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176 results for “qtl”
QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat
<p>The mapping population comprises of 180 RILs developed from a cross between GW322 and KAUZ.</p> <p><strong>Phenotypic data</strong><br>Phenotypic evaluation was conducted across two consecutive crop seasons (2021-22 and 2022-23) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at ICAR-IARI, New Delhi. Various physiological and agronomic traits of importance were measured. The component traits of yield including days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY) were measured under heat and combined stress conditions.</p> <p><strong>Genotypic data</strong><br>DNA was isolated from 21-day-old seedlings using the CTAB method (Murray and Thompson, 1980). DNA quality check was done using 0.8% agarose gel electrophoresis. The Axiom Breeders' array containing 35K Single Nucleotide Polymorphism (SNP) was employed for the genotyping of RILs and parents.</p>
SNP markers used for QTL mapping in the inbred lines
<p><span>Young leaves of the 175 inbred lines and their seven parents were collected from seedlings grown in a greenhouse. </span><span>About 200 mg bulk leaf sample from three plants of a line was placed in 2 ml safe-lock </span><span>Eppendorf tube and stored at ‒80 </span><span>˚C for one night prior to crushing using a Mixer Mill (TissueLyser II, Qiagen, Germany). Genomic DNA was extracted using SIGMA DNA extraction kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer's instruction. DNA concentration and purity of the samples were assessed using a NanoDrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The samples were processed and sequenced using tunable genotyping-by-sequencing (tGBS®) method by Data2Bio (Ames, IW, USA). Genomic DNA was digested using two restriction enzymes NSpI (5′-RCATG^Y-3′) and BfuCI/Sau3AI (5′-^GATC-3′) which created 3´and 5´overhangs, respectively. Two single-stranded oligos, one containing a sample-specific internal barcode and the other a universal oligo, were ligated to the complementary 3´ and 5´ overhangs, respectively. </span>All 175 inbred lines' and seven parents' treated DNA was pooled for construction of the tGBS library and sequencing. The raw sequence data were demultiplexed by barcode, which was subsequently removed bioinformatically from each sequence. The barcode-trimmed sequence reads of genotype were further trimmed using the trimming software, Lucy (Chou & Holmes, 2001; Li & Chou 2004) to remove low-quality reads based on Phred quality scores of Q15.</p>
Efficient statistical method for single-cell QTL analysis
<p>This upload contains data objects associated with our paper "Efficient statistical method for single-cell QTL analysis" introducing the SAIGE-QTL method (preprint available soon!).</p>
Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover
<p>Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (<i>Trifolium repens</i>). This widespread species displays a well-studied chemical defense polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F<sub>2</sub> mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL X E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL co-localization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favored early investment in flowering at the cost of multi-year survival in the southernmost site vs. delayed flowering and multi-year persistence in the northern environments. Our findings demonstrate that multi-locus genetic tradeoffs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.</p>
CAGE and txrevise promoter usage QTL summary statistics
<p>This dataset contains promoter usage QTL summary statistics obtained using <a href="https://github.com/eQTL-Catalogue/qtlmap">QTLmap</a>. QTLmap_summary_CAGE.txt contains summary statistics for CAGE, QTLmap_summary_txrevise-25.txt for regular <a href="https://github.com/kauralasoo/txrevise">txrevise</a> and QTLmap_summary_txrevise-supplemented-20.txt for txrevise with the new generated annotations.</p> <p>This dataset contains the promoter annotations obtained with CAGE as part of the FANTOM5 project, cleaned and reformatted using <a href="https://github.com/andreasvija/cage/blob/master/qtlmap_prep/clean_promoters.R">this code</a> for the purpose of QTL mapping, that were used to obtain the aforementioned summary statistics. They can be found in Cleaned_FANTOM5_promoter_annotations.tsv.</p> <p> </p> <p>QTL summary statistics column descriptions:</p> <p>molecular_trait_object_id - gene</p> <p>molecular_trait_id - top promoter for the gene</p> <p>n_traits - how many promoters were tested for the gene</p> <p>n_variants - how many genetic variants were tested for the promoter</p> <p>variant - top genetic variant for the promoter</p> <p>chromosome - chromosome</p> <p>position - promoter's top genetic variant start position</p> <p>pvalue - nominal p-value of the association between the promoter and genetic variant</p> <p>beta - the fitted linear model's regression coefficent</p> <p>p_perm - empirical p-value calculated using permutations</p> <p>p_beta - estimated empirical p-value based on the beta distribution, this is the recommended p-value column</p>
Root penetration index 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis.
