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References

  • Ballaré, C.L., Sanchez, R.A., Scopel, A.L. and Ghersa, C.M. (1988) Morphological responses of Datura ferox L seedlings to the presence of neighbors – their relationships with canopy microclimate. Oecologia, 76, 288293.
  • Ballaré, C.L., Scopel, A.L. and Sánchez, R.A. (1990) Far-red radiation reflected from adjacent leaves: an early signal of competition in plant canopies. Science, 247, 329332.
  • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Methodol, 57, 289300.
  • Blanco, F., Garretón, V., Frey, N., Dominguez, C., Pérez-Acle, T., Van der Straeten, D., Jordana, X. and Holuigue, L. (2005) Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis. Plant Mol. Biol. 59, 927944.
  • Bowling, S.A., Ailan, G., Hui, C., Gordon, A.S., Klessig, D.F. and Dong, X. (1994) A mutation in Arabidopsis that leads to constitutive expression of systemic acquired resistance. Plant Cell, 6, 18451857.
  • Cao, H., Glazebrook, J., Clarke, J.D., Volko, S. and Dong, X. (1997) The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell, 88, 5763.
  • Cerrudo, I., Keller, M.M., Cargnel, M.D., Demkura, P.V., De Wit, M., Patitucci, M.S., Pierik, R., Pieterse, C.M.J. and Ballaré, C.L. (2012) Low Red:Far-Red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism. Plant Physiol. 158, 20422052.
  • Chini, A., Fonseca, S., Fernández, G. et al. (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature, 448, 666671.
  • Chow, W.S., Melis, A. and Anderson, J.M. (1990) Adjustments of photosystem stoichiometry in chloroplasts improve the quantum efficiency of photosynthesis. Proc. Natl Acad. Sci. USA 87, 75077511.
  • Chung, H.S., Koo, A.J., Gao, X., Jayanty, S., Thines, B., Jones, A.D. and Howe, G.A. (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol. 146, 952964.
  • Cipollini, D. (2004) Stretching the limits of plasticity: can a plant defend against both competitors and herbivores? Ecology, 85, 2837.
  • Clack, T., Mathews, S. and Sharrock, R.A. (1994) The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Mol. Biol. 25, 413427.
  • Colcombet, J. and Hirt, H. (2008) Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. Biochem. J. 413, 217226.
  • De Vos, M., Van Oosten, V.R., Poecke, R.M.P.V. et al. (2005) Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol. Plant Microbe In. 18, 923937.
  • Després, C., DeLong, C., Glaze, S., Liu, E. and Fobert, P.R. (2000) The Arabidopsis NPR1/NIM1 protein enhances the DNA binding activity of a subgroup of the TGA family of bZIP transcription factors. Plant Cell, 12, 279290.
  • Devlin, P.F., Yanovsky, M.J. and Kay, S.A. (2003) A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol. 133, 16171629.
  • Djakovic-Petrovic, T., De Wit, M., Voesenek, L.A.C.J. and Pierik, R. (2007) DELLA protein function in growth responses to canopy signals. Plant J. 51, 117126.
  • Ellis, C. and Turner, J.G. (2001) The Arabidopsis mutant cev1 has constitutively active jasmonate and ethylene signal pathways and enhanced resistance to pathogens. Plant Cell, 13, 10251033.
  • Faigón-Soverna, A., Harmon, F.G., Storani, L., Karayekov, E., Staneloni, R.J., Gassmann, W., Más, P., Casal, J.J., Kay, S. and Yanovsky, M.J. (2006) A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. Plant Cell, 18, 29192928.
  • Fan, W. and Dong, X. (2002) In vivo interaction between NPR1 and transcription factor TGA2 leads to salicylic acid-mediated gene activation in Arabidopsis. Plant Cell, 14, 13771389.
  • Fernandez-Calvo, P., Chini, A., Fernandez-Barbero, G. et al. (2011) The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell, 23, 701715.
  • Finlayson, S.A., Lee, I.J., Mullet, J.E. and Morgan, P.W. (1999) The mechanism of rhythmic ethylene production in sorghum. The role of phytochrome B and simulated shading. Plant Physiol. 120, 10831089.
  • Fonseca, S., Chini, A., Hamberg, M., Adie, B., Porzel, A., Kramell, R., Miersch, O., Wasternack, C. and Solano, R. (2009) (+)-7-iso-Jasmonoyl-L-isoleucine is the endogenous bioactive jasmonate. Nat. Chem. Biol. 5, 344350.
  • Franklin, K.A. (2008) Shade avoidance. New Phytol. 179, 930944.
  • Franklin, K.A., Praekelt, U., Stoddart, W.M., Billingham, O.E., Halliday, K.J. and Whitelam, G.C. (2003) Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis. Plant Physiol. 131, 13401346.
  • Fu, Z.Q., Yan, S., Saleh, A. et al. (2012) NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants. Nature, 486, 228232.
  • Genoud, T., Buchala, A.J., Chua, N.-H. and Métraux, J.-P. (2002) Phytochrome signalling modulates the SA-perceptive pathway in Arabidopsis. Plant J. 31, 8795.
