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97 results for “quantitative trait loci”
Dataset - A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
<p>Plant immunity is often negatively impacted by heat stress. However, the underlying molecular mechanisms remain poorly characterized. Based on a genome-wide association mapping approach, this study aims to identify in <em>Arabidopsis thaliana</em> the genetic bases of robust resistance mechanisms to the devastating pathogen<em> Ralstonia solanacearum</em> under heat stress. A local mapping population was phenotyped against the <em>R. solanacearum</em> GMI1000 strain at 27 and 30 °C. To obtain a precise description of the genetic architecture underlying natural variation of quantitative disease resistance (QDR), we applied a genome-wide local score analysis. Alongside an extensive genetic variation found in this local population at both temperatures, we observed a playful dynamics of quantitative trait loci along the infection stages. In addition, a complex genetic network of interacting loci could be detected at 30 °C. As a first step to investigate the underlying molecular mechanisms, the atypical meiotic cyclin <em>SOLO DANCERS</em> gene was validated by a reverse genetic approach as involved in QDR to <em>R. solanacearum </em>at 30 °C. In the context of climate change, the complex genetic architecture underlying QDR under heat stress in a local mapping population revealed candidate genes with diverse molecular functions.</p>
Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult stages, but selected against as juvenile, so developmental decoupling of traits between ontogenetic stages may be necessary for the evolution of sexual dimorphism in adults. Resolving intralocus conflicts between sexes and ages is therefore a key to the evolution of age-specific expression of sexual dimorphism. We investigated the genetic architecture of divergence in the ontogeny of sexual dimorphism between two populations of the Japanese medaka (Oryzias latipes) that differ in the magnitude of dimorphism in anal and dorsal fin length. Quantitative trait loci (QTL) mapping revealed that few QTL had consistent effects throughout ontogenetic stages and the majority of QTL change the sizes and directions of effects on fin growth rates during ontogeny. We also found that most QTL were sex-specific, suggesting that intralocus sexual conflict is almost resolved. Our results indicate that sex- and age-specific QTL enable the populations to achieve optimal developmental trajectories of sexually dimorphic traits in response to complex natural and sexual selection.
Data from: Quantitative trait loci for cold tolerance in chickpea
Fall-sown chickpea (Cicer arietinum L.) yields are often double those of spring-sown chickpea in regions with Mediterranean climates that have mild winters. However, winter kill can limit the productivity of fall-sown chickpea. Developing cold-tolerant chickpea would allow the expansion of the current geographic range where chickpea is grown and also improve productivity. The objective of this study was to identify the quantitative trait loci (QTL) associated with cold tolerance in chickpea. An interspecific recombinant inbred line population of 129 lines derived from a cross between ICC 4958, a cold-sensitive desi type (C. arietinum), and PI 489777, a cold-tolerant wild relative (C. reticulatum Ladiz), was used in this study. The population was phenotyped for cold tolerance in the field over four field seasons (September 2011–March 2015) and under controlled conditions two times. The population was genotyped using genotyping-by-sequencing, and an interspecific genetic linkage map consisting of 747 single nucleotide polymorphism (SNP) markers, spanning a distance of 393.7 cM, was developed. Three significant QTL were found on linkage groups (LGs) 1B, 3, and 8. The QTL on LGs 3 and 8 were consistently detected in six environments with logarithm of odds score ranges of 5.16 to 15.11 and 5.68 to 23.96, respectively. The QTL CT Ca-3.1 explained 7.15 to 34.6% of the phenotypic variance in all environments, whereas QTL CT Ca-8.1 explained 11.5 to 48.4%. The QTL-associated SNP markers may become useful for breeding with further fine mapping for increasing cold tolerance in domestic chickpea.
Data from: Development of a genomic resource and quantitative trait loci mapping of male calling traits in the lesser wax moth, Achroia grisella
In the study of sexual selection among insects, the Lesser Waxmoth, Achroia grisella (Lepidoptera: Pyralidae), has been one of the more intensively studied species over the past 20 years. Studies have focused on how the male calling song functions in pair formation and on the quantitative genetics of male song characters and female preference for the song. Recent QTL studies have attempted to elucidate the genetic architecture of male song and female preference traits using AFLP markers. We continued these QTL studies using SNP markers derived from an EST library that allowed us to measure both DNA sequence variation and map loci with respect to the lepidopteran genome. We report that the level of sequence variation within A. grisella is typical among other Lepidoptera that have been examined, and that comparison with the Bombyx mori genome shows that macrosynteny is conserved. Our QTL map shows that a QTL for a male song trait, pulse-pair rate, is situated on the Z chromosome, a prediction for sexually selected traits in Lepidoptera. Our findings will be useful for future studies of genetic architecture of this model species and may help identify the genetics associated with the evolution of its novel acoustic communication.
