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opencc-by-4.0Jul 2017View details →

Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, All SNP markers

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.

opencc-by-4.0Jul 2017View details →

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

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.

Fig. 3 in Vision-Linked Traits Associated With Antenna Size and Foraging Ecology Across Ants

Fig. 3. Mapped lateral eye positions according to ecology. Species indicated by circles, squares represent mean values for ecological binnings. (A) Eye position, both dorsoventral and anteroposterior, mapped on a theoretical ant head. Colors are indicative of foraging niche. (B) Eye position measurements with colors indicating trophic level. Illustrated head proportions based on ratio of mean head length and depth in lateral view across taxa sampled; head length is approximately 40% greater than head depth in profile view on average.

Fig. 1 in Vision-Linked Traits Associated With Antenna Size and Foraging Ecology Across Ants

Fig. 1. Variation among vision-based traits across sampled taxa. Pruned phylogenetic tree from Blanchard and Moreau (2017) with log adjusted ommatidia density mapped along branches.The raw units for ommatidia density are ommatidia per 1mm2. Ecological niche occupation indicated with icons and bar graph colors, includes foraging niche and trophic level. (Right) Eye area normalized by frontal head area across sampled species. Corresponding PGLS results in Fig. 2, Table 2.

Fig. 5 in Vision-Linked Traits Associated With Antenna Size and Foraging Ecology Across Ants

Fig. 5. Visual acuity and trophic level. (Left) Variation between eye area and ommatidia number across sampled ant species.Trophic level information displays omnivorous (n = 31) and predatory (n = 28) ant species. Unknowns are also included (n = 11).Trendline shows linear regression of ommatidia number and eye area (R2 = 0.7908, P = <2.2 x 10–16). Both measurements are scaled by frontal head area. (Right) Simplified, hypothetical representation of visual acuity based on ommatidia number.

Fig. 4 in Vision-Linked Traits Associated With Antenna Size and Foraging Ecology Across Ants

Fig. 4. Phylogenetic Generalized Least Squares regression of scape length and eye traits. Results of linear regressions of visual traits against scape length; (A) ommatidia density R2 = 0.1754, P = 0.0004615; (B) eye height R2 = 0.4735, P = 5.40 x 10–10; (C) dorsoventral eye position R = 0.1365, P = 0.001975; (D) anteroposterior eye position R2 = 0.1286, P = 0.002643. Scape and eye height are scaled by head area. All specimens were included in analyses (n = 64); PGLS relationships from Blanchard and Moreau 2017. ** denotes P ≤ 0.01; *** P ≤ 0.001.

opencc-by-4.0Apr 2024View details →

Unprocessed PROSAIL-generated datasets of plant functional traits with associated spectra

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opencc-by-4.0Nov 2024View details →

Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa

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opencc-zeroJan 2023View details →

Megafruit and megafauna diversity are positively associated, while megafruit traits are related to abiotic factors, in Tropical Asia

Aim For tens of millions of years, herbivorous megafauna were abundant across the globe, fulfilling important ecological roles including seed dispersal. Megafruits are very large fruits that are dispersed most effectively by megafauna. However, megafruits also occur in ecosystems where megafauna are extinct or were never present, emphasizing our incomplete understanding of megafauna-megafruit relationships. Here we use the complex biogeography of tropical Asia to investigate how megafruit diversity and traits are associated with the diversity of megafauna, smaller animals, and abiotic factors. Location Tropical Asia, from the Indian subcontinent in the west to tropical China in the north to the Maluku archipelago (Indonesia) in the east. Time period Late Pleistocene to the present day. Major taxa studied Megafauna (body weight >500 kg) that consume fruits, including stegodons, elephants, rhinoceroses, giant tapirs, and large bovids. Fleshy-fruited plant species across the region with a fruit width >40 mm (i.e., megafruits). Methods We compiled a list of all megafruits along with selected plant, fruit, and seed traits in 16 subregions across tropical Asia. We explored biogeographic patterns in megafruit diversity and traits in relation to the diversities of past and present megafauna, large- and medium-sized animals and abiotic factors (mean temperature, mean precipitation, precipitation seasonality, insularity). Results We identified 496 megafruits in tropical Asia. Megafruit diversity was highest in subregions with high megafaunal diversity, particularly extant species. Megafruit traits were influenced most strongly by abiotic factors (mainly temperature and land area), and weakly by megafauna and smaller dispersers. Main conclusions Our results are consistent with megafauna maintaining or responding to megafruit diversity, but variation in megafruit traits is primarily associated with abiotic factors. Given the massive megafaunal losses in tropical Asia since the Late Pleistocene, it is important to identify fruit traits that can increase megafauna-dependence and thus vulnerability to these losses.

opencc-zeroJul 2022View details →

Data from: Genome-wide association study for grain yield and component traits in wheat (Triticum aestivum L.)

