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85 results for “SSR”
SSR genotypes of oak parents and progeny in Pentalofos Forest Greece
<p>Two files (datasets) with multi-locus genotypes at 17 nuclear microsatellites; one containing the genotypes of all 59 adult trees within a mixed oak forest stand in the Pentalofod Forest in Evros County in Greece and the other the genotypes of 110 juvenile trees in the same stand. A comparison can be performed for parentage assignement and studies of hybridization. Oak species: <em>Quercus frainetto, Q. petraea, Q pubescens.</em></p>
Developing a new genic SSR primer database for Vicia faba molecular breeding
<p>Accelerating breeding programs require the use of efficient molecular tools and enhance the diversity of local faba bean cultivars. The aim of this study is to develop a new genetic database of available SSR primers, to classify these PCR primers according to the target genes and their respective cell processes, to assess the diversity and efficacy of the microsatellite markers applied to faba bean and to study the genetic structure of some selected faba bean cultivars. Approximately 75,605 and 148,196 previously published genomic and transcriptomic sequences were used to detect possible simple sequence repetitions in faba genomic content. The number of identified SSRs was 25502 and 12319, where the distribution to different repeat type classes shows that, the trinucleotide was the highest number of repeat counts followed by dinucleotide repeats. These genic SSR sequences were used to design 1091 PCR primers, out of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers target transcriptomic sequences. The annotation of gene-targeted SSRs has shown that approximately 897 genes are targeted through our designed SSR primers. About 1890 gene ontology (GO) identification code has been obtained. The GOs keywords distributed between distinct cell molecular features, where the highest amount of redundant sentences is the technical word, domain and molecular feature phrases with 554, 196 and 160 GOs, respectively. These GOs belong to the general level of gene ontology, such as molecular function, cellular component and biological process with 544, 670 and 676 GOs, respectively. Twenty-seven SSR PCR primers were synthesized to genotype 12 Egyptian faba bean genotypes. About 11 SSR gave from 1 to 2 PCR bands, other gave only one sharp band with polymorphic band size. The number of polymorphic primers was 13 primers. The polymorphic mean polymorphism information content was 0.3 which implies moderate informativeness.</p>
Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Dataset: SSR Mining Inc. (SSRM) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
SSR data of Betula humilis
<p>The file contains microsatellite data of the shrub birch <em>Betula humilis</em>, used in the paper: Bona, A., Kulesza, U., Jadwiszczak, K. A. (2019). Clonal diversity, gene flow and seed production in endangered populations of <em>Betula humilis</em> Schrk. <em>Tree Genetics & Genomes</em>, <em>15</em>(4), 1-12. DOI: 10.1007/s11295-019-1357-2</p>
Data from: Altitude difference might contribute to the genetic divergence of giant panda' staple food Bamboo (Fargesia spathacea complex) based on 14 SSR markers
<p>The taxonomy in woody bamboo faces a lot of difficulties due to its long blooming intervals and complicated morphological variation. Whether the current taxonomy would reflect the genuine species divergence within woody bamboo is an intriguing question. <i>Fargesia spathacea</i> complex comprises fifteen closely related species with sympatric distribution in China. Their classification has long been controversy because of only a handful of vegetative traits available, thus providing a good opportunity to explore the evolutionary relationship and genetic differentiation in woody bamboo. Here we presented a study with 750 individuals from 39 representative populations in <i>Fargesia spathacea</i> complex using 14 SSR markers. We found varying degrees of genetic diversity across populations of the <i>Fargesia spathacea</i> complex (<i>He</i>=0.07-0.81) and largely negative <i>F</i> values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (cluster A and B), with the majority of fifteen species representing distinct genetic lineages. Based on the population genetic analysis along with morphological evidence, we confirmed the identity of three species (<i>F. decurvata</i>, <i>F. spathacea</i> and <i>F. murielae</i>) and suggested invalidation of four other species (<i>scabrida</i>, <i>F. robusta</i>, <i>F. denudata</i> and <i>F. nitida</i>). The delimitation of the rest eight species was yet to be explored. The ecological factor and spatial autocorrelation analysis supported that altitude difference might account for the distinct genetic divergence between two major groups.</p>
Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
<p>Pea (<em>Pisum</em> <em>sativum</em> L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (<em>Pisum</em> sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of <em>Pisum</em>, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of <em>Pisum</em> utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of <em>Pisum fulvum</em>, <em>Pisum</em> <em>abyssinicum</em> and some wild <em>P. sativum</em> accessions, whereas groups II and III consisted of the two genetic groups under <em>P. sativum </em>representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of <em>Pisum</em>, <em>P. fulvum</em> and <em>P. abyssinicum</em> possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of <em>P. sativum</em> described by some authors were not supported in this study, with the exception of several genotypes of <em>P. sativum</em> subsp. <em>elatius</em> that were clustered with <em>P. fulvum</em> and <em>P. abyssinicum</em>. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.</p>