  • Griebel, T. and Zeier, J. (2008) Light regulation and daytime dependency of inducible plant defenses in Arabidopsis: phytochrome signaling controls systemic acquired resistance rather than local defense. Plant Physiol. 147, 790801.
  • Islam, S.Z., Honda, Y. and Arase, S. (1998) Light-induced resistance of broad bean against Botrytis cinerea. J. Phytopathol. 146, 479485.
  • Islam, S.Z., Babadoost, M., Bekal, S. and Lambert, K. (2008) Red light-induced systemic disease resistance against root-knot nematode Meloidogyne javanica and Pseudomonas syringae pv. tomato DC 3000. J. Phytopathol. 156, 708714.
  • Izaguirre, M.M., Mazza, C.A., Biondini, M., Baldwin, I.T. and Ballaré, C.L. (2006) Remote sensing of future competitors: impacts on plants defenses. Proc. Natl Acad. Sci. USA 103, 71707174.
  • Keuskamp, D.H., Pollmann, S., Voesenek, L.A.C.J., Peeters, A.J.M. and Pierik, R. (2010) Auxin transport through PIN-FORMED 3 (PIN3) controls shade avoidance and fitness during competition. Proc. Natl Acad. Sci. USA 107, 2274022744.
  • King, E.O., Ward, M.K. and Raney, D.E. (1954) Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 44, 301307.
  • Kinkema, M., Fan, W. and Dong, X. (2000) Nuclear localization of NPR1 is required for activation of PR gene expression. Plant Cell, 12, 23392350.
  • Koornneef, A., Leon-Reyes, A., Ritsema, T., Verhage, A., Den Otter, F.C., Van Loon, L.C. and Pieterse, C.M.J. (2008) Kinetics of salicylate-mediated suppression of jasmonate signaling reveal a role for redox modulation. Plant Physiol. 147, 13581368.
  • Kozuka, T., Kobayashi, J., Horiguchi, G., Demura, T., Sakakibara, H., Tsukaya, H. and Nagatani, A. (2010) Involvement of auxin and brassinosteroid in the regulation of petiole elongation under the shade. Plant Physiol. 153, 16081618.
  • Kunkel, B.N. and Brooks, D.M. (2002) Cross talk between signaling pathways in pathogen defense. Curr. Opin. Plant Biol. 5, 325331.
  • Kurashige, N.S. and Agrawal, A.A. (2005) Phenotypic plasticity to light competition and herbivory in Chenopodium album (Chenopodiaceae). Am. J. Bot. 92(1), 2126.
  • Li, L., Ljung, K., Breton, G. et al. (2012) Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 26, 785790.
  • Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402408.
  • Lorenzo, O., Piqueras, R., Sanchez-Serrano, J.J. and Solano, R. (2003) ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. Plant Cell, 15, 165178.
  • Lorenzo, O., Chico, J.M., Sanchez-Serrano, J.J. and Solano, R. (2004) JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell, 16(7), 19381950.
  • Lorrain, S., Allen, T., Duek, P.D., Whitelam, G.C. and Fankhauser, C. (2008) Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 53, 312323.
  • Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 34483449.
  • Millenaar, F.F., Cox, M.C.H., van Berkel-de Jong, Y.E.M., Welschen, R.A.M., Pierik, R., Voesenek, L.A.J.C. and Peeters, A.J.M. (2005) Ethylene-induced differential growth of petioles in Arabidopsis. Analyzing natural variation, response kinetics, and regulation. Plant Physiol. 137, 9981008.
  • Mittler, R. (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci. 11, 1519.
  • Moreno, J.E., Tao, Y., Chory, J. and Ballaré, C.L. (2009) Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity. Proc. Natl Acad. Sci. USA 106, 49354940.
  • Morgan, D.C. and Smith, H. (1976) Linear relationship between phytochrome photoequilibrium and growth in plants under simulated natural radiation. Nature, 262, 210212.
  • Mou, Z., Fan, W. and Dong, X. (2003) Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell, 113, 935944.
  • Peng, J. and Harberd, N.P. (1997) Gibberellin deficiency and response mutations suppress the stem elongation phenotype of phytochrome-deficient mutants of Arabidopsis. Plant Physiol. 113, 10511058.
  • Pierik, R., Visser, E.J.W., De Kroon, H. and Voesenek, L.A.C.J. (2003) Ethylene is required in tobacco to successfully compete with proximate neighbours. Plant, Cell Environ. 26, 12291234.
  • Pierik, R., Whitelam, G.C., Voesenek, L.A.C.J., de Kroon, H. and Visser, E.J.W. (2004) Canopy studies on ethylene-insensitive tobacco identify ethylene as a novel element in blue light and plant-plant signaling. Plant J. 38, 310319.
  • Pieterse, C.M.J., Van der Does, D., Zamioudis, C., Leon-Reyes, A. and Van Wees, S.C.M. (2012) Hormonal modulation of plant immunity. Annu. Rev. Cell Dev. Biol. 28, 489521.
