List of all studies
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Study NameDescription#PhenotypesDate Added
Mejion201 different accessions of A. thaliana from different geographic origins. These accessions were part of the RegMap. Seeds were obtained by growing the parental generation of all lines used side by side in the same growth chambers under the same conditions. The seeds were surface sterilized in 2.8% hypochlorite for 4 min and washed three times in MonoQ sterile water. They were then stratified for 72 h at 4 °C in water and darkness and put to grow on our custom Confocal Chamber System (CCs). The seeds were grown for 3 d in vertically oriented CCs containing 1× Murashige and Skoog (MS) salt mixture, 1% (wt/vol) sucrose and 0.8% (wt/vol) agar. To provide a sterile environment for the CCs and prevent them from drying out, we embedded the CCs into conventional agar plates 2Aug/13/2016
trichome_development_epidermis_metal_traitsA genome-wide association screen for genes affecting trichome development and epidermal metal accumulation in Arabidopsis Radek Bezvoda, Yazmín Mónica Landeo Ríos, Zdeňka Kubátová, Eva Kollárová, Ivan Kulich, Viktor Žárský, Fatima Cvrčková Manuscript in preparation18May/17/2023
Pb Mine soilArabidopsis thaliana (360 accessions) were cultivated in two soil types with contrasted Pb concentration placed in a growth chamber. Germination and survival were monitored and rosette diameter (RD) of 3 individuals per accession and soil type was measured weekly for 4 weeks. Growth rate of each accession was calculated as mean(RDMine) / mean(RD Control) of the last RD measure. Fifty-day old plants were harvested to measure its nutrient mineral contents.15Aug/06/2021
Gravitropic setpoint angle (GSA)Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Data from the Nature Communications paper by Waidmann et. al. 2019.
Root growth rates under nutrient deficiencyData from the paper by Bouain et all. , bioRxiv 2018 "Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation" Root growth of different Arabidopsis accessions has been measured on MS plates lacking different nutrients in the early phase of seedling growth. doi:
Lifetime fitness in Germany and Spain under rainfall manipulationData from Exposito-Alonso et al. (2019). A map of climate change-driven natural selection in Arabidopsis thaliana. Nature. The data is comprised of three fitness traits in eight experimental environments and 98 climate variables of origin. Fitness traits include Survival from germination to reproductive adult, the number of Seeds produced per individual adult, and the product of both (Fitness). The traits have already been scaled by the mean of the experimental population, so they are relative fitness traits. The codes of each experiment follow a three letter format. The first position is either "m" from Madrid (Spain), "t" from Tuebingen (Germany). The second position is either "h" from high rainfall or "l" from low rainfall. The third position is either "p" from population replicate pot (where plants are at high density), or "i" from an individual replicate pot (where there was one plant per pot). In combination, for example, the code "mlp" refers to the fitness in the experiment of Madrid, at low precipitation, and high plant population density in the plot. Climate variables were used to understand the relationship between genome variation and environment of origin. They were derived intersecting the geographic coordinates where natural lines were originally collected and climate maps from (and derived metrics).122Jun/27/2019
Root growth under Zn deficiency Bouain et al. 2018Data from the Plos Genetics paper by Bouain et al. 2018
Inter-specific pollination of Arabidopsis thaliana and Malcolmia littoreaDegree of Malcolmia littorea (Brassicaceae) pollen tube entrance into pistils of Arabidopsis thaliana strains. Pollen tubes were stained with aniline blue. Values indicate arbitrary compatibility scores based on the numbers of pollen tubes in the styles: 1: No tubes observed; 2: 1–19 tubes; 3: 20–39 tubes; 4: 40–59 tubes; 5: ≥60 tubes.1May/10/2019
