR) enriched libraries were used to develop 16 microsatellite markers for C. fimbriata. All markers were polymorphic when tested against isolates from four host-specialized lineages of the pathogen. These markers will be valuable for phylogenetic and population genetic studies, as well as for tracking accidental introductions of host-specialized forms of the pathogen. [source] A set of polymorphic microsatellites for Vochysia ferruginea, a promising tree for land reclamation in the NeotropicsMOLECULAR ECOLOGY RESOURCES, Issue 3 2002A. J. Lowe Abstract Vochysia ferruginea Mart. (Vochysiaceae) is a gap colonist of Neotropical forest. Because of its high tolerance of low-nutrient acidic conditions and high aluminium and iron concentrations, and its high potential seed and pollen dispersal, it is a promising timber species for commercial development as reclaimed forest on degraded land. We present here primer sequences for 10 polymorphic simple sequence repeat (SSR) loci for use with V. ferruginea to assess fine scale genetic structure and gene flow dynamics. [source] Development and characterization of SSR markers in Ribes speciesMOLECULAR ECOLOGY RESOURCES, Issue 3 2002R. Brennan Abstract Eleven microsatellite loci were identified and characterized in blackcurrant (Ribes nigrum L.) and related species. An enriched library was constructed and screened with simple sequence repeat (SSR) oligonucleotides. Positive clones were sequenced and primers were designed flanking the repeat motifs. These 11 microsatellites produce amplification products polymorphic across a range of Ribes germplasm, predominantly from the Eucoreosma section of the genus. The number of alleles varied from 2 to 18 with levels of diversity ranging from 0.18 to 0.91. [source] Development of novel polymerase chain reaction (PCR) based microsatellite markers in Armillaria gallica by cross-species amplification and species-specific cloningMOLECULAR ECOLOGY RESOURCES, Issue 2 2002J.-B. Lefrancois Abstract 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. [source] Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan)MOLECULAR ECOLOGY RESOURCES, Issue 4 2001M. J. Burns Abstract Pigeonpea (Cajanus cajan) is an important subsistence crop in India where traditional landraces and improved hybrids are grown alongside each other. Gene flow may result in genetic erosion of these landraces and their wild relatives, whilst transgene escape from future genetically engineered varieties is another potential hazard. To assess the impact of these factors gene flow needs to be measured. A set of 10 simple sequence repeat markers have been developed, which exhibit polymorphism across a range of pigeonpea varieties. Use of these markers also offers an efficient system for the assessment of genetic diversity within populations of pigeonpea. [source] Populations do not become less genetically diverse or more differentiated towards the northern limit of the geographical range in clonal Vaccinium stamineum (Ericaceae)NEW PHYTOLOGIST, Issue 2 2008Sarah B. Yakimowski Summary ,,Geographically peripheral populations are expected to exhibit lower genetic diversity and higher differentiation than central populations because of their smaller size and greater spatial isolation. In plants, a shift from sexual to clonal asexual reproduction may further reduce diversity and increase differentiation. ,,Here, these predictions were tested by assaying 36 inter-simple sequence repeat (ISSR) polymorphisms in 21 populations of the woody, clonal plant Vaccinium stamineum in eastern North America, from the range center to its northern limit where it has ,threatened' status. Populations decline in frequency, but not size or sexual reproductive output, across the range. ,,Within-population diversity did not decline towards range margins. Modest genetic differentiation among populations increased slightly towards range margins and in small populations with high clonal propagation and low seed production, although none of these trends was significant. Low seed production and high clonal propagation were not associated with large-scale clonal spread. ,,By combining demographic and genetic data, this study determined that increased population isolation, rather than reduced population size, can account for the weak increase in genetic differentiation at range margins. [source] Quantitative trait loci for glucosinolate accumulation in Brassica rapa leavesNEW PHYTOLOGIST, Issue 4 2008Ping Lou Summary ,,Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica rapa. ,,Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. ,,An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F1s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. ,,Both comparative genomic analyses based on Arabidopsis,Brassica rapa synteny and mapping of candidate orthologous genes in B. rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL. [source] Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolatesPLANT BREEDING, Issue 4 2010S. Gupta With 2 figures and 5 tables Abstract Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between ,Pompadour' and ,Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from ,Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from ,Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from ,Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines. 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