The study material in GWAS panel with 280 common bread wheat genotypes was selected from All India Coordinated Research Project on Wheat and Barley to map the genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY). Phenotypic data: The GWAS panel was evaluated at five different environments during the 2020-21 Rabi (winter) season: E1-University of Agricultural Sciences, research farm, Dharwad (15°29'20.71"N, 74°59'3.35"E, 750m AMSL), E2-ICAR-Indian Agricultural Research Institute, New Delhi (28°38′30.5″N, 77°09′58.2″E, 228 m AMSL), E3-Indian Agricultural Research Institute, Jharkhand (24°16'58.4"N, 85°21'16.1"E, 651m AMSL), E4-ICAR-Indian Institute of Wheat and Barley, Karnal (29°41'8.2644''N, 76°59'25.9692''E, 250m AMSL), and E5-Punjab Agricultural University, Ludhiana (30o54' N, 75o48'E, 247m AMSL). The genotypes were planted in an augmented block design along with repeated checks (DBW187, MACS6222, WH1124, and WH1142). All the genotypes of a GWAS panel were phenotyped for six quantitative traits i.e. GWPS (gm), GY (gm), PH (cm) at five locations, GFD (days), DH (days) at four locations and GNPS (number) at two locations. Phenotypic data were analyzed using the R package 'augmentedRCBD' Genotypic data: Genomic DNA of the GWAS panel was extracted from the leaves of 21 days-old seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 14,790 high-quality SNPs was used in GWAS analysis.

opencc-by-4.0Jul 2022View details →

Data files associated with the article entitled: "High-throughput behavioral phenotyping of tiny arthropods: chemosensory traits in a mesostigmatic hematophagous mite" (accepted in Journal of Experimental Zoology - part A))

Here are provided three groups of datasets, corresponding respectively to the data obtained from MiteMap bioassays (1) with the monomolecular reference substances (geraniol and NH3), (2) with the patented blend MIX1.0, (3) with the odors emitted by the mites' bodies. These datasets were analyzed using the script provided in RMarkdown format in the Zenodo repository DOI 10.5281/zenodo.6109388. A folder is also provided with the heatmaps associated with these data grouped in subfolders by farm x modality.

opencc-by-4.0Aug 2022View details →

Mediating effects of Trait Emotional Intelligence on the association between Adverse Childhood Experiences (ACEs) and Self-reported Health

Data for two studies which investigate the role of trait emotional intelligence in resilience following adverse childhood experiences.

opencc-zeroAug 2022View details →

Genome-wide association mapping for component traits of drought and heat tolerance in wheat

The study material in GWAS panel with 282 advanced breeding line of bread wheat genotypes from IARI stress breeding program was selected to map the genomic regions responsible for Drought and heat tolerance component traits. Phenotypic data: The GWAS panel was evaluated at multiple locations namely, IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m), ARI, Pune - PUNE (18.5204° N, 73.8567° E, MSL 560m), IIWBR, Karnal - IIWBR (29.6857° N, 76.9905°E, MSL 243m), IARI, Jharkhand - JR (24.1929° N, 85.3756° E, MSL 580m) and IARI RS, Indore - IND (22.7196° N, 75.8577° E, MSL 553 m) with augmented RCBD design. Three tratments viz, IR (Irrigated), RI (Restricted irrigated) and LS (Late sown) were imposed for control, drought and heat stress, respectively. Data was collected on traits like Days to heading (DH), Days to maturity (DM), Normalized Difference Vegetation Index (NDVI) at anthesis and grain filling stage, chlorophyll content (SPAD) of flag leaf at post anthesis stage, Plant height (PH), Canopy temperature (CT), Grain weight per spike (GWPS), Thousand Grain weight (TGW), Plot Yield (PLTY) and Biomass. Genotypic data: Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 10546 high-quality SNPs was used in GWAS analysis. The detailed information of the methods and software used, data analysis and GWAS is provided at doi: 10.3389/fpls.2022.943033

opencc-by-4.0May 2024View details →

Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix

Data on studied willows, their traits, associated arthropod herbivore species, and script to perform analyses for the manuscript: "Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix".

opencc-by-4.0Jul 2022View details →

Datasets associated with Dale et al. 2022 Diversification and trait evolution in New Zealand woody lineages across changing biomes

Biome occupancy and trait datasets for New Zealand Melicytus, Myrsine, and Pseudopanax species used in Dale et al. 2022 Diversification and trait evolution in New Zealand woody lineages across changing biomes (https://doi.org/10.1080/03036758.2022.2108071). The datasets are biomes occupied, Specific Leaf Area, stem density, leaf nutrient content (N, P, K), and cold sensitivity. "dataset info.txt" outlines the variable names and their units.

opencc-by-4.0Jul 2019View details →

Transcriptome association studies of neuropsychiatric traits in African Americans implicates PRMT7 in schizophrenia

Genome-wide association study of Schizophrenia and Bipolar Disorder in African Americans 2019

opencc-zeroSep 2019View details →

Data from: Genome-wide association mapping of date palm fruit traits

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial crop species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crop species, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

opencc-zeroAug 2021View details →

Data from: Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize

Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within populations. However, it usually cannot capture the complex effects due to combination of alleles in haplotypes. Therefore, accuracy across populations has usually been low. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE, RNA expression of genes by haplotype), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked cis acting causal variants in the immediate vicinity of the gene, while excluding trans effects from diffusion and metabolism, so it would be more transferrable across different tissues and populations. We showed that HARE estimates captured one-third of the variation in gene expression and were more transferable across diverse tissues than the measured transcript expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels – a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel) – for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues whereas accuracy using HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations.

opennotspecifiedMay 2014View details →

Figure 9 in Two new species of asterocherid (Copepoda: Siphonostomatoida) associated with a sponge from the Strait of Messina, Italy: taxonomic and ecological traits

Figure 9. Psilomyzon sarcotragusicola sp. nov.: adult male. (A) habitus dorsal; (B) first urosomal somite and genital somite; (C) leg 4; (D) detail of the second endopodal segment of leg 4.