Find research datasets worth reusing

Brachypodium distachyon images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Brachypodium distachyon images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

Euphorbia peplus images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Euphorbia peplus images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

Arabidopsis thaliana images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Arabidopsis thaliana images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

Oryza sativa images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Oryza sativa images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

Solanum lycopersicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Solanum lycopersicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

Ocimum basilicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Ocimum basilicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

opencc-by-4.0Nov 2021View details →

Image dataset for the evaluation of a low-cost high-throughput plant phenotyping system

This dataset contains the raw and processed images from a low-cost high-throughput plant phenotyping (HTP) system, as well as the raw and processed images that were manually acquired for comparison. The HTP images were automatically and wirelessly acquired for entire benches of plants with a system composed of a Raspberry Pi and eight GoPro cameras. The entire file system of each GoPro camera was copied directly into a subfolder of finalGoProImages (numbered by camera). The raw HTP images were processed by correcting for lens distortion, computing the "greenness index" for each individual pixel, and filtering out extreme high and low values.  These processed HTP images were then saved in the "greenness" subfolder of finalGoProImages. The manually acquired images in the finalDSLR folder each represent an individual plant from one of five time points during the same greenhouse experiment. The raw manually acquired images were processed in the same manner as the raw HTP images by computing the greenness index for each individual pixel and filtering out extreme high and low values. The two tab-delimited text files include the number of green pixels and mean greenness index for each HTP (greennessGoProTable2.txt) and manually acquired (greennessDSLRTable2.txt) image.

opencc-by-4.0Mar 2022View details →

Analysis scripts for the evaluation of a low-cost high-throughput plant phenotyping system

Data analyses to complement "Image dataset for the evaluation of a low-cost high-throughput plant phenotyping system" (DOI: 10.5281/zenodo.5725224). "README_SetupAndAnalyses.pdf" contains instructions for setting up the high-throughput phenotyping (HTP) system and analyzing the resulting image datasets. The analyses are split into two parts. First, the automatically acquired HTP and manually acquired (DSLR) images are processed using the Python script labeled "finalGreennessAnalyses.py". The csv file labeled "labelTable.csv" is used to rename the DSLR images in terms of the date acquired and experimental conditions and must be included for the Python script to process the DSLR images. The output of the Python script includes "greennessGoProTable.txt" containing tab-delimited data regarding foliar size and greenness for each HTP image and "greennessDSLRTable.txt" containing tab-delimited data regarding foliar size and greenness for each DSLR image. The second step of the analyses includes inferential statistics (e.g., correlations and linear mixed effects modeling) and is based on the R script labeled "ghGoProAndDSLR_toPublish2.R". The csv file labeled "parAllBenches.csv" includes average solar daily light integral (solar DLI) data that were used as part of the linear mixed effects models in R.

opencc-by-4.0Jul 2019View details →

Contemporary phenotypic change in plant quantitative traits

This is a new version of the Gorné & Díaz 2017 database (doi:10.5281/zenodo.580095). We cheked the categorization of each case, fixed of some mistakes. Also, we disambiguated the trait type moderator and add a new (mean based) measure of change. This database included studies that provide data of changes in quantitative traits of angiosperms within a known temporal framework (<300 years). The search was performed by Scopus (www.scopus.com), up to 22 December 2015 (search strings in Gorné and Díaz 2017). The database includes studies that measured intraspecific change in a quantitative trait and which report the elapsed time when the phenotypic change occurred. The studies recorded a single population before and after a change in the environment or compared two (or more) populations by measuring a quantitative trait across two situations, where one of them was a new condition of known age. Both, by measuring change directly in the field or by performing common condition experiments (e.g. common garden experiments or reciprocal transplants). Studies reporting results from artificial selection or interspecific hybridization were excluded. The environmental changes included expansions of distributional range, soil or air pollution, exposure to herbicides, changes in salinity, pH, climate, disturbance or irrigation regime, and addition or loss of species in the local community. All data available in each study were recorded, including several observations of the same species. These procedures resulted in a database containing 1716 observations from 128 studies, with changes in populations of 152 species from 34 families, in elapsed times of < 260 years, and covering a wide range of traits, lifespan, growth forms and environmental situations. All data points were categorized according to biological properties of the study system (lifespan, growth form, trait type) and methodological ones. The amount and rate of phenotypic change is expresed as the standardized mean difference Hedges g (Hedges 1981, 1982), a rate of change which is the Hedges g over the elapsed time in years, and the log-transformation of both of them. The standardized mean difference is equal to the haldane numerator, which is a standard rate of evolution (Haldane 1949; Gingerich 1993). In addition, we upgraded the Díaz and Gorné (2017) database, computing the response ratio effect size (logRR) (Hedges et al. 1999) whenever possible. The response ratio is a mean-scaled metric equal to the darwins numerator (Haldane 1949). So that we compute a rate of change similar to darwins (time expressed as years instead of million years).   contact email address: gorneld@gmail.com

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Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes

Data associated with "Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes" (DOI: 10.3389/fmicb.2024.1452534). These data include soil resource measurements and various phenotypic measurements of associated Streptomyces isolates/populations. Specifically, these data note population level inhibition phenotypes according to Herr's Assays, isolate level antibiotic resistance phenotypes against 9 standard antibiotics, and isolate level resource use phenotypes quantified with Biolog SF-P2 96 well plates.

openCC0Sep 2024View details →

opencc-by-4.0Apr 2020View details →

Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits

Dataset associated with the manuscript "Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits" (Arroyo-Correa et al. 2020), including plant-pollinator interactions, individual plant attributes and the plant polygon map created with drone flights.

opencc-by-4.0Nov 2020View details →

Code and Data for: "Signs of local adaptation and phenotypic plastic response to elevation shifted between environmental backgrounds in Snapdragon plants"

