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Dataset results
18 results for “genetic background effects”
Data from: Stoichiometric traits of stickleback: effects of genetic background, rearing environment, and ontogeny
Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem-effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwa- ter fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichio- metric composition of bodies and excretion) of threespine stickleback. We use two populations from distinct freshwater lineages with contrasting lateral plating pheno- types (full vs. low plating) and their hybrids, which are mostly fully plated. We found that ontogeny, rearing environment, and body condition were the most important pre- dictors of organismal stoichiometry. Although elemental composition was similar be- tween both populations and their hybrids, we found significant divergence in phosphorus allocation among body parts and in phosphorus excretion rates. Overall, body armor differences did not explain variation in whole body phosphorus, phospho- rus allocation, or phosphorus excretion. Evolutionary divergence between these line- ages in both allocation and excretion is likely to have important direct consequences for ecosystems, but may be mediated by evolution of multiple morphological or physi- ological traits beyond plating phenotype.
Data from: Mutualism effectiveness and vertical transmission of symbiotic fungal endophytes in response to host genetic background
Certain species of the Pooideae subfamily develop stress tolerance and herbivory resistance through symbiosis with vertically-transmitted, asexual fungi. This symbiosis is specific, and genetic factors modulate compatibility between partners. Although gene flow is clearly a fitness trait in allogamous grasses, since it injects hybrid vigor and raw material for evolution, it could reduce compatibility and thus, mutualism effectiveness. To explore the importance of host genetic background in modulating the performance of symbiosis, Lolium multiflorum plants, infected and non-infected with Neotyphodium occultans, were crossed with genetically distant plants of isolines (susceptible and resistant to diclofop-methyl herbicide) bred from two cultivars, and exposed to stress. The endophyte improved seedling survival in genotypes susceptible to herbicide, while it had a negative effect on one of the genetically resistant crosses. Mutualism provided resistance to herbivory independently of the host genotype, but this effect vanished under stress. While no endophyte effect was observed on host reproductive success, it was increased by inter-population plant crosses. Neither gene flow nor herbicide had an important impact on endophyte transmission. Host fitness improvements due to gene flow do not appear to result in direct conflict with mutualism while this seems to be an important mechanism for the ecological and contemporary evolution of the symbiotum.
Data from: Stoichiometric traits of stickleback: effects of genetic background, rearing environment, and ontogeny
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Data from: Mutualism effectiveness and vertical transmission of symbiotic fungal endophytes in response to host genetic background
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Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis
The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist, nor about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression, and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear. To investigate the genetic basis and genomic consequences of genetic background dependence of the scallopedE3 allele on the Drosophila melanogaster wing, we generated multiple novel genome-level datasets from a mapping-by-introgression experiment and a tagged RNA gene expression dataset. In addition we used whole genome re-sequencing of the parental lines—two commonly used laboratory strains—to predict polymorphic transcription factor binding sites for SD. We integrated these data with previously published genomic datasets from expression microarrays and a modifier mutation screen. By searching for genes showing a congruent signal across multiple datasets, we were able to identify a robust set of candidate loci contributing to the background-dependent effects of mutations in sd. We also show that the majority of background-dependent modifiers previously reported are caused by higher-order epistasis, not quantitative non-complementation. These findings provide a useful foundation for more detailed investigations of genetic background dependence in this system, and this approach is likely to prove useful in exploring the genetic basis of other traits as well.
Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis
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Data from: Sensitivity of the distribution of mutational fitness effects to environment, genetic background, and adaptedness: a case study with Drosophila
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Data from: Do males matter? Testing the effects of male genetic background on female meiotic crossover rates in Drosophila melanogaster
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Data from: Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas
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The effect of genetic background on cognitive and pathological traits: AD-BXD
GEO Series GSE101144. Mus musculus. 133 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNA-seq on isogenic PTEN panel iPSC-derived neural progenitor cells to study the effect of ASD specific PTEN mutation and the effects of autism genetic background
GEO Series GSE214323. Homo sapiens. 54 samples. Type: Expression profiling by high throughput sequencing.
Combined effects of genetic background and diet on mouse metabolism and gene expression
GEO Series GSE260764. Mus musculus. 160 samples. Type: Expression profiling by high throughput sequencing.
Genetic background effect on Scn5a mutant cardiac right ventricle gene expression
GEO Series GSE19741. Mus musculus. 12 samples. Type: Expression profiling by array.
The effect of genetic background on cognitive and pathological traits: AD-BXD [dataset 2]
GEO Series GSE119215. Mus musculus. 88 samples. Type: Expression profiling by high throughput sequencing.
Analysis of Aire effects on individual mice of different genetic backgrounds
GEO Series GSE8564. Mus musculus. 20 samples. Type: Expression profiling by array.
Effect of summer daylight exposure and genetic background on growth in growth hormone deficient children
GEO Series GSE72439. Homo sapiens. 60 samples. Type: Expression profiling by array.
HCV tumor promoting effect is dependent on host genetic background
GEO Series GSE12185. Mus musculus. 50 samples. Type: Expression profiling by array.
Glomerular transcriptomic analysis of the influence of Genetic background effect during anti-GBM glomerulonephritis in mice
GEO Series GSE56236. Mus musculus. 12 samples. Type: Expression profiling by array.
ScienceDex guides
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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.