|1001 Genomes & easyGWAS||Phenotypes from the 1001 Genomes Project and the easyGWAS publication||8||Jun/26/2019|
|1001genomes flowering time phenotypes||Study of flowering time at 16°C (FT16) and flowering time at 10°C (FT10) that where phenotype for the 1001genomes project.||2||Aug/14/2016|
|Abscisic acid (ABA) treatment||Ristova et al., (2018): Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis. Plant Journal. DOI: 10.1111/tpj.14034.||9||Jan/16/2019|
|Adaptive diversification of growth allometry in the plant Arabidopsis thaliana||The file contains average trait values per accession for plant life cycle duration ('LifeCyleDuration', days), total fruit number ('FruitNumber'), final rosette dry mass ('rosetteDM', mg), absolute growth rate ('GrowthRate', mg d-1), relative growth rate ('RGR', mg d-1 g-1), and the scaling exponent ('ScalingExponent').
Accessions are identified with their 1001-genomes IDs (http://1001genomes.org/).||5||Apr/03/2019|
|Atwell et. al, Nature 2010||GWAS of 107 phenotypes in Arabidopsis thaliana inbred lines using ~250k SNPs in 199 accessions||107||Aug/13/2016|
|Auxin (IAA) treatment||Ristova et al., (2018): Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis. Plant Journal. DOI: 10.1111/tpj.14034.||9||Jan/16/2019|
|Control (C) treatment||Ristova et al., (2018): Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis. Plant Journal. DOI: 10.1111/tpj.14034.||9||Jan/16/2019|
|Cytokinin (CK) treatment||Ristova et al., (2018): Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis. Plant Journal. DOI: 10.1111/tpj.14034.||9||Jan/16/2019|
|DAAR||GWAS of three mass features of N-malonyl-D-allo-isoleucine in Arabidopsis thaliana inbred lines using ~250k SNPs in 416 accessions||3||Sep/05/2017|
|Flowering time in simulated seasons||Two independent experiments were conducted in this study. Experiment 1 was done with a mapping population of 360 accessions (33), and Experiment 2 used a set of 473 accessions. Each accession in each experiment had four replicates under each of the four growth conditions (two planting seasons by two locations).
Both experiments were conducted in two walk-in growth chambers (AR-916, Percival Scientific) that were programmed to cycle the local climates every 5 min from the simulated weather files. The simulated climates were generated by using SolarCalc (35) with sunrise and sunset, light spectrum, temperature, and relative humidity programmed to cycle throughout the day and the season according to 1975?2000 averages (Fig. S5). One chamber was simulating Spain (latitude 41.72091, longitude 2.957075) starting from March 1, and the other chamber was simulating Sweden (latitude 55.71226, longitude 13.207352) starting from May 1st on the first day when plants were put into the chambers.||34||Aug/13/2016|
|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).||28||Aug/20/2020|
|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. https://doi.org/10.1038/s41467-019-11483-4||1||Aug/27/2019|
|Inter-specific pollination of Arabidopsis thaliana and Malcolmia littorea||Degree 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.||1||May/10/2019|
|Ion Concentration||Plants 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 . 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 ) 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.||19||Mar/21/2017|
|Kerdaffrec et al. 2016||Germination 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.||1||Mar/15/2018|
|Kerdaffrec et al. 2017||Germination 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).||6||Mar/15/2018|
|Lifetime fitness in Germany and Spain under rainfall manipulation||Data 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 worldclim.org (and derived metrics).||122||Jun/27/2019|
|Mejion||201 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 ||2||Aug/13/2016|
|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
|Root growth rates under nutrient deficiency||Data 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.