<p><span>Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized <em>Arabidopsis thaliana</em> responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins and inhibitor treatments suggest that </span><span>auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. </span><span>The assessment of 21 Arabidopsis accessions revealed that primary root penetrability (PRP) varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population (RIL) derived from Landsberg erecta (Ler-0, with a high PRP) and Shahdara (Sha, with a low PRP) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3 (<em>q</em>-<em>RPI3</em>), which accounted for 29.98% (LOD = 8.82) of the total phenotypic variation. Employing an introgression line (IL-321), with a homozygous <em>q</em>-<em>RPI3</em>region from Sha in the Ler-0 genetic background, we demonstrated that <em>q-RPI3</em> plays a crucial role in root penetrability. This multiscale study revels new insights into root plasticity during the penetration process in hard agar layers, natural variation and genetic architecture behind primary root penetrability in Arabidopsis.</span></p>
Test data for C-QTL analysis of barley Recombinant Chromosome Substitution Lines
<p>This data shows the testing of C-QTL approach to visualise the influence of ensembles of groups of genetic markers on plant traits from a selection of Recombinant Chromosome Substitution Lines. The analysis was performed on of 29 genotypes and two traits: Heading Date and plant height. For heading date, the two major QTLs on 2H and 7H associated with heading date using the REML approach (de la Fuente Canto 2016) are also detected using the CQTL analysis, getting the highest 'rank' or score with this approach. Similarly, marker main effect for plant height at the region of the sdw1 seems to be detected with the CQTL analysis.</p>
Gene expression QTL lead variants in macrophages stimulated with IFNg and Salmonella
<p>Lead eQTL variants from RASQUAL and FastQTL analyses.</p> <p>Columns in the RASQUAL results:</p> <ul> <li>snp_id - id of the lead eQTL variant</li> <li>gene_id - id of the gene</li> <li>chisq - Chi-square statistics from RASQUAL</li> <li>p_nominal - Nominal p-value from RASQUAL</li> <li>p_eigen - Nominal p-value corrected by EigenMT for the number of indepedent tests in the cis region of the gene.</li> <li>n_tests - Number of independent tests estimated by EigenMT</li> <li>fdr_thresh - Empirical FDR 10% threshold. Those eQTLs for which p_eigen < fdr_threshold are significant at the 10% FDR level.</li> </ul> <p> </p>
Coordinates of genetic variants used for QTL mapping
<p>Column names</p> <ol> <li>chr - chromosome name</li> <li>pos - position</li> <li>snp_id - variant id</li> <li>ref - reference allele</li> <li>alt - alternate allele</li> <li>type - variant type (SNP or INDEL)</li> <li>AC - alternate allele count</li> <li>AN - total allele count</li> </ol>
Gene, Splice and Transcript based QTL association in the human sACC and Amygdala
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R/QTL datasets for fusiform rust resistance QTL mapping
<p>Fusiform rust disease, caused by the endemic fungus <i>Cronartium quercuum</i> f. sp. <i>fusiforme</i>, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in <i>Pinus taeda </i>L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three QTL distributed on two linkage groups. The two QTL on linkage group 2 were additive with respect to their effects on the probability of disease outcome. All three QTL were validated using a population of 2057 cloned pine genotypes in a six-year-old multi-environmental field trial. As a complement to the QTL mapping approach, bulked segregant RNAseq analysis revealed a small number of candidate nucleotide binding leucine rich repeat genes harboring SNP significantly associated with disease resistance. The results of this study demonstrate that single qualitative resistance genes can confer effective resistance against genetically diverse mixtures of an endemic pathogen.</p>
QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat
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QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations
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Data from: Validation of grain yield QTL from soft winter wheat using a CIMMYT spring wheat panel
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Dissecting the genetic basis of variation in Drosophila sleep using a multiparental QTL mapping resource
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Data from: Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: estimates of selection and QTL mapping
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Data from: Major QTL controls adaptation to serpentine soils in Mimulus guttatus
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SNP markers used for QTL mapping in the inbred lines
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Variants and QTL associated with variation in genome-wide crossover number
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Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover
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