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Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

https://doi.org/10.1101/031088
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS‐1A promoter.
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Phytochrome regulated gene expression
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Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716
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Weighted gene coexpression network analysis strategies applied to mouse weight
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Control of carbon partitioning by light quality mediated by phytochrome
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Principal component analysis
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Different Plant Hormones Regulate Similar Processes through Largely Nonoverlapping Transcriptional Responses
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Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants
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Analysis of a tomato introgression line, IL8-3, with increased Brix content
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PIFs: pivotal components in a cellular signaling hub
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Interaction of a GATA factor with -acting elements involved in light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in
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Critical Role for CCA1 and LHY in Maintaining Circadian Rhythmicity in Arabidopsis
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Proximity signal and shade avoidance differences between early and late successional trees
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Regulation of flowering time by light quality
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Spatially restricted microRNA directs leaf polarity through ARGONAUTE1
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The tomato genome sequence provides insights into fleshy fruit evolution
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Is photomorphogenic shade avoidance adaptive? Perspectives from population biology
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The Arabidopsis Athb‐2 and ‐4 genes are strongly induced by far‐red‐rich light
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The rosette habit of Arabidopsis thaliana is dependent upon phytochrome action: novel phytochromes control internode elongation and flowering time
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The tomato I‐box binding factor LeMYBI is a member of a novel class of Myb‐like proteins
inferredcites →https://doi.org/10.1073/pnas.1210955109openalex-snapshot
Models and tests of optimal density and maximal yield for crop plants
inferredcites →https://doi.org/10.1073/pnas.1309606110openalex-snapshot
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
inferredcites →https://doi.org/10.1073/pnas.85.19.7089openalex-snapshot
An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene.
inferredcites →https://doi.org/10.1073/pnas.95.12.7197openalex-snapshot
High temperature promotes auxin-mediated hypocotyl elongation in Arabidopsis
inferredcites →https://doi.org/10.1086/285860openalex-snapshot
Testing the Adaptive Plasticity Hypothesis: Density-Dependent Selection on Manipulated Stem Length in Impatiens capensis
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/genetics/141.3.1147openalex-snapshot
An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL.
inferredcites →https://doi.org/10.1093/icb/43.3.459openalex-snapshot
The Adaptive Evolution of Plasticity: Phytochrome-Mediated Shade Avoidance Responses
inferredcites →https://doi.org/10.1093/jxb/eri070openalex-snapshot
Application of metabolite profiling to the identification of traits in a population of tomato introgression lines
inferredcites →https://doi.org/10.1093/pcp/pch125openalex-snapshot
Degradation of Phytochrome Interacting Factor 3 in Phytochrome-Mediated Light Signaling
inferredcites →https://doi.org/10.1101/gad.1201404openalex-snapshot
The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
inferredcites →https://doi.org/10.1101/gad.14.15.1958openalex-snapshot
FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of Arabidopsis development
inferredcites →https://doi.org/10.1101/gad.364005openalex-snapshot
A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis
inferredcites →https://doi.org/10.1101/gad.432607openalex-snapshot
Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity
inferredcites →https://doi.org/10.1101/gad.5.3.484openalex-snapshot
AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes.
