VirtualPlant: A Software Platform to Support Systems Biology Research

Self Cite

Significance Species display a range of plastic phenotypes that presumably have evolved as a result of adaptation to heterogeneous environments. We asked whether the genetic mechanisms that underlie adaptation across populations also determine the response of an individual plant to environmental cues in Arabidopsis . Using an integrative root phenotyping approach, genes that underlie natural variation in root architecture across populations were shown to control plasticity responses within an individual. Together, our results uncover a genetic mechanism underlying the phenotypic plasticity of an individual and phenotypic diversity across natural variants.

Section: Identification Of Candidate Genes Underlying Natural Variatimentioning

confidence: 95%

Integration of responses within and acrossArabidopsisnatural accessions uncovers loci controlling root systems architecture

Rosas

Cibrián-Jaramillo

Ristova

et al. 2013

Self Cite

“…To simplify the analysis of our results and to provide an initial insight into how AFB3 regulates gene expression in response to nitrate, we analyzed our data using the Sungear tool (18) available at the VirtualPlant webpage (http://www.virtualplant.org) (19). Sungear allows for the visualization and analysis of multiple datasets to identify genes that are unique or are shared by different gene lists (18,20).…”

Section: Resultsmentioning

confidence: 99%

Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response ofArabidopsis thalianaroots

Vidal

Moyano

Riveras

et al. 2013

196

179

Auxin is a key phytohormone regulating central processes in plants. Although the mechanism by which auxin triggers changes in gene expression is well understood, little is known about the specific role of the individual members of the TIR1/AFB auxin receptors, Aux/IAA repressors, and ARF transcription factors and/or molecular pathways acting downstream leading to plant responses to the environment. We previously reported a role for AFB3 in coordinating primary and lateral root growth to nitrate availability. In this work, we used an integrated genomics, bioinformatics, and molecular genetics approach to dissect regulatory networks acting downstream of AFB3 that are activated by nitrate in roots. We found that the NAC4 transcription factor is a key regulatory element controlling a nitrate-responsive network, and that nac4 mutants have altered lateral root growth but normal primary root growth in response to nitrate. This finding suggests that AFB3 is able to activate two independent pathways to control root system architecture. Our systems approach has unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate.systems biology | nitrogen | Sungear

“…The functional processes impacted by IMI, CLO, and SA were determined using MapMan (16) and BioMaps in Virtual Plant (17). Results with the three compounds were qualitatively similar, but the magnitude of the response (number of genes associated with a given process) was consistently greater with IMI treatment compared with SA and CLO.…”

Section: Neonicotinoids Induce Global Transcriptional Response Similamentioning

confidence: 99%

Neonicotinoid insecticides induce salicylate-associated plant defense responses

Ford

Casida²,

Chandran³

et al. 2010

167

136

Neonicotinoid insecticides control crop pests based on their action as agonists at the insect nicotinic acetylcholine receptor, which accepts chloropyridinyl-and chlorothiazolyl-analogs almost equally well. In some cases, these compounds have also been reported to enhance plant vigor and (a)biotic stress tolerance, independent of their insecticidal function. However, this mode of action has not been defined. Using Arabidopsis thaliana, we show that the neonicotinoid compounds, imidacloprid (IMI) and clothianidin (CLO), via their 6-chloropyridinyl-3-carboxylic acid and 2-chlorothiazolyl-5-carboxylic acid metabolites, respectively, induce salicylic acid (SA)-associated plant responses. SA is a phytohormone best known for its role in plant defense against pathogens and as an inducer of systemic acquired resistance; however, it can also modulate abiotic stress responses. These neonicotinoids effect a similar global transcriptional response to that of SA, including genes involved in (a)biotic stress response. Furthermore, similar to SA, IMI and CLO induce systemic acquired resistance, resulting in reduced growth of a powdery mildew pathogen. The action of CLO induces the endogenous synthesis of SA via the SA biosynthetic enzyme ICS1, with ICS1 required for CLO-induced accumulation of SA, expression of the SA marker PR1, and fully enhanced resistance to powdery mildew. In contrast, the action of IMI does not induce endogenous synthesis of SA. Instead, IMI is further bioactivated to 6-chloro-2-hydroxypyridinyl-3-carboxylic acid, which is shown here to be a potent inducer of PR1 and inhibitor of SA-sensitive enzymes. Thus, via different mechanisms, these chloropyridinyl-and chlorothiazolylneonicotinoids induce SA responses associated with enhanced stress tolerance.N eonicotinoids are the newest of the three major classes of insecticides, which also include the organophosphorus compounds and pyrethroids. Imidacloprid (IMI), with a chloropyridinyl (Cl-pyr) substituent, is the most important neonicotinoid, used primarily as a systemic compound absorbed and translocated by plants to control sucking insect pests (1). The neonicotinoids clothianidin (2) (CLO) and a metabolic precursor, the oxadiazine compound thiamethoxam (3, 4), which have chlorothiazolyl (Cl-thia) substituents, are also extensively used as systemic insecticides in plants. The neonicotinoids IMI and CLO are oxidatively cleaved in planta to 6-chloropyridinyl-3-carboxylic acid (CPA) and 2-chlorothiazolyl-5-carboxylic acid (CTA), respectively, among other metabolites (5). In studying metabolism of neonicotinoids in spinach (5) under insect-free conditions, we sometimes observed enhancement of foliage growth, plant vigor, and drought-tolerance. These remarkable effects of neonicotinoids directly on plants, independent of controlling insect pests, have also been noted by many researchers and farmers and documented in both research publications and patent disclosures, especially for IMI (6-8) and the CLO precursor, thiamethoxam (9). In addition, treatment with IMI...