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23 results for “Genetic Content”
CONTENT -- Multi-context genetic modeling TWAS and eAssociation summary statistics
<p>We provide the summary statistics of running CONTENT, the context-by-context approach, and UTMOST on over 22 phenotypes. The phenotypes are listed in the manuscript, and their respective studies and sample size can be found in a table under the supplementary section of the manuscript. All 3 methods were trained on GTEx v7 as well as CLUES, a single-cell RNA sequencing dataset of PBMCs. The data include the gene name, model, cross-validated R^2, prediction pvalue, TWAS p value, TWAS Z score, and a column titled "hFDR" indicating whether the association was statistically significant while employing hierarchical FDR. The benefits of employing such an approach for all methods can be found in the manuscript.</p> <p> </p> <p>We also include the eAssociations that we obtain by training prediction models on GTEx and CLUES alone. For the CxC and UTMOST approaches, these files contain the gene, context, pvalue and adjusted R^2. For CONTENT, these include the gene, context and pvalue and adjusted R^2 for each CONTENT model--the column names are described like a regression of y~x, rsq_y_x, so rsq_observed_full is the adjusted R^2 from regressing the observed expression onto the cross-validated full model predictions. In cases where the R^2 is higher from the specific or shared models, it's best to use either of those rather than the full model for out of sample prediction.</p>
Figure 2 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 2. Idiograms of the accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa - PI" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D), "Cateto Roxo 99" (E), "Roxo de Minas" (F), and "Sergipe" (G). Yellow dash and circle represent the CMA+/DAPI- band. Chromosomal order (CO), chromosome morphology (CM), metacentric (M), submetacentric (SM), short arm (p), and long arm (q). Vertical bar in karyogram and ideogram = 10 µm.
Figure 1. Allium sativum L in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 1. Allium sativum L.cytological data obtained by conventional Giemsa staining.Prophase and interphase nucleus (A), prometaphase (B), and metaphase (C) obtained with the use of antimitotic. Mitotic cycle is shown in d-f: anaphase (D), end of anaphase (E), and telophase (F). Dots and red arrow indicate the distended nucleolar organiser region (NOR). Bar = 10 µm.
Data for: Assessment of genetic diversity and protein content of Scandinavian peas (Pisum sativum)
<p>We produced homogeneous lines of 227 pea accessions from the Nordic Genetic Resource Center by single seed descent. The genetic diversity among these, mostly Scandinavian accessions, was investigated using three microsatellite markers, A9, AC58 and AA5. The microsatellites were highly informative and separated 153 of 194 accessions on a Neighbor Joining topology. The high polymorphism information content (PIC) values between 0.87 and 0.91 indicated that the gene bank material contains a large number of pea accessions with different breeding. The peas were grown in the field for two years and seed protein content showed variation between 9.3% and 34.1% over years and accessions. Mean thousand seed weight was 152.05 g. More than 10 accessions had protein content above 28% showing that the collection has potential as a breeding nursery for high-protein pea.</p>
Data for: Assessment of genetic diversity and protein content of Scandinavian peas (Pisum sativum)
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Quantitative genetics of phosphorus content in the freshwater herbivore, Daphnia pulicaria
<p>1. Phosphorus (P) is essential for growth of all organisms, and P content is correlated with growth in most taxa. Although P content was initially considered to be a trait fixed at the species level, there is growing evidence for considerable intraspecific variation. Selection on such variation can thus alter the rates at which P fluxes through food webs.</p> <p>2. Nevertheless, prior work describing the sources and extent of intraspecific variation in P content were not genetically explicit, confounded by unknown genetic background and evolutionary history. We constructed an F2 recombinant population of the dominant freshwater grazer, Daphnia pulicaria to mitigate such issues.</p> <p>3. F2 recombinants exhibited considerable variation in growth rate, P content (0.49% to 1.97%), P use efficiency (PUE; 51 to 208 mg biomass/mg P), and correlated traits such as hatching time of resting eggs, in common garden conditions.</p> <p>4. These results clearly demonstrate the scope of genetic recombination in generating variation in ecologically-relevant traits. The absence of environmental selection is a likely component driving such variation not observed in natural settings.</p> <p>5. Although phosphoglucose isomerase (PGI) genotype was significantly associated with variation in hatching time of resting eggs, contrary to prior work with less rigorous designs, allelic variation at the PGI locus did not explain variation in P content and PUE of Daphnia, indicating that such quantitative traits are under polygenic control.</p> <p>6. Together, these results suggest that although there is considerable genetic scope for variation in key ecologically-relevant traits, such as P content and efficiency of P use, these traits are likely under strong stabilizing selection, most likely due to selection on growth rate and size. Importantly, our observations suggest that anthropogenic alterations to P supply due to eutrophication could alter selection on these traits, thereby rapidly altering the role Daphnia plays in the P cycle of lakes.</p>
Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites' performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.
