Find research datasets worth reusing

Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.

1,715

datasets available to search

ShareScore release 0.7.1

Dataset results

1,715 results for “Arabidopsis thaliana; Arabidopsis”

Learn how ShareScore rates datasets ↗

dryad28/100

Data from: Extreme QTL mapping of germination speed in Arabidopsis thaliana

Seed germination is a key life history transition for annual plants and partly determines lifetime performance and fitness. Germination speed, the elapsed time for a nondormant seed to germinate, is a poorly understood trait important for plants' competitiveness and fitness in fluctuating environments. Germination speed varied by 30% among 18 Arabidopsis thaliana populations measured, and exhibited weak negative correlation with flowering time and seed weight, with significant genotype effect (P < 0.005). To dissect the genetic architecture of germination speed, we developed the extreme QTL (X-QTL) mapping method in A. thaliana. The method has been shown in yeast to increase QTL mapping power by integrating selective screening and bulk-segregant analysis in a very large mapping population. By pooled genotyping of top 5% of rapid germinants from ~100 000 F3 individuals, three X-QTL regions were identified on chromosomes 1, 3 and 4. All regions were confirmed as QTL regions by sequencing 192 rapid germinants from an independent F3 selection experiment. Positional overlaps were found between X-QTLs and previously identified seed, life history and fitness QTLs. Our method provides a rapid mapping platform in A. thaliana with potentially greater power. One can also relate identified X-QTLs to the A. thaliana physical map, facilitating candidate gene identification.

opencc-zeroDec 2015View details →

dryad28/100

Data from: Chromosomal loci important for cotyledon opening under UV-B in Arabidopsis thaliana

BACKGROUND: Understanding of the genetic architecture of plant UV-B responses allows extensive targeted testing of candidate genes or regions, along with combinations of those genes, for placement in metabolic or signal transduction pathways. RESULTS: Composite interval mapping and single-marker analysis methods were used to identify significant loci for cotyledon opening under UV-B in four sets of recombinant inbred lines. In addition, loci important for canalization (stability) of cotyledon opening were detected in two mapping populations. One candidate locus contained the gene HY5. Mutant analysis demonstrated that HY5 was required for UV-B-specific cotyledon opening. CONCLUSIONS: Structured mapping populations provide key information on the degree of complexity in the genetic control of UV-B-induced cotyledon opening in Arabidopsis. The loci identified using quantitative trait analysis methods are useful for follow-up testing of candidate genes.

opencc-zeroDec 2011View details →

dryad28/100

Data from: The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluskan herbivores

Although slugs and snails play important roles in terrestrial ecosystems and cause considerable damage on a variety of crop plants, knowledge about the mechanisms of plant immunity to mollusks is limited. We found slugs to be natural herbivores of Arabidopsis thaliana and therefore investigated possible resistance mechanisms of this species against several molluskan herbivores. Treating wounded leaves with the mucus residue ("slime trail") of the Spanish slug Arion lusitanicus increased wound-induced jasmonate levels, suggesting the presence of defense elicitors in the mucus. Plants deficient in jasmonate biosynthesis and signaling suffered more damage by molluskan herbivores in the laboratory and in the field, demonstrating that JA-mediated defenses protect A. thaliana against slugs and snails. Furthermore, experiments using A. thaliana mutants with altered levels of specific glucosinolate classes revealed the importance of aliphatic glucosinolates in defending leaves and reproductive structures against mollusks. The presence in mollusk feces of known and novel metabolites arising from glutathione conjugation with glucosinolate hydrolysis products suggests that molluskan herbivores actively detoxify glucosinolates. Higher levels of aliphatic glucosinolates were found in plants during the night compared to the day, which correlated well with the nocturnal activity rhythms of slugs and snails. Our data highlight the function of well-known anti-herbivore defense pathways in resistance against slugs and snails and suggest an important role for the diurnal regulation of defense metabolites against nocturnal molluskan herbivores.

opencc-zeroDec 2012View details →

dryad28/100

Data from: Identification of the submergence tolerance QTL come quick drowning1 (CQD1) in Arabidopsis thaliana

