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45 results for “SSR markers”
Data from: Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers
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Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
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Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea
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Data from: SSR Markers for Filago subgen. Filago (Gnaphalieae: Asteraceae) and cross-amplification in three other subgenera
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SSR results of 13 markers of 609 Pyricularia oryzae isolates in Vietnam
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SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
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Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers
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Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes
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Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstruction: A comparison in sea buckthorn
<p>Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non-model species. We identified SSRs from expressed sequence tags (EST-SSRs) and whole genome sequences (gSSRs), by analyzing the transcriptome and genome of the Mongolian sea buckthorn (<i>Hippophae rhamnoides</i> subsp. <i>Mongolica</i>) cultivar 'Sunny'<i>.</i> Using the same number of loci, EST-SSRs showed higher transferability to <i>Hippophae </i>than gSSRs, and phylogenetic trees based on EST-SSRs demonstrated higher resolution for classifying <i>Hippophae </i>species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST-SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST-SSRs and gSSRs would provide insight into the trade-off between differentiation and polymorphism in marker selection for breeding programs.</p>
Data from: De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing.
Recent developments in sequencing technologies and bioinformatics analyses provide an unprecedented opportunity for cost and time effective high quality microsatellite marker discovery in non-model organisms for which no genomic information is available. Here, we use shotgun pyrosequencing of a microsatellite-enriched library to develop, for the first time, microsatellite markers for Alnus glutinosa, a keystone tree species of European riparian woodland communities. From a total of 17,855 short sequences, we identified 590 perfect microsatellites from which 392 had designed primers. A subset of 48 loci were tested for amplification, twelve of which were polymorphic in A. glutinosa. These twelve loci were successfully co-amplified in a single multiplex PCR experiment and validated for population genetics applications. In addition, ten and eight of these microsatellites were found to be transferable to the related A. incana and A. cordata species. The developed multiplex of 12 microsatellite markers therefore provides new opportunities for experimental evolutionary and forest genetics research in Alnus.
Data from: Worldwide core collections of tea (Camellia sinensis) based on SSR markers
Tea (Camellia sinensis (L.) O. Kuntze) is the world's most popular beverage crop. However, to date, no core collection has been selected from worldwide germplasm resources on the basis of genotype data. In this study, we analyzed 788 tea germplasm accessions using 23 simple sequence repeat (SSR) markers. Our population structure analysis divided the germplasms into a Japanese group and an exotic group. The latter could be divided into var. sinensis and var. assamica. The genetic diversity was higher in germplasms from China, Taiwan, India, and Sri Lanka than in those from other countries, and low in germplasms from Japan. Using the number of SSR alleles as a measure of genetic diversity, we developed a core collection consisting of 192 accessions and three subcore collections with 96, 48, and 24 accessions. Although the results might be affected by marker-selection bias, the core 192 collection adequately covered the range of variation of the 788 accessions in floral morphology, and the chemical composition of first-flush leaves. These collections will be powerful tools for breeding and genetic research in tea.
Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes
Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.
Fig. 4 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 4. HPTLC profile of (a) MeOH extract of L. speciosa (LS1197) of population 7 (b) CRA standard.
Fig. 1 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 1. Chemical structure of corosolic acid (CRA).
Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
<p>Ethiopia is a center of diversity for barley (<i>Hordeum vulgare </i>L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic as well as overall environmental changes on the stability and persistence of populations. Here, we examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades (1976-2017), using simple sequence repeat (SSR) markers. Our objective was to evaluate spatial and temporal changes in barley population connectivity associated with the closure of geographic origin and time periods. Low to strong genetic diversity was observed among the landraces and STRUCTURE, Neighbour joining tree and Discriminant Analysis of Principal Component analysis revealed three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. The grouping of landraces based on altitudinal classes was influenced by geographic proximity. From AMOVA year categories, it was observed that within population genetic diversity much higher than between population genetic diversity and that the temporal differentiation is considerably smaller. The low to strong genetic differentiation between landraces from various geographic origins could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Nevertheless, we found some connectivity between changes in population dynamics as well as contemporary gene flow. The results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of barley germplasms. Furthermore, our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that <i>in-situ</i> conservation strategies based on farmers use can conserve the genetic identity of landraces while allowing adaptation to local-environments.</p>
Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
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Data from: Worldwide core collections of tea (Camellia sinensis) based on SSR markers
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Data from: SSR-marker analysis of the intracultivar phenotypic variation discovered within 3 soybean cultivars
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Genomic SSR and EST-SSR markers for phylogenetic and pedigree reconstruction: A comparison in sea buckthorn
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Data from: The population genetic diversity and pattern of Pteroceltis tatarinowii, a relic tree endemic to China, inferred from SSR markers
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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