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Repeat Markers (repeat + marker)
Kinds of Repeat Markers Selected AbstractsGenetic Analysis and Mapping of the Dominant Dwarfing Gene D-53 in RiceJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 4 2006Li-Rong Wei Abstract The dwarfing gene D-53 is one of a few dominant genes for dwarfing in rice (Oryza sativa L.). In the present study, our genetic analysis confirmed that mutant characteristics including dwarfing, profuse tillering, thin stems and small panicles are all controlled by the dominant D-53 gene. We measured the length of each internode of KL908, a D-53- carrying line, and classified the dwarfism of KL908 into the dn-type. In addition, we measured elongation of the second sheath and ,-amylase activity in the endosperm, and we characterized KL908 as a dwarf mutant that was neither gibberellic acid-deficient nor gibberellic acid-insensitive. Using a large F2 population obtained by crossing KL908 with a wild-type variety, NJ6, the D-53 gene was mapped to the terminal region of the short arm of chromosome 11, with one simple sequence repeat marker, Ds3, co-segregating, and the other, K81114, located 0.6 cM away. (Managing editor: Li-Hui Zhao) [source] Genetic diversity and migration patterns of the aquatic macrophyte Potamogeton malaianus in a potamo-lacustrine systemFRESHWATER BIOLOGY, Issue 6 2009YUANYUAN CHEN Summary 1.,Previously, the Yangtze River connected thousands of shallow lakes which together formed a potamo-lacustrine system capable of sustaining a rich variety of submerged macrophytes. 2.,Potamogeton malaianus is one of the dominant submerged macrophytes in many lakes of this area. Genetic variation and population structure of P. malaianus populations from ten lakes in the potamo-lacustrine system were assessed using inter-simple sequence repeat markers. 3.,Twelve primer combinations produced a total of 166 unambiguous bands of which 117 (70.5%) were polymorphic. Potamogeton malaianus exhibited a moderate level of population genetic diversity (PP = 70.5%, HE = 0.163 and I = 0.255), as compared with that of plants in the same habitat and range. The main factors responsible for this moderate value were the plant's mixed breeding system (both sexual and asexual) and the hydrological connectivity among habitats. 4.,F statistics, calculated using different approaches, consistently revealed a moderate genetic differentiation among populations, contributing about 20% of total genetic diversity. An estimate of gene flow (using FST) suggested that gene flow played a more important role than genetic drift in the current population genetic structure of P. malaianus (Nm = 1.131). 5.,The genetic diversity of P. malaianus did not increase downstream. A high level of linkage,disequilibrium at the whole population level suggested that metapopulation processes may affect genetic structure. The migration pattern of P. malaianus was best explained by a two-dimensional stepping stone model, indicating that bird-mediated dispersal could greatly influence gene movements among lakes. [source] Population Genetic Structure of the Medicinal Plant Vitex rotundifolia in China: Implications for its Use and ConservationJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2008Yuan Hu Abstract Vitex rotundifolia L. is an important plant species used in traditional Chinese medicine. For its efficient use and conservation, genetic diversity and clonal variation of V. rotundifolia populations in China were investigated using inter-simple sequence repeat markers. Fourteen natural populations were included to estimate genetic diversity, and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure. The overall genetic diversity (GD) of V. rotundifolia populations in China was moderate (GD = 0.190), with about 40% within-population variation. Across all populations surveyed, the average within-population diversity was moderate (P = 22.6%; GD = 0.086). A relatively high genetic differentiation (Gst = 0.587) among populations was detected based on the analysis of molecular variance data. Such characteristics of V. rotundifolia are likely attributed to its sexual/asexual reproduction and limited gene flow. The genotypic diversity (D = 0.992) was greater than the average values of a clonal plant, indicating its significant reproduction through seedlings. Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m. Genetic diversity patterns of V. rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds, and by sampling individuals in a population at >20 m spatial intervals to avoid collecting individuals with identical or similar genotypes. [source] Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2009ZHIWU QUAN Abstract Eleven polymorphic microsatellite markers were isolated and identified in the aquatic plant Euryale ferox Salisb. (Nymphaeaceae). This species, which belongs to basal Magnoliophyta, reproduces sexually. All of these 11 microsatellite markers yielded 25 alleles in a survey of a wild population of 34 individuals. Two or three alleles per locus were detected, with expected heterozygosity ranging from 0.056 to 0.634 and observed heterozygosity from 0.000 to 0.088. These simple sequence repeat markers will be useful for evaluating the genetic structure of the E. ferox population in the future. [source] Transferability and characterization of nine microsatellite markers for the tropical tree species Tabebuia roseo-albaMOLECULAR ECOLOGY RESOURCES, Issue 1 2009JULIANA MASSIMINO FERES Abstract Microsatellite loci that were previously developed in the tropical tree Tabebuia aurea were used for the genetic analysis of Tabebuia roseo-alba populations. Nine of 10 simple sequence repeat markers were amplified, and the polymorphism was assessed in 58 individuals sampled from two stands in southeastern Brazil. All loci were polymorphic with Mendelian inheritance. The allele numbers were high, ranging from 5 to 13 in population I and 3 to 7 in population II, with means of 8.9 and 5.5, respectively. We conclude that these markers can be efficiently used for parentage and gene-flow studies. [source] EST-derived polymorphic microsatellites from cultivated strawberry (Fragaria×ananassa) are useful for diversity studies and varietal identification among Fragaria speciesMOLECULAR ECOLOGY RESOURCES, Issue 4 2006D. J. GIL-ARIZA Abstract Microsatellite or simple sequence repeat markers derived from expressed sequence tags (ESTs) provide genetic markers within potentially functional genes, which could be very useful for breeding programs. To date, the development of microsatellite markers in the genus Fragaria has focused mainly on Fragaria vesca. However, most of the interests of breeding programs relate to specific characteristics of cultivated strawberry. Here, we describe a set of 10 EST-derived microsatellites from Fragaria × ananassa. These markers showed high levels of polymorphism within strawberry cultivars and among different Fragaria species, indicating their potential for genetic studies not only on strawberry but also in other species within the genus. [source] Development of EST-SSRs in Cucumis sativus from sequence databaseMOLECULAR ECOLOGY RESOURCES, Issue 4 2006Q. KONG Abstract Simple sequence repeat markers derived from expressed sequence tags (EST-SSR) are potentially valuable tools for plant breeding and germplasm collection conservation, and increasingly, efforts have been made for developing this type of marker. We have identified 20 polymorphic SSR markers from cucumber ESTs deposited in public sequence database. The average allele number was 3.3 per locus, ranging from two to six alleles during screening 20 cucumber genotypes with the mean expected heterozygosity of 0.477. Amplification products were also detected by 13 pairs of primer in Cucumis melo. These informative EST-SSR markers can be used in cucumber genetic improvement projects. [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 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] Simple sequence repeat-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance to Fusarium wilt and sterility mosaic diseasePLANT BREEDING, Issue 2 2010R. K. Saxena With 1 figure and 3 tables Abstract In order to maximize polymorphism in the mapping populations for mapping loci for Fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea, a set of 32 pigeonpea lines were screened for polymorphism with 30 microsatellite or simple sequence repeat markers. A total of 23 marker loci showed polymorphism with 2,4 alleles and the polymorphism information content for these markers ranged from 0.12 to 0.65 with an average of 0.43 per marker. High number of polymorphic markers, higher genetic dissimilarity coefficient and contrasting phenotypic data taken into consideration and five parental combinations were identified and crosses initiated for developing five genetically diverse mapping populations. Of these crosses, one cross segregates for FW resistance, two for SMD resistance and the remaining two crosses segregate for resistance to both FW and SMD. Development of mapping populations is in progress for mapping loci for resistance to FW and SMD in pigeonpea. [source] Identification of quantitative trait loci for drought tolerance at seedling stage by screening a large number of introgression lines in maizePLANT BREEDING, Issue 4 2009Z. Hao Abstract The maize genome hosts tremendous phenotypic and molecular diversity. Introgression lines (ILs), developed by continuous backcrossing to recurrent parents, could provide a unique genetic stock for quantitative trait locus (QTL) mapping. Using maize lines from six heterotic groups of different ecological zones, we developed >500 BC2F2 IL sets by crossing 11 inbred lines (as recurrent parents) with >200 local maize inbred lines (as donor parents). Of them, 34 IL sets were selected as a subset for drought tolerance screening and a total of 417 ILs survived under severe water stress at seedling stage. One set of 32 surviving ILs, derived from Chang7-2/DHuang212, was used for QTL mapping with simple sequence repeat markers covering the whole genome, with seven QTL detected. Furthermore, investigating all surviving ILs, we identified two common regions in bin 3.04, corresponding to marker intervals bnlg1904,umc1772 and umc1223,bnlg1957, respectively, which shared high genetic variation in three IL sets. Our results indicated that selective genotyping can be used to identify genetic loci for complex traits. The ILs, highly selected for drought tolerance in this study, provide a unique set of materials for both genomic studies and development of enhanced germplasm resources. [source] Detection of QTLs for bread-making quality in wheat using a recombinant inbred line populationPLANT BREEDING, Issue 3 2009Y. Li Abstract Whereas gluten fraction accounts for 30,60% of the variation in wheat bread-making quality, there remains substantial variation determined by non-gluten factors. The objective of this study was to detect new loci for wheat quality. The genetics of sodium dodecyl sulphate-sedimentation volume (Ssd), grain hardness (GH), grain protein content, wet gluten content (WGC) and water absorption (Abs) in a set of 198 recombinant inbred lines derived from two commercial varieties was studied by quantitative trait loci (QTL) analysis. A genetic map based on 255 marker loci, consisting of 250 simple sequence repeat markers and five glutenin loci, Glu-A1, Glu-B1, Glu-D1, Glu-B3 and Glu-D3, was constructed. A total of 73 QTLs were detected for all traits. A major QTL for GH was detected on chromosome 1B and its relative contribution to phenotypic variation was 27.7%. A major QTL for Abs on chromosome 5D explained more than 30% of the phenotypic variation. Variations in Ssd were explained by four kinds of genes. Some QTLs for correlated traits mapped to the same regions forming QTL clusters or indicated pleiotropic effects. [source] Effects of Hordeum chilense cytoplasm on agronomic traits in common wheatPLANT BREEDING, Issue 1 2007S. G. Atienza Abstract The genome of bread wheat, AABBDD, was substituted into the cytoplasm of Hordeum chilense by repeated backcrossing to produce alloplasmic lines. The aim of this work was to investigate the effect of H. chilense cytoplasm on agronomic traits in common wheat. Three cytolines were developed. The alloplasmic nature of these lines was confirmed using chloroplast simple-sequence repeat markers. Each cytoline was compared with its respective euplasmic control for agronomic performance during 2 years of field trials. The interaction between H. chilense cytoplasm and common wheat genome greatly affected most of the traits evaluated. Among them, alloplasmic lines showed delayed anthesis date, lower yield and lower plant height. These effects are similar to those caused by Aegilops cytoplasm. The main conclusion of this work is that H. chilense cytoplasm is of limited value for wheat breeding. [source] Fusarium head blight resistance derived from Lophopyrum elongatum chromosome 7E and its augmentation with Fhb1 in wheatPLANT BREEDING, Issue 5 2006X. Shen Abstract The objective of this study was to assess the effectiveness of Fusarium head blight (FHB) resistance derived from wheatgrass Lophopyrum elongatum chromosome 7E and to determine whether this resistance can augment resistance in combination with other FHB resistance quantitative trait loci (QTL) or genes in wheat. The ,Chinese Spring',Lophopyrum elongatum disomic substitution line 7E(7B) was crossed to three wheat lines: ,Ning 7840', L3, and L4. F2 populations were evaluated for type II resistance with the single-floret inoculation method in the greenhouse. Simple sequence repeat markers associated with Fhb1 in ,Ning 7840' and L4 and markers located on chromosome 7E were genotyped in each population. Marker,trait association was analysed with one-way or two-way analysis of variance. The research showed that, in the three populations, the average number of diseased spikelets (NDS) in plants with chromosome 7E is 1.2, 3.1 and 3.2, vs. NDS of 3.3, 7.2 and 9.1 in plants without 7E, a reduction in NDS of 2.1, 4.1 and 5.9 in the respective populations. The QTL on 7E and the Fhb1 gene augment disease resistance when combined. The effect of the QTL on 7E was greater than that on 3BS in this experiment. Data also suggest that the FHB resistance gene derived from L. elongatum is located on the long arm of 7E. [source] Role of sexual reproduction in the spread of an invasive clonal plant Solidago canadensis revealed using intersimple sequence repeat markersPLANT SPECIES BIOLOGY, Issue 1 2006MEI DONG Abstract Invasive species, second