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2,785 results for “Genotype”
Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing
<p>In this study, genotyping-by-sequencing (GBS) was performed on 1041 <em>Aegilops</em> accessions, representing 23 different species. These accessions have been maintained by the Wheat Genetics and Resource Center (WGRC) at Kansas State University. The GBS FASTQ files have been uploaded to the NCBI SRA public repository under the BioProject accession number # PRJNA985892. We have provided other files related to data analysis, such as the barcode key file, SNP matrices, and taxonomic information of the accessions in this Dryad repository, which can be accessed through the provided link. The aim of the study was to explore the genetic and genomic characteristics of wild wheat relatives, <em>Aegilops,</em> using a larger number of SNP markers. Here, we also curated the WGRC gene bank <em>Aegilops</em> collection via the identification of misclassified accessions and genetically identical redundant accessions. Further, we explored the genomic relationship between wheat and the different <em>Aegilops</em> species. </p>
ddRAD genotyping data
<p>This dataset includes raw sequences and metadata (barcodes) used for ddRAD genotyping in the publication:</p> <blockquote> <p>Stelzer, C.P., M. Pichler, P. Stadler, Genome streamlining and clonal erosion in nutrient-limited environments: a test using genome-size variable populations, <em>Evolution</em>, Volume 77, Issue 11, November 2023, Pages 2378–2391, <a href="https://doi.org/10.1093/evolut/qpad144">https://doi.org/10.1093/evolut/qpad144</a></p> </blockquote> <p>Please cite this study if you use the data.</p>
Data from: Genotype-by-environment interactions influence the composition of the Drosophila seminal proteome
<p>Ejaculate proteins are key mediators of post-mating sexual selection and sexual conflict, as they can influence both male fertilization success and female reproductive physiology. However, the extent and sources of genetic variation and condition dependence of the ejaculate proteome are largely unknown. Such knowledge could reveal the targets and mechanisms of post-mating selection and inform about the relative costs and allocation of different ejaculate components, each with its own potential fitness consequences. Here, we used liquid chromatography coupled with tandem mass spectrometry to characterize the whole-ejaculate protein composition across twelve isogenic lines of Drosophila melanogaster that were reared on a high- or low-quality diet. We discovered new proteins in the transferred ejaculate and inferred their origin in the male reproductive system. We further found that the ejaculate composition was mainly determined by genotype identity and genotype-specific responses to larval diet, with no clear overall diet effect. Nutrient restriction increased proteolytic protein activity and shifted the balance between reproductive function and RNA metabolism. Our results open new avenues for exploring the intricate role of genotypes and their environment in shaping ejaculate composition, or for studying the functional dynamics and evolutionary potential of the ejaculate in its multivariate complexity.</p>
Genotype, phenotype and linkage data for Mimulus parishii x M. cardinalis hybrid incompatibility study
<p>The evolution of genomic incompatibilities causing postzygotic barriers to hybridization is a key step in species divergence. Incompatibilities take two general forms – structural divergence between chromosomes leading to severe hybrid sterility in F<sub>1</sub> hybrids and epistatic interactions between genes causing reduced fitness of hybrid gametes or zygotes (Dobzhansky-Muller incompatibilities). Despite substantial recent progress in understanding the molecular mechanisms and evolutionary origins of both types of incompatibility, how each behaves across multiple generations of hybridization remains relatively unexplored. Here, we use genetic mapping in F<sub>2</sub> and RIL hybrid populations between the phenotypically divergent but naturally hybridizing monkeyflowers <em>Mimulus cardinalis</em> and <em>M. parishii</em> to characterize the genetic basis of hybrid incompatibility and examine its changing effects over multiple generations of experimental hybridization. In F<sub>2</sub>s, we found severe hybrid pollen inviability (< 50% reduction vs. parental genotypes) and pseudolinkage caused by a reciprocal translocation between Chromosomes 6 and 7 in the parental species. RILs retained excess heterozygosity around the translocation breakpoints, which caused substantial pollen inviability when interstitial crossovers had not created compatible heterokaryotypic configurations. Strong transmission ratio distortion and inter-chromosomal linkage disequilibrium in both F<sub>2</sub>s and RILs identified a novel two-locus genic incompatibility causing sex-independent gametophytic (haploid) lethality. The latter interaction eliminated three of the expected nine F<sub>2</sub> genotypic classes via F<sub>1</sub> gamete loss without detectable effects on the pollen number or viability of F<sub>2</sub> double heterozygotes. Along with the mapping of numerous milder incompatibilities, these key findings illuminate the complex genetics of plant hybrid breakdown and are an important step toward understanding the genomic consequences of natural hybridization in this model system.</p>
Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease
<p>Leaf scald caused by the bacteria <em>Xanthomonas albilineans</em> is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against <em>X. albilineans</em> using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5-144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of <em>X. albilineans</em> and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi) The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.</p>
Genotype of expression quantitative loci (eQTL) analyses for bovine blood and liver
<p>To identify expression quantitative loci (eQTL) operating in bovine blood and liver, 238 animals were genotyped uisng Illumina BovineHD genotyping arrary. For this file minor allele is used as ref as the default in plink.</p>
Effects of genotype and host environment on the cuticular hydrocarbon profiles of Lysiphlebus parasitoids and aggression by aphid-tending ants
Parasitoids in the genus Lysiphlebus specialize on ant-tended aphids and have previously been reported to mimic the CHC profiles of their aphid hosts to avoid detection by ants. However, the precise mechanisms that mediate reduced ant aggression toward Lysiphlebus spp. are not known, nor is it clear whether such mechanisms are broadly effective or specialized to particular aphid hosts. Here we explore the effects of wasp genotype and host environment on Lysiphlebus cuticular hydrocarbon (CHC) profiles and ant aggression. Rearing asexual Lysiphlebus lines in different host aphid environments revealed effects of both wasp line and aphid host on wasp CHCs. However, variation in genotype and host affected different features of the CHC profile, with wasp genotype explaining most variation in linear and long-chain methyl alkanes, while aphid host environment primarily influenced short-chain methyl alkanes. Subsequent behavioral experiments revealed no effects of host environment on ant aggression, but stronger evidence for genotypic effects. The presence of genotypic variation in experienced ant aggression and relevant chemical traits is particularly relevant in light of recent evidence for genetic divergence among Lysiphlebus parasitoids collected from different aphid hosts.
Non-additive interaction between genotypes: implications for competitive fitness assays
<p>Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged <em>Drosophila simulans</em> populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: 1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. 2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype x environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.</p>
The Study of CYP2C19 Genotype-Guided Clopidogrel Treatment Models
ClinicalTrials.gov study NCT06665919. IPD Sharing: YES. Countries: 1. Publications: 50.
Data used in: Heritability and variance components of seed size in wild species: influences of breeding design and the number of genotypes tested
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Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales
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Data from: The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family
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Effects of genotype and host environment on the cuticular hydrocarbon profiles of Lysiphlebus parasitoids and aggression by aphid-tending ants
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SNPs genotypes of southern beech Nothofagus dombeyi
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Knockdown resistance (kdr) genotypes and collection information for Aedes aegytpi from Iquitos, Peru (2000 - 2017)
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Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
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Variation in personality shaped by evolutionary history, genotype, and developmental plasticity in response to feeding modalities in the Arctic charr
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Structure and dynamics of enterovirus genotype networks
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Phenotypes and genotypes of brown trout used for breeding experiments in 2014
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Patch quality and genotype-by-environment interactions shape dispersal and post-settlement survival in a butterfly metapopulation
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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
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.