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2,785 results for “Genotype”
mass spectrometry metabolomic analysis of Drosophila head extracts: 3 genotypes (control, RNAi Opa1 in muscle, RNAi Marf in muscle), 2 ages (30 days, 65 days)
<p>RNAi of the Drosophila mitochondrial fusion genes Opa1 and Marf (Mitofusin 2) in the muscle results in an extended lifespan. In order to detect metabolic changes in lipid in the neural tissue, we analysed the metabolome of fly heads by mass spectroscopy, comparing the two knock-down genotypes to a wild type control at two ages: 30 days (young flies) and 65 days (old flies).</p>
NMR metabolomic analysis of Drosophila extracts: 3 genotypes (control, RNAi Opa1 in muscle, RNAi Marf in muscle), 3 body regions (head, thorax, abdomen), 2 ages (30 days, 65 days)
<p>RNAi of the Drosophila mitochondrial fusion genes Opa1 and Marf (Mitofusin 2) in the muscle results in an extended lifespan. In order to unravel the metabolic changes in the long-living flies we analysed the metabolome by NMR spectroscopy, comparing the two knock-down genotypes to a wild type control at two ages: 30 days (young flies) and 65 days (old flies). In order to detect autonomous and non-autonomous changes, we also divided the samples in three anatomical regions: head (mostly neural tissue) thorax (mostly muscle), and abdomen (visceral, reproductive, metabolic control)</p>
Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima
Understanding the effects of the demographic dynamics and environmental heterogeneity on the genomic variation of forest species is important not only for uncovering the evolutionary history of the species but also for predicting their ability to adapt to climate change. In this study, we combined a common garden experiment with range-wide population genomics analyses to infer the demographic history and characterize patterns of local adaptation in a subtropical oak species, Quercus acutissima. We scanned about 8% of the oak genome using a balanced representation of both genic and non-genic regions and identified a total of 55,361 SNPs in 167 trees. Genomic diversity analyses revealed an east-west split in the species distribution range. Coalescent-based model simulations inferred a late Pleistocene divergence in Q. acutissima between the east and west groups as well as subsequent pre-glaciation population expansion events. Consistent with observed genetic differentiation, morphological traits also showed east-west differentiation and the biomass allocation in seedlings was significantly associated with precipitation. Environment was found to have a significant and stronger impact on the non-neutral than the neutral SNPs, and also significantly associated with the phenotypic differentiation, suggesting that apart from the geography, environment had played a role in determining non-neutral and phenotypic variation. Our approach, which combined a common garden experiment with landscape genomics data, validated the hypothesis of local adaptation of this long-lived oak tree of subtropical China. Our study joins the small number of studies that have combined genotypic and phenotypic data to detect patterns of local adaptation.
Alfalfa genotyping-by-sequencing (GBS) data
<p>Alfalfa (<i>Medicago</i> <i>sativa</i> L.) quantitative trait loci (QTL) mapping population (184 F<sub>1</sub>) derived from cultivars 3010 (cold-tolerant) as female parent and CW 100 (cold-sensitive) as male parent were genotyped using genotyping-by-sequencing (GBS). Polymorphic SNPs unique to either 3010 (AB x AA) or CW 1010 (AA x AB) were identified as single dose allele (SDA) markers and used to generate the genetic linkage maps. Two sets of linkage maps, a set for each parent, were used to map the traits and the QTL were identified. With the genotyping and phenotyping informations we were able to map various alfalfa traits such as fall dormancy, winter-hardiness, freezing tolerance, flowering time, yield and leaf-rust resistance. The raw sequence data were deposited at NCBI SRA with the accession number SRP150116. This study identified several genomic regions and associated markers that can be further utilized in marker-assisted breeding to improve the alfalfa. </p>
Genotype data not consistent with clonal transmission of sea turtle fibropapillomatosis or goldfish schwannoma
<p>Recent<b> </b>discoveries of transmissible cancers in multiple bivalve species suggest that direct transmission of cancer cells within species may be more common than previously thought, particularly in aquatic environments. Fibropapillomatosis occurs with high prevalence in green sea turtles (Chelonia mydas) and the geographic range of disease has increased since fibropapillomatosis was first reported in this species. Widespread incidence of schwannomas, benign tumours of Schwann cell origin, reported in aquarium-bred goldfish (Carassius auratus), suggest an infectious aetiology. We investigated the hypothesis that cancers in these species arise by clonal transmission of cancer cells. Through analysis of polymorphic microsatellite alleles, we demonstrate concordance of host and tumour genotypes in diseased animals. These results imply that the tumours examined arose from independent oncogenic transformation of host tissue and were not clonally transmitted. Further, failure to experimentally transmit goldfish schwannoma via water exposure or inoculation suggest that this disease is unlikely to have an infectious aetiology.</p>
Fig. 1 in Among-Genotype Variation For Sediment Rejection In The Reef-Building Coral Diploastrea Heliopora (Lamarck, 1816)
Fig. 1. Location of sampling site.