  • Pré, M., Atallah, M., Champion, A., De Vos, M., Pieterse, C.M.J. and Memelink, J. (2008) The AP2/ERF domain transcription factor ORA59 integrates jasmonic acid and ethylene signals in plant defense. Plant Physiol. 147, 13471357.
  • Rahman, M.Z., Khanam, H., Ueno, M., Kihara, J., Honda, Y. and Arase, S. (2010) Suppression by red light irradiation of Corynespora leaf spot of cucumber caused by Corynespora cassiicola. J. Phytopathol. 158, 378381.
  • R Development Core Team (2009) R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. ISBN 3-900051-07-0, URL http://www.R-project.org.
  • Reed, J.W., Nagpal, P., Poole, D.S., Furuya, M. and Chory, J. (1993) Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell, 5, 147157.
  • Ryals, J., Weymann, K., Lawton, K. et al. (1997) The Arabidopsis NIM1 protein shows homology to the mammalian transcription factor inhibitor IκB. Plant Cell, 9, 425439.
  • Salter, M.G., Franklin, K.A. and Whitelam, G.C. (2003) Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature, 426, 680683.
  • Sessa, G., Carabelli, M., Sassi, M., Ciolfi, A., Possenti, M., Mittempergher, F., Becker, J., Morelli, G. and Ruberti, I. (2005) A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev. 19, 28112815.
  • Smith, H. (2000) Phytochromes and light signal perception by plants - an emerging synthesis. Nature, 407, 585591.
  • Smith, H. and Holmes, M.G. (1977) The function of phytochrome in the natural environment? III. Measurement and calculation of phytochrome photoequilibria. Photochem. Photobiol. 25, 547550.
  • Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 3. doi: 10.2202/1544-6115.1027.
  • Spoel, S.H. and Dong, X. (2008) Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe, 3, 348351.
  • Spoel, S.H., Koornneef, A., Claessens, S.M.C. et al. (2003) NPR1 modulates cross-talk between salicylate- and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell, 15, 760770.
  • Spoel, S.H., Mou, Z., Tada, Y., Spivey, N.W., Genschik, P. and Dong, X. (2009) Proteasome-mediated turnover of the transcription coactivator NPR1 plays dual roles in regulating plant immunity. Cell, 137, 860872.
  • Sultan, S.E. (2010) Plant developmental responses to the environment: eco-devo insights. Curr. Opin. Plant Biol. 13, 96101.
  • Suzuki, A., Suriyagoda, L., Shigeyama, T. et al. (2011) Lotus japonicus nodulation is photomorphogenetically controlled by sensing the red/far red (R/FR) ratio through jasmonic acid (JA) signaling. Proc. Natl Acad. Sci. USA 108, 1683716842.
  • Tada, Y., Spoel, S.H., Pajerowska-Mukhtar, K., Mou, Z., Song, J., Wang, C., Zuo, J. and Dong, X. (2008) Plant immunity requires conformational changes of NPR1 via S-nitrosylation and thioredoxins. Science, 321, 952956.
  • Tao, Y., Ferrer, J.-L., Ljung, K. et al. (2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell, 133, 164176.
  • Thines, B., Katsir, L., Melotto, M., Niu, Y., Mandaokar, A., Liu, G., Nomura, K., He, S.Y., Howe, G.A. and Browse, J. (2007) JAZ repressor proteins are targets of the SCFCOI1 complex during jasmonate signalling. Nature, 448, 661665.
  • Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R. and Leunissen, J.A. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35, W71W74.
  • Vandenbussche, F., Pierik, R., Millenaar, F.F., Voesenek, L.A.C.J. and Van der Straeten, D. (2005) Reaching out of the shade. Curr. Opin. Plant Biol. 8, 462468.
  • Walters, R.G. (2005) Towards an understanding of photosynthetic acclimation. J. Exp. Bot. 56, 435447.
  • Wang, D., Amornsiripanitch, N. and Dong, X. (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog. 2, 10421050.
  • Wang, H., Jiang, Y.P., Yu, H.J., Xia, X.J., Shi, K., Zhou, Y.H. and Yu, J.Q. (2010) Light quality affects incidence of powdery mildew, expression of defence-related genes and associated metabolism in cucumber plants. Eur. J. Plant Pathol. 127, 125135.
  • Wu, Y., Zhang, D., Chu, J.Y., Boyle, P., Wang, Y., Brindle, I.D., De Luca, V. and Després, C. (2012) The Arabidopsis NPR1 protein is a receptor for the plant defense hormone salicylic acid. Cell, 28, 639647.
  • Xu, L., Liu, F., Lechner, E., Genschik, P., Crosby, W.L., Ma, H., Peng, W., Huang, D. and Xie, D. (2002) The SCFCOI1 ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis. Plant Cell, 14, 19191935.
  • Zhai, Q., Li, C.-B., Zheng, W., Wu, X., Zhao, J., Zhou, G., Jiang, H., Sun, J., Lou, Y. and Li, C. (2007) Phytochrome chromophore deficiency leads to overproduction of jasmonic acid and elevated expression of jasmonate-responsive genes in Arabidopsis. Plant Cell Physiol. 48, 10611071.