Global climate change is predicted to increase water precipitation fluctuations and lead to localized prolonged floods in agricultural fields and natural plant communities. Thus, understanding the genetic basis of submergence tolerance is crucial in order to improve plant survival under these conditions. In this study, we performed a quantitative trait locus (QTL) analysis in Arabidopsis to identify novel candidate genes for increased submergence tolerance by using Kas-1 and Col (gl1) parental accessions and their derived recombinant inbred lines (RILs). We measured survival after submergence in dark for a 13-day period and used median lethal time, LT50 values for the QTL analysis. A major QTL, the Come Quick, Drowning (CQD1) locus, was detected in 2 independent experiments on the lower arm of chromosome 5 involved in higher submergence tolerance in the parental accession Kas-1. For fine-mapping, we then constructed near isogenic lines (NILs) by backcrossing the CQD1 QTL region. We also analyzed QTL regions related to size, leaf number, flowering, or survival in darkness and none of the QTL related to these traits overlapped with CQD1. The submergence tolerance QTL, CQD1, region detected in this study includes genes that have potential to be novel candidates effecting submergence tolerance such as trehalose-6-phosphate phosphatase and respiratory burst oxidase protein D. Gene expression and functional analysis for these genes under submergence would reveal the significance of these novel candidates and provide new perspectives for understanding genetic basis of submergence tolerance.

opencc-zeroDec 2016View details →

dryad28/100

Data from: Multiple simultaneous treatments change plant response from adaptive parental effects to within-generation plasticity, in Arabidopsis thaliana

In general, studies on plant phenotypic plasticity concentrate on plant responses to different levels of a single environmental factor. Under natural conditions, however, multiple environmental factors often vary simultaneously. I studied the consequences for lifetime fitness caused by single treatments or treatment combinations by investigating patterns of phenotypic plasticity within and between generations. The parental plants (3 genotypes of the annual plant Arabidopsis thaliana) received zero, one or two stress treatments at an early life-stage. The treatments included wounding, shading, chilling, and their pairwise combinations. In the second generation, offspring of treated plants received either the parental or no treatment. Offspring of non-treated plants were reared under all treatment conditions. Plants responded strongly to the treatments, especially through delayed reproduction, which positively affected lifetime fitness. Notably, treatment combinations triggered stronger plastic responses on average. Because the delay in reproduction was offset by a delay in senescence, the treatments resulted in a fitness gain instead of a loss. However, under adverse environmental conditions, this delay represents a potential fitness cost, especially when the time for reproduction is limited. The treatments wounding and shading triggered parental effects that increased fitness only in plants that themselves received the treatment. Untreated offspring of wounded or shaded parents performed like control plants. Also, these parental effects were not accompanied by potential fitness costs, such as delayed reproduction. Chilling triggered genotype-specific parental effects that increased or reduced fitness. Of the treatment combinations only wounding and shading resulted in genotype-specific parental effects that increased or reduced fitness independently of offspring treatment. These results suggest that the response of annual plants to treatment combinations triggers predominantly within-generation plastic responses that include potential fitness costs, which cannot be inferred from studies that manipulate environmental factors individually. Therefore, single treatment studies likely underestimate the costs of plasticity in natural environments.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Phenological and fitness responses to climate warming depend upon genotype and competitive neighborhood in Arabidopsis thaliana

1. Increasing temperatures during climate change are known to alter the phenology across diverse plant taxa, but the evolutionary outcomes of these shifts are poorly understood. Moreover, plant temperature-sensing pathways are known to interact with competition-sensing pathways, yet there remains little experimental evidence for how genotypes varying in temperature responsiveness react to warming in realistic competitive settings. 2. We compared flowering time and fitness responses to warming and competition for two near isogenic lines (NILs) of Arabidopsis thaliana transgressively segregating temperature-sensitive and -insensitive alleles for major-effect flowering time genes. We grew focal plants of each genotype in intraspecific and interspecific competition in four treatments contrasting daily temperature profiles in summer and fall under contemporary and warmed conditions. We measured phenology and fitness of focal plants to quantify plastic responses to season, temperature, and competition and the dependence of these responses on flowering time genotype. 3. The temperature-insensitive NIL was constitutively early-flowering and less fit, except in a future-summer climate in which its fitness was higher than the later flowering, temperature-sensitive NIL in low competition. The late-flowering NIL showed accelerated flowering in response to intragenotypic competition and to increased temperature in the summer but delayed flowering in the fall. However, its fitness fell with rising temperatures in both seasons, and in the fall its marginal fitness gain from decreasing competition was diminished in the future. 4. Functional alleles at temperature-responsive genes were necessary for plastic responses to season, warming, and competition. However, the plastic genotype was not the most fit in every experimental condition, becoming less fit than the temperature-canalized genotype in the warm summer treatment. 5. Climate change is often predicted to have deleterious effects on plant populations, and our results show how increased temperatures can act through genotype-dependent phenology to decrease fitness. Furthermore, plasticity is not necessarily adaptive in rapidly changing environments since a non-plastic genotype proved fitter than a plastic genotype in a warming climate treatment.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