Genetics of mercury accumulation in Stickleback, genotypes and metal accumulation phenotypes
<p>Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome wide association study (GWAS) between 28,450 SNPs and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs (Single Nucleotide Polymorphism) suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kbp distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback.</p>
Normalized NMR integration values from the metabolomic analysis of Drosophila larvae extracts from 2 genotypes at 3 time points.
<p>We measured the metabolites related to energy production using 1H nuclear magnetic resonance spectroscopy (NMR). No alterations in the levels of carbohydrate stores or free amino acids were found between control and Sema1ai animals, corroborating the notion that the main metabolic changes are in the lipid metabolism. The exception is the glycolytic amino acid alanine (elevated in Sema1ai animals), confirming alterations in glycolysis. The levels of the ß-alanine amino acid are markedly reduced in 256 h AEL or 10.5-day-old Sema1ai animals, probably indicating muscle degeneration in the severely obese larvae that is consistent with the deteriorated state and reduced movement of the 10-day-old (256 hours) mutant larvae. Gluconeogenesis is stimulated by high lactate, and the concentration of lactate is higher in Sema1ai larvae than controls, though the difference is not statistically significant. Glycolysis is stimulated by glucose and inhibited by citrate, an early intermediate of the citric acid cycle. The increased citrate levels in the 10.5-day-old Sema1ai larvae suggest that glycolysis is lower at this age, consistent with the increased level of glucose in the severely obese larvae. The fact that both gluconeogenesis and glycolysis pathways are simultaneously enhanced in Sema1ai larvae support the hypothesis that the animals defecting in adiposity signaling are in a state of perceived energy insufficiency despite having sufficient energy stored.</p>
Fraxinus excelsior genotype data for "Genetic resources of common ash (Fraxinus excelsior L.) in Poland"
<p>The data set contains microsatellite genotypes (3 chloroplast + 10 nuclear loci) of Fraxinus excelsior trees, together with the information about sampling sites.<br> </p>
Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles
<p>We aimed to simplify our fetal <i>RHD</i> genotyping protocol by changing the method to attach Illumina's sequencing adaptors to PCR products from the ligation-based method to a PCR-based method, and to improve its quantitative accuracy by introducing unique molecular indexes, which allow us to count the numbers of DNA fragments used as PCR templates and to minimize the effects of PCR and sequencing errors. Both of the newly established protocols reduced time and cost compared with our conventional protocol. Removal of PCR duplicates using UMIs reduced the frequencies of erroneously mapped sequences reads likely generated by PCR and sequencing errors. The modified protocols will help us facilitate implementing fetal <i>RHD</i> genotyping for East Asian populations into clinical practice.</p>
SNP genotype matrix for GWAS and Machine Learning analyses
<p><strong>SNP datasets used for GWAS and Machine Learning analyses</strong></p> <p>All datasets come from the easyGWAS website: <a href="https://easygwas.ethz.ch/down/1/">https://easygwas.ethz.ch/down/1/</a></p> <p> </p> <p><strong>=== Horton et al. 2012 ===</strong></p> <p><strong>1307 Arabidopsis genotypes x 214,057</strong> <strong>SNPs</strong></p> <p><strong>1) In the form of a genotype matrix </strong></p> <p>The file is called <a href="https://zenodo.org/api/files/d862e79f-02f2-4176-9b8e-04e48a2cf72c/horton2012.raw?versionId=2b05fb8d-b486-4f00-b7bf-bb024b892dc9">Horton2012.raw</a></p> <p><a href="https://www.nature.com/articles/ng.1042">https://www.nature.com/articles/ng.1042</a></p> <p>Preview of the first lines and columns:</p> <p>FID Chr1_657_T Chr1_3102_G Chr1_4648_A Chr1_4880_T Chr1_5975_G Chr1_6063_T Chr1_6449_C<br> 9381 2 2 2 0 0 0 0<br> 9380 0 0 0 0 0 0 2<br> 9378 2 2 2 0 0 0 0<br> 9371 2 2 2 0 0 0 0<br> 9367 0 0 0 2 0 0 0<br> 9363 2 2 2 0 0 0 0<br> 9356 0 2 2 0 0 0 0<br> 9355 2 2 2 0 0 0 0<br> 9354 2 2 2 0 0 0 0</p> <p>...etc...</p> <p>PLINK 1.9 was used to convert the .ped and .map file to a .raw format with: </p> <pre><code class="language-bash">plink --file original_data/genotype --recodeA --tab</code></pre> <p>Genotypes are encoded as 0, 1 or 2 with:</p> <pre> SNP SNP_A --- ----- A A -> 0 A C -> 1 C C -> 2 0 0 -> NA </pre> <p>Then only the Family ID was kept (same as individual ID) and other columns (Paternal ID, Maternal ID, Sex, Phenotype) were removed.</p> <p>The corresponding PLINK manual page used is here: <a href="https://zzz.bwh.harvard.edu/plink/dataman.shtml#recode">https://zzz.bwh.harvard.edu/plink/dataman.shtml#recode</a></p> <p><strong>1) In the form of set of files compatible with PLINK out of the box</strong></p> <p>The archive file is called <a href="https://zenodo.org/api/files/b34fd40e-2db1-47b0-92c8-0ad51ad92d46/AtPolyDB_call_method_75_Horton2012.tar.gz">AtPolyDB_call_method_75_Horton2012.tar.gz</a> and contains three files:</p> <ul> <li>genotype.ped: pedigree information from the 1307 ecotypes</li> <li>genotype.map: the SNP positions on the genome</li> <li>phenotypes.pheno: the phenotype value of the 1307 ecotypes</li> </ul> <p> </p>