Dataset for Quantitative Trait Loci Associated with Lodging in Dry Field Peas. Data for PR Population (Carerra x Striker).
<p>Dataset for Quantitative Trait Loci Associated with Lodging in Dry Field Peas. Data for PR Population (Carerra x Striker). Here is data on lodging, height, stem diameter, side branch diameter, and epicotyl diameter for both site years with the PR population.</p>
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, All SNP markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas. All SNP markers were included in the dataset. U designates a missing datapoint. The data was not inputed.</p>
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers. This dataset is associated with the dissertation entitled, Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas.</p>
Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition
<p>Robert Ferguson<sup>1,2,3*</sup>, Vylyny Chat<sup>1,2,3*</sup>, Leah Morales<sup>1,2,3</sup>, Danny Simpson<sup>1,2,3</sup>, Kelsey Monson<sup>1,2,3</sup>, Elisheva Cohen<sup>1,2,3</sup>,Sarah Zusin<sup>1,2,3</sup>, Gabriele Madonna<sup>4</sup>, Mariaelena Capone<sup>4</sup>, Ester Simeone<sup>4</sup>, Anna Pavlick<sup>5</sup>, Jason Luke<sup>6,7</sup>, Thomas F Gajewski<sup>8,9,10</sup>, Iman Osman<sup>1,3,11,12</sup>, Paolo Antonio Ascierto<sup>4</sup>, Jeffrey Weber<sup>1,3,11</sup>, Tomas Kirchhoff<sup>1,2,3</sup></p> <p>1Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA<br> 2Departments of Population Health and Environmental Medicine, New York University- Grossman School of Medicine, New York, NY, USA<br> 3The Interdisciplinary Melanoma Cooperative Group, New York University-Grossman School of Medicine, New York, NY, USA<br> 4Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy<br> 5Division of Hematology & Medical Oncology, the Cutaneous Oncology Program, Weill Cornell Medicine and New York-Presbyterian, New York, USA<br> 6Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA.<br> 7UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.<br> 8Department of Pathology, University of Chicago, Chicago, IL, USA.</p> <p>9Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA.<br> 10Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA.<br> 11Department of Medicine, New York University-Grossman School of Medicine, New York, NY, USA<br> 12Ronald O. Perelman Department of Dermatology, New York University-Grossman School of Medicine, New York, NY, USA</p> <p>*These authors contributed equally to the work</p> <p>Corresponding author: Tomas Kirchhoff, PhD</p> <p><strong>ABSTRACT</strong><br> <strong>Background:</strong> Immune-checkpoint inhibition (ICI) has improved clinical outcomes for metastatic melanoma patients, however, 65-80% of patients treated with ICI experience immune-related adverse events (irAEs). Given the plausible link of irAEs with underlying host immunity, we explored if germline genetic variants controlling the expression of 42 immunomodulatory genes<br> were associated with the risk of irAEs in melanoma patients treated with the single-agent anti- CTLA-4 antibody ipilimumab (IPI).<br> <strong>Methods:</strong> We identified 42 immunomodulatory expression quantitative trait loci (ieQTLs) most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped in IPI-treated melanoma patients, collected as part of a multiinstitutional collaboration. We tested the association of ieQTLs with irAEs in a discovery cohort of 95 patients followed by validation in an additional 97 patients.<br> Results: We found that the alternate allele of rs7036417, a variant linked to increased expression of SYK, was strongly associated with an increased risk of grade 3-4 toxicity (OR= 7.46; 95% CI=2.65-21.03; p=1.43E-04). This variant was not associated with response (OR= 0.90; 95% CI=0.37-2.21; p=0.82).<br> Conclusion: We report that rs7036417 associates with increased risk of severe irAEs, independent of IPI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with autoimmune disease. The association between rs7036417 and IPI irAEs in our data suggests a role of SYK over-expression in irAE development. These findings support the hypothesis that inherited variation in immune-related pathways modulate ICI toxicity and suggest SYK as a possible future target for therapies to reduce irAEs.</p> <p> </p> <p><strong>Keywords:</strong> irAEs; germline variants; immune checkpoint inhibition; melanoma</p> <p><strong>Funding:</strong> This research was funded by the Italian Ministry of Health (IT-MOH) through “Ricerca Corrente”, grants number M2/2 and L2-1.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
A Genome-Wide Scan For Quantitative Trait Loci of Serum Bilirubin - A Framingham Study
ClinicalTrials.gov study NCT00340509. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Dataset - A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
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Data from: Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations
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Data from: Quantitative trait loci for cold tolerance in chickpea
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Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations
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Data from: Development of a genomic resource and quantitative trait loci mapping of male calling traits in the lesser wax moth, Achroia grisella
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Data from: Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population
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Data from: CLIP test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis
An important question arises when mapping quantitative trait loci (QTLs) for genetically correlated traits: is the correlation due to pleiotropy (a single QTL affecting more than one trait) and/or close linkage (different QTLs that are physically close to each other and influence the traits)? In this article, we propose the Close Linkage versus Pleiotropism (CLIP) test, a fast, simple and powerful method to distinguish between these two situations. The CLIP test is based on the comparison of the square of the observed correlation between a combination of apparent effects at the marker level to the minimal value it can take under the pleiotropic assumption. A simulation study was performed to estimate the power and alpha risk of the CLIP test and compare it to a test that evaluated whether the confidence intervals of the two QTLs overlapped or not (CI test). On average, the CLIP test showed a higher power (68%) to detect close-linked QTLs than the CI test (43%) and a same alpha risk (4%).
Data from: Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis
Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line, the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes and each explained around 5-14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping the candidate gene CG16700 for cold tolerance co-localizing with a QTL was identified.
Data from: Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits
The crop seed is a complex organ that may be composed of the diploid embryo, the triploid endosperm and the diploid maternal tissues. According to the genetic features of seed characters, two genetic models for mapping quantitative trait loci (QTLs) of crop seed traits are proposed, with inclusion of maternal effects, embryo or endosperm effects of QTL, environmental effects and QTL-by-environment (QE) interactions. The mapping population can be generated either from double back-cross of immortalized F2 (IF2) to the two parents, from random-cross of IF2 or from selfing of IF2 population. Candidate marker intervals potentially harboring QTLs are first selected through one-dimensional scanning across the whole genome. The selected candidate marker intervals are then included in the model as cofactors to control background genetic effects on the putative QTL(s). Finally, a QTL full model is constructed and model selection is conducted to eliminate false positive QTLs. The genetic main effects of QTLs, QE interaction effects and the corresponding P-values are computed by Markov chain Monte Carlo algorithm for Gaussian mixed linear model via Gibbs sampling. Monte Carlo simulations were performed to investigate the reliability and efficiency of the proposed method. The simulation results showed that the proposed method had higher power to accurately detect simulated QTLs and properly estimated effect of these QTLs. To demonstrate the usefulness, the proposed method was used to identify the QTLs underlying fiber percentage in an upland cotton IF2 population. A computer software, QTLNetwork-Seed, was developed for QTL analysis of seed traits.
Data from: Quantitative trait loci for growth and body size in the nine-spined stickleback Pungitius pungitius L.
Body size is an ecologically important trait shown to be genetically variable both within and among different animal populations as revealed by quantitative genetic studies. However, few studies have looked into underlying genetic architecture of body size variability in the wild using genetic mapping methods. With the aid of quantitative trait loci (QTL) analyses based on 226 microsatellite markers, we mapped body size and growth rate traits in the nine-spined stickleback (Pungitius pungitius) using an F2-intercross (n = 283 offspring) between size divergent populations. In total, 15 QTL locations were detected. The proportion of phenotypic variation explained by individual body size-related QTL ranged from 3% to 9%, and those related to growth parameters and increments from 3% to 7%. Several of the detected QTL affected either early or late growth. These results provide a solid starting point for more in depth investigations of structure and function of genomic regions involved in determination of body size in this popular model of ecological and evolutionary research.
Data from: Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr23 and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h²=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency. Three of the four QTLs controlling pvr23 breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr23 and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long term farmer selection.
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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.
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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.
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