Seed longevity (Renard et. al., 2020)Four different seed aging treatments (3 artificial treatments (AAT, CDT and EPPO) and dry seed storage (NAT)) were scored in 269 Arabidopsis thaliana ecotypes.4Aug/26/2020
Atwell et. al, Nature 2010GWAS of 107 phenotypes in Arabidopsis thaliana inbred lines using ~250k SNPs in 199 accessions107Aug/13/2016
DAARGWAS of three mass features of N-malonyl-D-allo-isoleucine in Arabidopsis thaliana inbred lines using ~250k SNPs in 416 accessions3Sep/05/2017
Kerdaffrec et al. 2016Germination rate of seeds after-ripened for 21 days (GR21) measured for 161 Swedish lines. A more detailed description can be found in Kerdaffrec et al. 2016.1Mar/15/2018
Kerdaffrec et al. 2017Germination rate of seeds after-ripened for 21, 63 and 105 days measured for 92 Swedish lines grown under two different temperature treatments, cold (15ºC) and warm (21ºC).6Mar/15/2018
Genetic dissection of shoot regeneration from root explants in Arabidopsis (Lardon et al., 2020)In the frame of a genome-wide association study, we have subjected 170 natural Arabidopsis thaliana accessions to two protocol variants for shoot regeneration from root explants and recorded substantial variation in regenerated shoot numbers and several related in vitro traits. The results of this study are reported in "The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors" (Lardon et al., Commun. Biol., 2020).28Aug/20/2020
Satbhai et. al. Nature Communications 2017Low availability of Fe significantly limits crop yields in many parts of the world. However, it is largely unknown which genes and alleles adjust plant growth in Fe limited environments. Using natural variation of a geographically restricted panel of Arabidopsis thaliana accessions, we identify allelic variation at the FRO2 locus associated with root length under iron deficiency. We show that non-coding sequence variation at the FRO2 locus leads to variation of FRO2 transcript levels, as well as ferric chelate reductase activity, and is causal for a portion of the observed root length variation. These FRO2 allele dependent differences are coupled with altered seedling phenotypes grown on iron-limited soil. Overall, we show that these natural genetic variants of FRO2 tune its expression. These variants might be useful for improvement of agronomically relevant species under specific environmental conditions, such as in podzols or calcareous soils (Reference: doi:10.1038/ncomms15603).5Sep/05/2017
Natural variation in stomata size (Dittberner et al. 2018)Measurements of stomata site, density and water use efficiency as described by Dittberner et al. 2018 in Molecular Ecology DOI: 10.1111/mec.148386Jul/31/2019
Isoprenoid concentrationNatural variation of seven different isoprenoids in 118 different accessions7Oct/25/2020
1001 Genomes & easyGWASPhenotypes from the 1001 Genomes Project and the easyGWAS publication8Jun/26/2019
Ion ConcentrationPlants were grown in a controlled environment with 10 h light/ 14 h dark (90 mmol m22s21 photosynthetically active light) and 19 to 22uC, as previously described [31]. Briefly, seeds were sown onto moist soil (Promix; Premier Horticulture) in 10.506210 20 row trays with various elements added to the soil at subtoxic concentrations (As, Cd, Co, Li, Ni, Rb, and Se [31]) and the tray placed at 4uC for 3 days to stratify the seeds and help synchronize germination. Each tray contained 108 plants, six plants each from 18 accessions, with three plants of each accession planted in two different parts of the tray. Each tray contained four common accessions (Col-0, Cvi-0, Fab-2 and Ts-1) used as controls, and 14 test accessions. Trays were bottom-watered twice per week with 0.25-strength Hoagland solution in which Fe was replaced with 10 mM Fe-HBED[N,N9-di(2-hydroxybenzyl)ethyle- nediamine-N,N9-diacetic acid monohydrochloride hydrate; Strem Chemicals, Inc.). After 5 weeks plants were non-destructively sampled by removing one or two leaves and the elemental composition of the tissue analyzed by Inductively Couple Plasma Mass Spectroscopy (ICP-MS). The plant material was rinsed with 18 MV water and placed into Pyrex digestion tubes.19Mar/21/2017
Raffinose (22°C and 32°C)Raffinose measurements at 22°C and 32°C published in Reichelt et al. 2023