The SV information of A02 and the genotype information based on super-pangenome
<p>A02.SV.vcf is the SV information between the A02 genome and Nipponbare genome.</p> <p>238rice.all.bamSV.vcf is the raw data of the SV genotyping information based on the super pan-genome.</p> <p> </p>
STR genotypes of 195 black grouse individuals
<p>The data file contains the individual genotypes of 195 black grouse (Lyrurus tetrix) individuals, genotyped at 9 STR (microsatellite) loci.</p> <p>The data is curated into 10 subpopulations as decribed in the accompanied publication.</p> <p>The data is uploaded in the commonly used genepop file format.</p>
Dataset associated with the manuscript: Soil management legacy interacts with wheat genotype to determine access to organic N in a dryland system
<p>Organic nutrient management through the application of compost and/or cover crops provides mineralizable sources of nutrients for plants while often building soil organic matter (SOM) and various aspects of soil health. Variability in nutrient acquisition strategies between crop genotypes may confer advantages under different soil health contexts and could be important for crop selection and breeding, but crop response under field conditions remains unexplored. We investigated the ability of different genotypes of winter wheat (<em>Triticum aestivum</em> L.) to access nitrogen (N) from newly added cover crop residues in two soils with contrasting levels of SOM and biological activity. We planted three previously characterized wheat genotypes in a long-term dryland compost amendment field trial: 1) Byrd (modern, deep roots, low exudation), 2) Cheyenne (historic, drought susceptible, intermediate exudation), and 3) Snowmass (modern, drought-susceptible, high exudation). <sup>15</sup>N-labelled cover crop residue was added to each plot and traced into wheat tissue. In the low SOM soil, the high exudate genotype Snowmass and historic genotype Cheyenne took up the most residue-derived N (6.4-8.1 kg N ha<sup>-1</sup>) compared to the low-exudate genotype Byrd (4.4 kg N ha<sup>-1</sup>), suggesting a strong exudate effect in the more carbon-limited soil. However, the low-exudate, deep rooted genotype, Byrd, took up the most residue N in the high SOM soils (4.6 kg N ha<sup>-1 </sup>vs. 2.8 and 3.3 hg N ha<sup>-1</sup> for Cheyenne and Snowmass, respectively), which indicated higher native N cycling activities and great importance of drought resistance. Enzyme activity, inorganic N, and microbial communities were not influenced by genotype, though did show strong effects of compost application legacy. Our results show that belowground allocation strategies that favor microbial stimulation may be less successful under water limitation, especially when high SOM can support mineralization of residue N without added investment in root inputs. Increased soil health through SOM-building management likely enhances nutrient cycling, and may better support root strategies that invest less in microbial stimulation in favor of other limiting resources.</p>
Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation
<div class="abstract">A long-standing goal in the field of polyploid biology has been the derivation of mathematical models of gamete mode formation. These models form the basis of statistical inference and evolutionary theory. Here, we present 3-locus models of gamete mode formation in autotetraploids without and with preferential cross-over formation. The three loci are assumed to occur on one arm of the same chromosome. For preferential cross-over formation, one of the three loci affects the tendency for sets of sister chromatids to pair and therefore affects rates of recombination. The models are derived such that the process of double reduction is a function of rates of synaptic partner switches and recombination, as opposed to being independent of these processes. We assume potentially one synaptic partner switch per meiosis. We also assume the coefficient of coincidence is one, such that cross-over events are independent, given a set of cross-over rates. Illustrative cases are examined demonstrating differences in the gamete mode probabilities without and with preferential cross-over formation. Lastly, we explore the accuracy of maximum likelihood estimates of the probability of synaptic partner switches and preferential cross-over formation when the locus controlling preferences is at a proximal, middle or distal location on the chromosome arm. All Supplementary Information is available at https://github.com/ckgriswold/3-locus-autotetraploid-meiosis.</div>