only to habitat loss as a cause of biodiversity loss, pose serious threats to native biodiversity and ecosystems. Little is known about the mechanisms that some exotic plants use to become invasive in their non-native ranges. Solidago canadensis, native to North America, was intentionally introduced to many countries where it has become an invasive plant. To understand the roles that reproductive mode plays in successful invasion of exotic plants, and the relative importance of sexual reproduction and clonal growth, the genetic diversity and clonal structure of two S. canadensis populations from Shanghai, China were investigated using intersimple sequence repeats. Samples were collected in a grid pattern with intervals of 2 m among adjacent individuals within the studied area (approximately 30 m × 30 m) for each population. Results showed that the percentages of polymorphic loci for the two populations were 97.9% and 96.5% and clonal diversity measured using the Simpson Diversity Index was 1.00 for both populations. No identical genotypes were found among the analyzed samples. It is suggested from this study that sexual reproduction facilitates the establishment of new S. canadensis populations, whereas clonal expansion maintains and enlarges the established populations. Thus, limiting sexual reproduction of S. canadensis may effectively control the invasion of this species. [source] Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markersANNALS OF APPLIED BIOLOGY, Issue 2 2009A.A.J. Raji Abstract Molecular-marker-aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within-population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within-population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (He) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base. [source] Application of random amplified polymorphic DNA and inter-simple sequence repeat markers in the genus CrataegusANNALS OF APPLIED BIOLOGY, Issue 2 2009H. Dai Abstract Hawthorn (Crataegus spp.) has a long history as an ornamental and a source of medicine. We report the use of random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers to determine genetic relationships in the genus Crataegus. Twenty-eight accessions, including eight species (Crataegus pinnatifida, Crataegus bretschneideri, Crataegus maximowiczii, Crataegus kansuensis, Crataegus altaica, Crataegus songarica, Crataegus dahurica and Crataegus sanguinea) and two botanical varieties (C. pinnatifida var. major and C. maximowiczii var. ninganensis) were analysed. Twelve RAPD primers reproducibly and strongly amplified 128 fragments of which 116 were polymorphic; similarly, 13 ISSR primers generated 127 products of which 119 were polymorphic. Dendrograms based on unweighted pair group method with arithmetic average analysis were constructed from both the RAPD and the ISSR data. Similarity coefficient based on RAPD and ISSR markers ranged from 0.22 to 0.98 and 0.23 to 0.98, respectively. The range in similarity coefficient indicated that the genus has a high level of genetic diversity. The Mantel test on the similarity matrices produced by RAPD and ISSR markers gave r = 0.86, showing high correlation between RAPD and ISSR markers in their ability to detect genetic relationships between Crataegus accessions. RAPD and ISSR appear to be reliable methods for the analysis of genetic relationships among hawthorns. [source] Further evidence of genetic heterogeneity segregating with hereditary gingival fibromatosisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 8 2009Xiaoqian Ye Abstract Aim: To clinically characterize and map the disease-associated locus in a five-generation Chinese family with autosomal dominant early-onset hereditary gingival fibromatosis (HGF). Material and Methods: A complete oral examination was conducted. Genomic DNA samples were obtained from 14 individuals. Short tandem repeats markers, which encompass four previously known loci related to HGF, were genotyped. Two-point log of the odds (LOD) scores were calculated using MLINK program of the LINKAGE software, multipoint and non-parametric linkage (NPL) analysis were performed using the GENEHUNTER software. Results: Clinical evaluation and histological examination of this family suggested typical features of HGF. The onset age was early in the generations, ranging between 1 and 2 years. None of the tested markers showed cosegregation among affected individuals. Genotyping data from four putative regions yielded significant negative two-point LOD scores (<,2.0) at ,=0. The maximum multipoint LOD scores and NPL analysis revealed exclusion of these loci as well. Conclusions: Exclusion of linkage in this family to any of the known HGF loci proved the existence of a novel locus for autosomal dominant HGF and showed that this rare disorder is far more heterogeneous than previously expected. [source] | ||||||||||