inferredcites →https://doi.org/10.1104/pp.008110openalex-snapshot
Molecular Characterization of a Heteromeric ATP-Citrate Lyase That Generates Cytosolic Acetyl-Coenzyme A in Arabidopsis,
inferredcites →https://doi.org/10.1104/pp.103.4.1115openalex-snapshot
Effects of Blue and Red Light on Expression of Nuclear Genes Encoding Chloroplast Glyceraldehyde-3-Phosphate Dehydrogenase of Arabidopsis thaliana
inferredcites →https://doi.org/10.1104/pp.104.042176openalex-snapshot
Genome-Wide ORFeome Cloning and Analysis of Arabidopsis Transcription Factor Genes
inferredcites →https://doi.org/10.1104/pp.108.133496openalex-snapshot
Auxin and Ethylene Regulate Elongation Responses to Neighbor Proximity Signals Independent of Gibberellin and DELLA Proteins in Arabidopsis
inferredcites →https://doi.org/10.1104/pp.110.156802openalex-snapshot
Involvement of Auxin and Brassinosteroid in the Regulation of Petiole Elongation under the Shade
inferredcites →https://doi.org/10.1104/pp.111.192518openalex-snapshot
The Developmental Trajectory of Leaflet Morphology in Wild Tomato Species
inferredcites →https://doi.org/10.1104/pp.112.201921openalex-snapshot
Stem Transcriptome Reveals Mechanisms to Reduce the Energetic Cost of Shade-Avoidance Responses in Tomato
inferredcites →https://doi.org/10.1104/pp.113.217802openalex-snapshot
Identification of Novel Loci Regulating Interspecific Variation in Root Morphology and Cellular Development in Tomato
inferredcites →https://doi.org/10.1104/pp.113.221549openalex-snapshot
Dynamics of the Shade-Avoidance Response in Arabidopsis
inferredcites →https://doi.org/10.1104/pp.119.3.909openalex-snapshot
Phytochrome D Acts in the Shade-Avoidance Syndrome in Arabidopsis by Controlling Elongation Growth and Flowering Time1
inferredcites →https://doi.org/10.1104/pp.122.3.621openalex-snapshot
Shade Avoidance Responses. Driving Auxin along Lateral Routes
inferredcites →https://doi.org/10.1104/pp.124.1.39openalex-snapshot
RSF1, an Arabidopsis Locus Implicated in Phytochrome A Signaling
inferredcites →https://doi.org/10.1104/pp.88.4.1323openalex-snapshot
Expression of Light-Harvesting Chlorophyll a/b-Protein Genes Is Phytochrome-Regulated in Etiolated Arabidopsis thaliana Seedlings
inferredcites →https://doi.org/10.1105/tpc.016097openalex-snapshot
An Arabidopsis Callose Synthase, GSL5, Is Required for Wound and Papillary Callose Formation
inferredcites →https://doi.org/10.1105/tpc.104.025643openalex-snapshot
A Novel Molecular Recognition Motif Necessary for Targeting Photoactivated Phytochrome Signaling to Specific Basic Helix-Loop-Helix Transcription Factors[W]
inferredcites →https://doi.org/10.1105/tpc.104.026211openalex-snapshot
Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-Citrate Lyase in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.105.031625openalex-snapshot
Auxin and Light Control of Adventitious Rooting in Arabidopsis Require ARGONAUTE1
inferredcites →https://doi.org/10.1105/tpc.105.035840openalex-snapshot
Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice andArabidopsis [W]
inferredcites →https://doi.org/10.1105/tpc.109.067728openalex-snapshot
Jasmonate and Phytochrome A Signaling in Arabidopsis Wound and Shade Responses Are Integrated through JAZ1 Stability
inferredcites →https://doi.org/10.1105/tpc.109.072280openalex-snapshot
Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes
inferredcites →https://doi.org/10.1105/tpc.113.112391openalex-snapshot
A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines
inferredcites →https://doi.org/10.1105/tpc.114.126037openalex-snapshot
SAUR Inhibition of PP2C-D Phosphatases Activates Plasma Membrane H+-ATPases to Promote Cell Expansion in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.114.130112openalex-snapshot
Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context
inferredcites →https://doi.org/10.1105/tpc.9.4.491openalex-snapshot
A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene.