237 rice cultivar genotype dataset with 91,800 SNPs
<p>This repository contains a genotype dataset for Shimono et al. 2022.</p> <p>DOI: https://doi.org/10.21203/rs.3.rs-1544941/v2</p> <p> </p>
Data for: Trinity assembled transcriptome of a Eurasian (Myriophyllum spicatum) and a hybrid (M. spicatum × M. sibiricum) genotype of watermilfoil
<p>Aquatic plant managers frequently treat Eurasian watermilfoil (<em>Myriophyllum spicatum</em> L.; EWM) and hybrid watermilfoil (<em>Myriophyllum spicatum</em> L. × <em>Myriophyllum sibiricum</em> Komarov) with 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide. However, watermilfoil genotypes can differ in their response to 2,4-D. In this study, we compared facultative and constitutive gene expression differences for two watermilfoil genotypes (one Eurasian and one hybrid) that differ in their sensitivity to 2,4-D. To do this, we compared between control and 0.5mg L-1 2,4-D treated plants at four time points after treatment. We also assembled the first de novo watermilfoil transcriptome. We found that while qualitatively similar, the facultative transcriptional response of the EWM genotype to 2,4-D treatment was much stronger than the hybrid genotype, indicated by a greater number and log-fold-change of differentially expressed genes at all time points after treatment. Further, we found that the EWM and hybrid genotype differed in their 9-cis-epoxycarotenoid dioxygenase (NCED) and abscisic acid (ABA) gene response, and that there was a greater amount of photosynthesis gene downregulation (both in number and log-fold-change) in the EWM than the hybrid genotype. At the constitutive level, overall, the hybrid expressed genes at a higher level than the EWM genotype, but not the genes of the 2,4-D response pathway. These differences in gene expression match with the degree of phenotypic difference in growth observed between these genotypes when exposed to 2,4-D. The hybrid genotype used here mitigates the effects of 2,4-D treatment better than the EWM genotype at both the molecular and phenotypic level. More study is needed to understand the mechanism(s) of mitigation and whether this is a cause of hybridity, or the specific genotypic backgrounds used here.</p>
Rum and Argyll red deer genotype files
<p>The red deer population inhabiting the north block of the Isle of Rum, Scotland (57°0'N, 6°20'W) has been studied at an individual level since 1971 and was the main focus of this study. After quality control 39,587 autosomal SNPs genotyped in 3046 individuals were retained for analysis. This study also used equivalent genotype data for 157 individuals from a mainland population of red deer from Argyll, Scotland. Data files are in plink readable format (.bed .bim .fam) and include a .txt file with estimated SNP positions in centimorgans (cM). If you plan to analyse the data, we request that you inform us, see README file for more information. </p>
Roe deer microsatellite genotype data
<p>In the early 1800s, the European roe deer (<em>Capreolus capreolus</em>) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonised Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonisation and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies and explore the opportunity for development of forensic traceability tools. The results concerning the recolonisation origin support natural, multidirectional immigration from neighbouring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad scale geographic origin assignment using nuclear markers to support law enforcement.</p>
Environment and genotype influence on Populus tremuloides condensed tannin composition
<p>This dataset contains concentration and molecular structural information (mean degree of polymerization, procyanidin:prodelphinidin ratios, stereochemistry) describing condensed tannins in <em>Populus tremuloides</em> (aspen) tree foliage in different genotypes and in response to altered environmental conditions (warming, freeze damage, ozone exposure, elevated carbon dioxide, elevated soil nutrients, altered soil microbiome, mammal browsing, and insect herbivory).</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.