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606 results for “association genetics”
FIGURE 1 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data
FIGURE 1 Bayesian inference tree of marine associated Ameronothroidea and terrestrial outgroups based on 18S sequences. Posterior probabilities>0.9 are shown near nodes; abbreviations: PRT – Portugal, DE – Germany, DR – Dominican Republic, JP – Japan, TW – Taiwan, MY – Malaysia; families are given in different colours. Photographs of selected species are given to provide an insight into the basic habitus of each larger group.
FIGURE 2 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data
FIGURE 2 Bayesian topology based on the combined data set of coi, D3 and 18S sequences. Posterior probabilities>0.9 are shown near nodes; abbreviations: PRT – Portugal, DE – Germany, DR – Dominican Republic, TW – Taiwan.
Taking advantage from phenotype variability in a local animal genetic resource: identification of genomic regions associated with the hairless phenotype in Casertana pigs
<p>Ped and Map files for 96 Casertana breed pigs genotyped with Illumina BeadChip 60K Porcine.<br> The first field of the ped file contains the id of the farm (1az-6az).<br> The hairless phenotype, in the ped phenotype field, is codified as 1, the hairy phenotype is codified as 2.</p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (16S rRNA gene sequencing data)
<p>Microbiome data accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for alpha- and beta- diversity, as well as for individual taxa both in binary and quantitative phenotypic representation. Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (Metadata)
<p>Associated demographic, lifestyle, environmental and biochemical metadata accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals". Data is available for 827 individuals that gave consent for their data to be shared outside of the Milieu intérieur consortium. </p>
Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"
<p>Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"</p> <p>Multiple sclerosis (MS) is the most common neurological disorder in young adults. Despite extensive studies, only a fraction of MS heritability has been explained, with association studies focusing primarily on protein-coding genes, essentially for the difficulty of interpreting non-coding features. However, non-coding RNAs (ncRNAs) and functional elements, such as super-enhancers (SE), are crucial regulators of many pathways and cellular mechanisms, and they have been implicated in a growing number of diseases. In this work, we searched for possible enrichments in non-coding elements at MS genome-wide associated loci, with the aim to highlight their possible involvement in the susceptibility to the disease. We first reconstructed the linkage disequilibrium (LD) structure of the Italian population using data of 727,478 single-nucleotide polymorphisms (SNPs) from 1,668 healthy individuals. The genomic coordinates of the obtained LD blocks were intersected with those of the top hits identified in previously published MS genome-wide association studies (GWAS). By a bootstrapping approach, we hence demonstrated a striking enrichment of non-coding elements, especially of circular RNAs (circRNAs) mapping in the 73 LD blocks harboring MS-associated SNPs. In particular, we found a total of 482 circRNAs (annotated in publicly available databases) vs. a mean of 194 ± 65 in the random sets of LD blocks, using 1,000 iterations. As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the <em>STAT3</em> gene, can be modulated by the three genotypes at the disease-associated SNP. Finally, by evaluating RNA-seq data of two cell lines, SH-SY5Y and Jurkat cells, representing tissues relevant for MS, we identified 18 (two novel) circRNAs derived from MS-associated genes. In conclusion, this work showed for the first time that MS-GWAS top hits map in LD blocks enriched in circRNAs, suggesting circRNAs as possible novel contributors to the disease pathogenesis.</p> <p>GEO database</p> <p>URL: <a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a></p> <p>Numero di accesso del dataset: GSE110525</p>
Fig. 2 in Quantitative genetics of gastrointestinal strongyle burden and associated body condition in feral horses
Fig. 2. Predicted relationship between an individual's annual location and a) faecal egg count (measured as the natural logarithm of eggs per gram (EPG) + 25) and b) body condition. Location is scaled to a mean of 0 and standard deviation of 1, therefore 0 represents the centre of the island with −2 at the far west and 2 at the far east. The fitted line comes from the full univariate animal model in each case. In both cases, overlap between points is represented by darker point colour. In 2b. points have been jittered along the y axis to ease visualisation.
Data from: Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass
<ul> <li>Global change forecasts in ecosystems require knowledge of within species diversity, particularly of dominant species within communities. We assessed site-level diversity and capacity for adaptation of the dominant species of the shortgrass steppe biome of the Central US, Bouteloua gracilis.</li> <li>We quantified genetic diversity from 17 sites across regional scales, north-south from New Mexico to South Dakota, and local scales in Northern Colorado. We also quantified phenotype and plasticity within and among sites and determined the extent to which phenotypic diversity in B. gracilis was related to climate.</li> <li>Genome sequencing indicated pronounced population structure at the regional scale, and local differences indicated gene flow and/or dispersal may also be limited. Within a common environment, we found evidence for genetic divergence in biomass-related phenotypes, plasticity, and phenotypic variance, indicating functional divergence and different adaptive potential. Phenotypes differentiated according to climate, chiefly median Palmer Hydrological Drought Index and other aridity metrics.</li> <li>Our results indicate conclusive differences in genetic variation, phenotype, and plasticity in this species and suggest a mechanism explaining variation in shortgrass steppe community responses to global change. This analysis of B. gracilis intraspecific diversity across spatial scales will improve conservation and management of the shortgrass steppe ecosystem moving forward.</li> </ul>
Association of genetic variation at the GJA5 locus with motor progression in Parkinson's
<p>These are the GWAS summary statistics generated from the study described in the title</p>
GPAM: Genetic Programming with Associative Memory - datasets for symbolic regression
<p>This collection contains five data sets for symbolic regression generated using functions known as Koza-1, Nguyen-7, Nguyen-10, Korns-1, and Korns-4. In each function, we replaced some data points with randomly generated values from interval [−10, 10].</p>
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
Data for: Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster
<p>Fertility is a major component of fitness but its genetic architecture remains poorly understood. Using a full diallel cross of 50 <em>Drosophila</em> <em>melanogaster</em> Genetic Reference Panel inbred lines with whole genome sequences, we found substantial genetic variation in fertility largely attributable to females. We mapped genes associated with variation in female fertility by genome-wide association analysis of common variants in the fly genome. Validation of candidate genes by RNAi knockdown confirmed the role of the dopamine 2-like receptor (<em>Dop2R</em>) in promoting egg laying. We replicated the <em>Dop2R</em> effect in an independently collected productivity dataset and showed that the effect of the <em>Dop2R</em> variant was mediated in part by regulatory gene expression variation. This study demonstrates the strong potential of genome-wide association analysis in this diverse panel of inbred strains and subsequent functional analyses for understanding the genetic architecture of fitness traits.</p>
Host-associated genetic differentiation and origin of a recent host shift in the generalist parasitic weed Phelipanche ramosa
<p>The branched broomrape, <em>Phelipanche ramosa</em> (L.) Pomel, is a parasitic weed that can infest several crops, notably tobacco, hemp and tomato. In western France, it has recently adapted to a new host, oilseed rape. We collected <em>P. ramosa</em> samples from fields cultivated with six different crops across Europe. Data from SSR markers and DNA sequences showed strong host-associated genetic differentiation.</p> <p>File SSRdata-Pramosa1611.txt contains sampling locations, host crops and microsatellite genotypes.</p> <p>Files BO1aligned.fas, ITSaligned.fas, RPL16aligned.fas and trnKtrnQaligned.fas contain aligned DNA sequences.</p>
Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms
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Data for: Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster
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Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
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Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load
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Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass
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Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers
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Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens
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Allen Brain Atlas
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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.