Code and data for manuscript: "Signs of local adaptation and phenotypic plastic response to elevation shifted between environmental backgrounds in Snapdragon plants"

opencc-zeroNov 2023View details →

Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients

Background: Understanding the mechanisms by which genes control and regulate complex quantitative traits during periods of fluctuating resources remains a challenging and uncertain task in photosynthesis studies. Most studies have focused on the structure of photosynthesis, the photosynthetic response under stress, or the genetic mechanisms involved in photosynthetic effects and neglected the interactive genetic mechanism that governs various traits through significant quantitative trait loci (QTLs). Results In this study, we have developed a differential dynamic system that enables the identification of QTLs based on the photosynthetic phenotypic and genotypic data under varying levels of light intensity gradients. The framework not only allows for the assessment of the direct effects of QTLs on phenotypes but also captures how they influence interactions among phenotypes as light intensities change. We have analyzed the genetic effects and genetic variance, visualized the genetic network associated with photosynthesis interactions, and validated the effectiveness and stability of the DDS framework. Pivotal QTLs were identified individually to uncover the process and pattern of interaction. Through functional annotation, we made an intriguing discovery that seemingly unimportant QTLs can still have significant genetic effects on phenotypic changes through their regulation with other QTLs. Conclusions This finding emphasizes the significance of considering the interactive genetic architecture when seeking to understand the genetic interaction mechanism of photosynthesis in natural populations of woody plants. Moreover, our research provides a novel framework that can be extended to explore the interactive genetic architecture among organisms, contributing to a deeper understanding of stress resistance mechanisms in woody plants.

opencc-byDec 2021View details →

A case-study for improved reusability of plant phenotyping data with MIAPPE

Accompanying datasets for manuscript, "A case-study for improved reusability of plant phenotyping data with MIAPPE". The ZIP archives in this repository contain the source files and the output files that this manuscript refers to.

opencc-zeroJul 2022View details →

Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction

Pollinators are declining globally, with climate change implicated as an important driver. Climate change can induce phenological shifts and reduce floral resources for pollinators, but little is known about its effects on floral attractiveness and how this might cascade to affect pollinators, pollination functions and plant fitness. We used an in situ long-term drought experiment to investigate multiple impacts of reduced precipitation in a natural Mediterranean shrubland, a habitat where climate change is predicted to increase the frequency and intensity of droughts. Focusing on three insect-pollinated plant species that provide abundant rewards and support a diversity of pollinators (Cistus albidus, Salvia rosmarinus and Thymus vulgaris), we investigated the effects of drought on a suite of floral traits including nectar production and floral scent. We also measured the impact of reduced rainfall on pollinator visits, fruit set and germination in S. rosmarinus and C. albidus. Drought altered floral emissions of all three plant species qualitatively, and reduced nectar production in T. vulgaris only. Apis mellifera and Bombus gr. terrestris visited more flowers in control plots than drought plots, while small wild bees visited more flowers in drought plots than control plots. Pollinator species richness did not differ significantly between treatments. Fruit set and seed set in S. rosmarinus and C. albidus did not differ significantly between control and drought plots, but seeds from drought plots had slower germination for S. rosmarinus and marginally lower germination success in C. albidus. Synthesis. Overall, we found limited but consistent impacts of a moderate experimental drought on floral phenotype, plant reproduction and pollinator visits. Increased aridity under climate change is predicted to be stronger than the level assessed in the present study. Drought impacts will likely be stronger and this could profoundly affect the structure and functioning of plant-pollinator networks in Mediterranean ecosystems.

Data and scripts used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Images, script and data used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

opencc-zeroSep 2021View details →

Data from: Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection

Floral scent is a key mediator in plant–pollinator interactions; however, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. We recorded 289 scent compounds in deceptive moth fly-pollinated Arum maculatum from various populations north vs. south of the Alps, the highest number so far reported in a single plant species. Scent and fruit set differed between regions, and some, but not all differences in scent could be explained by differential phenotypic selection in northern vs. southern populations. Our study is the first to provide evidence that phenotypic selection is involved in shaping geographic patterns of floral scent in deceptive plants. The hyperdiverse scent of A. maculatum might result from the plant's imitation of various brood substrates of its pollinators.

opencc-zeroDec 2022View details →

Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly

In alpine systems, cushion plants act as foundation species by ameliorating local environmental conditions. Empirical studies indicate that contrasting phenotypes of alpine cushion species have different effects on understory plant species, either facilitative or competitive. Furthermore, dependent species within each community type might also exhibit different responses to each cushion phenotype, which can be clustered into several "response groups". Additionally, these species-groups specific responses to alpine cushion species phenotypes could alter community assembly. However, very few studies have assessed responses of dependent communities at species-group levels, in particular for both above- and below-ground communities. Here, we selected a loose and a tight phenotype of the alpine cushion species Thylacospermum caespitosum in two sites in northwest China, and use the relative intensity of interactions index to quantify cushion plant effects on subordinate communities of plants and soil fungi and bacteria. We assessed variations in responses of both above- and below-ground organisms to cushion plant effects at species-group level. Species-group level analyses showed that the effects of the phenotype varied among groups of each of the three community types, and different species-groups were composed of unique taxa. Additionally, we found that loose cushions enhanced stochastic processes in community assembly, for plants and soil fungi but not for soil bacteria. These variations of phenotypic effects on different species-group induced contrasting taxonomic composition between groups and altered community assembly thereby. Our study highlights the occurrence of contrasting effects of two phenotypes of a foundation cushion plant on understory plants, soil fungi and bacteria community composition, but not necessarily on their richness. We also showed that assessing responses of understory species at the species-group level allows a more realistic and mechanistic understanding of biotic interactions both for above- and below-ground communities.