Dataset from "Employing hidden Markov models to assess the genetic content of genome assemblies"
<p>Dataset used to reach the conclusions in "Employing hidden Markov models to assess the genetic content of genome assemblies".</p>
Fig. 4 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 4. (A) A map of Iran showing the relative geographic location of each habitat, (B) Representative of DNA fragments generated by the UBC807 primer in the nine juniper populations. The left-most (L) column corresponds to the biological ruler (Ladder) and the right-most column () is a negative control., (C) Dendrogram obtained from five ISSR primers using UPGMA method by Dice similarity coefficient for 27 juniper genotypes (D) Principal Component Analysis based on Dice matrix for 27 juniper genotypes.
Fig. 2 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 2. (A): Cluster analysis using an average of 40 compounds identified in the 27 individuals from across the Juniperus genus. (B): Cluster analysis dendrogram of juniper populations evaluated based on 13 morphological characters using SPSS 0.16 and Average Linkage method (Within Group). The abbreviations of the labels are given in Table S6.
Fig. 1 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 1. Typical representative GC-MS chromatograms of EOs collected from (A1): J. excelsa of Torbat-Heydaryeh (JET1), (A2): J. sabina of Ramsar (JSR) and (A3): J. communis of Tooskestan (JCT), (B1): Analysis of EO percentage among the studied populations (B2,3): Mean comparison of top 10 EO constituents.
Fig. 3 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 3. Mean comparison of morphological characteristics in 9 juniper populations. (Cwe: Cone weight, CL: Cone length, CD: Cone length, SN: Seed number of cone, SL: Seed length, Swi: Seed width, Swe: Cone weight, NL: Needle length, Nwi: Needle width, NLP5: Number of leaves per 5-mm section of ultimate lateral branchlet, RCL/D: Ratio of cone length to diameter, RCD/SN: Ratio of cone diameter to seed number, RSL/Wi: Ratio of seed length to width.)
Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
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Leveraging genetic resources and genomic prediction to enhance flavonol content in cranberry fruit
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Quantitative genetics of phosphorus content in the freshwater herbivore, Daphnia pulicaria
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Figure 3 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 3. Double staining with CMA/DAPI in accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Red arrows indicate CMA+ bands in the overlaid chromosome (B). White arrows indicate gaps formed by condensation (D). Dots indicate distended nucleolar organiser regions (NORs) (f). Bar = 10 µm. Figure 2. Double staining with CMA/DAPI in accessions "Cateto Roxo 99" (E), "Roxo de Minas" (F) and "Sergipe" (G). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Dots indicate distended nucleolar organiser regions (NORs) (F). Bar = 10 µm.
Data from: Tracking changes in chromosomal arrangements and their genetic content during adaptation
There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.
Data from: Tracking changes in chromosomal arrangements and their genetic content during adaptation
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A high-content arrayed CRISPR screen reveals genetic requirements for dynein-based trafficking
GEO Series GSE218249. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
High-content phenotypic analysis defines generalizable genetic and molecular regulators of lifespan in a C. elegans recombinant inbred population
GEO Series GSE252593. Caenorhabditis elegans. 96 samples. Type: Expression profiling by high throughput sequencing.
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