Anticipating the effect of climate change on plants requires understanding its evolutionary consequence on traits and genes in complex realistic environments. How seasonal variation has an impact on the dynamics of adaptation in natural populations remains unclear. We simulated adaptation to different climate change scenarios, grounding our analysis in experimental data and explicitly exploring seasonal variation. Seasonal variation dramatically affected the dynamics of adaptation: Marked seasonality led to genetic differentiation within the population to different seasonal periods, whereas low seasonality led to a single population with fast-evolving fitness. Our results suggest the prevalence of phenotypic plasticity across environmental conditions in determining how climate change will shift selection on traits and loci. In this unpredictable context, maintaining broad genomic diversity is critical.

opencc-zeroDec 2015View details →

dryad28/100

CLSM data of CLE40, CLV3, WUS, BAM1, and CLV1 reporter lines in Arabidopsis thaliana

Stem cell homeostasis in plant shoot meristems requires tight coordiantion between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)–receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.

opencc-zeroJun 2021View details →

zenodo28/100

Arabidopsis thaliana real dataset

Open the record for dataset details and reuse information.

opencc-by-4.0Nov 2023View details →

zenodo28/100

Chromatograms: Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana

Sei-0 and Col-0 Arabidopsis thaliana plants were inoculated with WT and mutant cabbage leaf curl virus and PCR amplicons targeting the Rep gene region were Sanger-sequenced, as documented (Hoyer et al. <a href="http://doi.org/10.1094/PBIOMES-12-21-0077-R">2022</a>).

opencc-by-4.0Nov 2021View details →

dryad28/100

Effects of primary seed dormancy on life-time fitness of Arabidopsis thaliana in the field

Background and Aims Seed dormancy determines the environmental niche of plants in seasonal environments, and has consequences for plant performance that potentially go far beyond the seed and seedling stages. In this study, we examined the cascading effects of seed dormancy on the expression of subsequent life-history traits and fitness in the annual herb Arabidopsis thaliana. Methods We planted seeds of >200 recombinant inbred lines (RIL) derived from a cross between two locally adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified the relationship between primary seed dormancy and the expression of subsequent life-history traits and fitness in the RIL population with path analysis. To examine effects of differences in dormancy on relative fitness of the two parental genotypes, we planted dormant seeds during the seed dispersal period and non-dormant seeds during the germination period of the local population. Key Results In the RIL population, strong primary dormancy was associated with high seedling survival, but with low adult survival and fecundity, and the path analysis indicated that this could be explained by effects on germination timing, rosette size, and flowering start. The relationship between primary seed dormancy and germination proportion varied among years, and this was associated with differences in seasonal changes in soil moisture. The planting of dormant and nondormant seeds indicated that the lower primary dormancy of the local Swedish genotype contributed to its higher germination proportion in two years, and to its higher fecundity in one year. Conclusions Our results show that seed dormancy affects trait expression and fitness components across the life cycle, and suggest that among-year variation in the incidence of drought during the germination period should be considered when predicting the consequences of climatic change for population growth and evolution.

opencc-zeroFeb 2022View details →

zenodo28/100

Impact of U2-type Introns on Splice Site Prediction in Arabidopsis Thaliana using Deep Learning

Open the record for dataset details and reuse information.

opencc-by-4.0May 2024View details →

zenodo28/100