inferredcites →https://doi.org/10.1111/j.1365-3040.1993.tb00489.xopenalex-snapshot
Impaired phytochrome‐mediated shade‐avoidance responses in the aurea mutant of tomato
inferredcites →https://doi.org/10.1111/j.1365-3040.1993.tb00903.xopenalex-snapshot
Modulation of leaf elongation, tiller appearance and tiller senescence in spring barley by far‐red light
inferredcites →https://doi.org/10.1111/j.1365-3180.2010.00781.xopenalex-snapshot
Shade avoidance: an integral component of crop–weed competition
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
inferredcites →https://doi.org/10.1111/ppl.12099openalex-snapshot
Auxin‐mediated plant architectural changes in response to shade and high temperature
inferredcites →https://doi.org/10.1146/annurev.arplant.53.100301.135302openalex-snapshot
P HYTOCHROMES C ONTROL P HOTOMORPHOGENESIS BY D IFFERENTIALLY R EGULATED , I NTERACTING S IGNALING P ATHWAYS IN H IGHER P LANTS
inferredcites →https://doi.org/10.1146/annurev.pp.28.060177.002035openalex-snapshot
Comparative Photosynthesis of Sun and Shade Plants
inferredcites →https://doi.org/10.1186/1471-2105-4-25openalex-snapshot
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot
WGCNA: an R package for weighted correlation network analysis
inferredcites →https://doi.org/10.1186/1471-2229-10-58openalex-snapshot
Salt tolerance in Solanum pennellii: antioxidant response and related QTL
inferredcites →https://doi.org/10.1186/1471-2229-9-122openalex-snapshot
Identification of flowering genes in strawberry, a perennial SD plant
inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1371/journal.pgen.1002589openalex-snapshot
A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response
inferredcites →https://doi.org/10.1371/journal.pone.0090587openalex-snapshot
Interactions between Auxin, Microtubules and XTHs Mediate Green Shade- Induced Petiole Elongation in Arabidopsis
inferredcites →https://doi.org/10.1387/ijdb.051973jcopenalex-snapshot
Regulation of gene expression by light
inferredcites →https://doi.org/10.3389/fpls.2012.00202openalex-snapshot
A High-Throughput Method for Illumina RNA-Seq Library Preparation
inferredcites →https://doi.org/10.4161/psb.25447openalex-snapshot
Homeodomain-Leucine zipper II family of transcription factors to the limelight
inferredcites →https://doi.org/10.4161/psb.4.6.8359openalex-snapshot
Callose synthesis in higher plants

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9780470015902.a0029555openalex-snapshot
Phenotypic and Developmental Plasticity in Plants
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2018.09.023openalex-snapshot
Blue light attenuation mediates morphological and architectural acclimation of Vitis vinifera cv. Malbec to shade and increases light capture
inferred← citeshttps://doi.org/10.1016/j.pbi.2016.03.005openalex-snapshot
Molecular control of crop shade avoidance
inferred← citeshttps://doi.org/10.1093/hr/uhac254openalex-snapshot
Promoter replacement of ANT1 induces anthocyanin accumulation and triggers the shade avoidance response through developmental, physiological and metabolic reprogramming in tomato
inferred← citeshttps://doi.org/10.1093/jxb/erx295openalex-snapshot
Multiple links between shade avoidance and auxin networks
inferred← citeshttps://doi.org/10.1093/plphys/kiag379openalex-snapshot
Phytochrome-interacting factors integrate environmental signals to regulate tomato growth and development
inferred← citeshttps://doi.org/10.1101/2025.03.18.643865openalex-snapshot
A tomato line hyposensitive to simulated proximity shade shows altered auxin-related gene expression and improved fruit yield under high-density field conditions
inferred← citeshttps://doi.org/10.1104/pp.20.00587openalex-snapshot
Mediator Subunit MED25 Physically Interacts with PHYTOCHROME INTERACTING FACTOR4 to Regulate Shade-Induced Hypocotyl Elongation in Tomato
inferred← citeshttps://doi.org/10.1111/nph.70384openalex-snapshot
A shade‐hyposensitive tomato line shows altered auxin homeostasis and higher fruit yield under high‐density field conditions
inferred← citeshttps://doi.org/10.1111/pce.12914openalex-snapshot
The shade‐avoidance syndrome: multiple signals and ecological consequences
inferred← citeshttps://doi.org/10.1111/ppl.14558openalex-snapshot
Evaluation of the roles of brassinosteroid, gibberellin and auxin for tomato internode elongation in response to low red:far‐red light
inferred← citeshttps://doi.org/10.3390/plants7040102openalex-snapshot
Multiple Pathways in the Control of the Shade Avoidance Response
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