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
<p>Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread <i>Elymus</i> species. <i>Elymus excelsus</i> Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of <i>E. excelsus</i> germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of <i>E. excelsus</i> from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of <i>E. excelsus</i> germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (<i>F</i><sub><i>st</i></sub> = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (<i>H</i><sub><i>e</i></sub> = 0.197) was greater than that of the GSC (<i>H</i><sub><i>e</i></sub> = 0.176) and XJC (<i>H</i><sub><i>e</i></sub> = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that <i>E. excelsus</i> accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable <i>E. excelsus</i> germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.</p>
GMATA derived ssr files containing Microsatellite data for 128 Phytophthora strains
<p>These 128 files are GMATA software-derived .ssr files, containing Microsatellite data for each Phytophthora strain.</p>
EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights
<p><em>Callicarpa subpubescens</em>, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.</p>
Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)
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EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights
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Data from: Enhanced correlations of EST-SSR based genetic distance with hybrid performance, specific hybridizing ability and heterosis using effect-increasing and effect-decreasing alleles: a case study in Eucalyptus L'Hér
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Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
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Data from: Altitude difference might contribute to the genetic divergence of giant panda' staple food Bamboo (Fargesia spathacea complex) based on 14 SSR markers
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Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers
In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.
Data from: SSR Markers for Filago subgen. Filago (Gnaphalieae: Asteraceae) and cross-amplification in three other subgenera
• Premise of the study: Microsatellite primers were developed for the first time in the genus Filago (Gnaphalieae: Asteraceae). These markers will facilitate low-scale phylogenetic, phylogeographic and population genetics studies within the genus Filago. • Methods and Results: Nine pairs of microsatellite primers were identified and optimized on two species of Filago using a microsatellite-enrichment library method and 454 GS-FLX technique. The set of primers amplified tri- to hexanucleotide repeats, and showed one to six alleles per locus for both species: F. gaditana and F. carpetana. Transferability was performed in 29 samples corresponding to nine representative species of Filago. • Conclusions: The results indicate the utility of the newly developed markers, which will be useful to go deeper into the phylogenetic relationships among the taxa within Filago. These microsatellites will enable phylogeographic, reproductive and genetic variation studies.
Data from: Analysis of microsatellite loci in tree of heaven (Ailanthus altissima (Mill.) Swingle) using SSR-GBS
Microsatellite markers are still the marker of choice for many research questions in the field of forest genetics. However, the number of available markers is often low for species that have not been studied intensively like the tree of heaven (Ailanthus altissima). During the last decade, next generation sequencing (NGS) has offered advanced techniques for efficiently identifying microsatellite markers and accurately genotyping samples. Here, we identify new microsatellite markers for the tree of heaven by applying an NGS-based method using the Illumina MiSeq platform. NGS technology was proved to be an effective method for fast and cost-efficient identification of microsatellite markers by implementing a genotyping-by-sequencing approach based on Illumina amplicon sequencing (SSR-GBS). We screened three populations from Eastern Austria for genetic variation at 19 newly identified microsatellite loci. We tested two different genotyping approaches: (1) considering only allele lengths (forming a so-called 'allele length dataset'), (2) taking also single nucleotide polymorphisms (SNPs) within the amplified fragments into account (forming a so-called 'SNP dataset'). The results revealed higher values for all genetic diversity parameters, as well as a better resolution of genetic assignment, when the latter approach was followed. Thus, by taking advantage of sequence information which is provided by SSR-GBS, one may achieve considerable gains in performance using the same marker set. The developed markers provide a cost-efficient tool for genotyping populations of tree of heaven and the approach presented here promises to be of high value for medium throughput genotyping applications in non-model forest tree species. We will use this method to widen the perspectives for further population genetic investigations of the tree of heaven.
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
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.