Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
Tóm tắt
Từ khóa
Tài liệu tham khảo
JJ Casal, 2013, Photoreceptor signaling networks in plant responses to shade, Annu Rev Plant Biol, 64, 403, 10.1146/annurev-arplant-050312-120221
CL Ballaré, 1987, Early detection of neighbour plants by phytochrome perception of spectral changes in reflected sunlight, Plant Cell Environ, 10, 551, 10.1111/1365-3040.ep11604091
S Lorrain, 2008, Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors, Plant J, 53, 312, 10.1111/j.1365-313X.2007.03341.x
P Hornitschek, 2012, Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling, Plant J, 71, 699, 10.1111/j.1365-313X.2012.05033.x
L Li, 2012, Linking photoreceptor excitation to changes in plant architecture, Genes Dev, 26, 785, 10.1101/gad.187849.112
T Kozuka, 2010, Involvement of auxin and brassinosteroid in the regulation of petiole elongation under the shade, Plant Physiol, 153, 1608, 10.1104/pp.110.156802
Y Tao, 2008, Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants, Cell, 133, 164, 10.1016/j.cell.2008.01.049
T Djakovic-Petrovic, 2007, DELLA protein function in growth responses to canopy signals, Plant J, 51, 117, 10.1111/j.1365-313X.2007.03122.x
LV Kurepin, 2007, The interaction of light quality and irradiance with gibberellins, cytokinins and auxin in regulating growth of <italic>Helianthus annuus</italic> hypocotyls, Plant Cell Environ, 30, 147, 10.1111/j.1365-3040.2006.01612.x
M Carabelli, 2007, Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity, Genes Dev, 21, 1863, 10.1101/gad.432607
JE Moreno, 2009, Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity, Proc Natl Acad Sci U S A, 106, 4935, 10.1073/pnas.0900701106
W Kegge, 2013, Canopy light cues affect emission of constitutive and methyl jasmonate-induced volatile organic compounds in <italic>Arabidopsis thaliana</italic>, New Phytol, 200, 861, 10.1111/nph.12407
R Sozzani, 2011, High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype, Genome Biol, 12, 219, 10.1186/gb-2011-12-3-219
EA Winzeler, 1999, Functional characterization of the <italic>S</italic>. <italic>cerevisiae</italic> genome by gene deletion and parallel analysis, Science, 285, 901, 10.1126/science.285.5429.901
B Neumann, 2010, Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes, Nature, 464, 721, 10.1038/nature08869
RA Green, 2011, A high-resolution <italic>C</italic>.<italic>elegans</italic> essential gene network based on phenotypic profiling of a complex tissue, Cell, 145, 470, 10.1016/j.cell.2011.03.037
MF Yanik, 2011, Technologies for micromanipulating, imaging, and phenotyping small invertebrates and vertebrates, Annu Rev Biomed Eng, 13, 185, 10.1146/annurev-bioeng-071910-124703
S Atwell, 2010, Genome-wide association study of 107 phenotypes in <italic>Arabidopsis thaliana</italic> inbred lines, Nature, 465, 627, 10.1038/nature08800
B Berger, 2012, High-throughput phenotyping in plants, 9
EP Spalding, 2013, Image analysis is driving a renaissance in growth measurement, Curr Opin Plant Biol, 16, 100, 10.1016/j.pbi.2013.01.001
T Dornbusch, 2012, Measuring the diurnal pattern of leaf hyponasty and growth in <italic>Arabidopsis</italic>—a novel phenotyping approach using laser scanning, Funct Plant Biol, 39, 860, 10.1071/FP12018
A Bruex, 2012, A gene regulatory network for root epidermis cell differentiation in <italic>Arabidopsis</italic>, PLoS Genet, 8, e1002446, 10.1371/journal.pgen.1002446
M Sentandreu, 2011, Functional profiling identifies genes involved in organ-specific branches of the PIF3 regulatory network in <italic>Arabidopsis</italic>, Plant Cell, 23, 3974, 10.1105/tpc.111.088161
R Khanna, 2006, Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in <italic>Arabidopsis</italic> are necessary for optimal deetiolation, Plant Cell, 18, 2157, 10.1105/tpc.106.042200
JN Maloof, 2013, LeafJ: An ImageJ plugin for semi-automated leaf shape measurement, J Vis Exp, 71, e50028
G Sessa, 2005, A dynamic balance between gene activation and repression regulates the shade avoidance response in <italic>Arabidopsis</italic>, Genes Dev, 19, 2811, 10.1101/gad.364005
M Carabelli, 1996, Twilight-zone and canopy shade induction of the Athb-2 homeobox gene in green plants, Proc Natl Acad Sci U S A, 93, 3530, 10.1073/pnas.93.8.3530
I Roig-Villanova, 2007, Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins, EMBO J, 26, 4756, 10.1038/sj.emboj.7601890
C Sorin, 2009, ATHB4, a regulator of shade avoidance, modulates hormone response in <italic>Arabidopsis</italic> seedlings, Plant J, 59, 266, 10.1111/j.1365-313X.2009.03866.x
MG Salter, 2003, Gating of the rapid shade-avoidance response by the circadian clock in plants, Nature, 426, 680, 10.1038/nature02174
SA Finlayson, 1999, The mechanism of rhythmic ethylene production in sorghum, Plant Physiol, 119, 1083, 10.1104/pp.119.3.1083
R Pierik, 2004, Interactions between ethylene and gibberellins in phytochrome-mediated shade avoidance responses in tobacco, Plant Physiol, 136, 2928, 10.1104/pp.104.045120
FF Millenaar, 2005, Ethylene-induced differential growth of petioles in Arabidopsis. Analyzing natural variation, response kinetics, and regulation, Plant Physiol, 137, 998, 10.1104/pp.104.053967
J Smalle, 1997, Ethylene can stimulate <italic>Arabidopsis</italic> hypocotyl elongation in the light, Proc Natl Acad Sci U S A, 94, 2756, 10.1073/pnas.94.6.2756
R Pierik, 2004, Canopy studies on ethylene-insensitive tobacco identify ethylene as a novel element in blue light and plant-plant signalling, Plant J, 38, 310, 10.1111/j.1365-313X.2004.02044.x
SK Reddy, 2013, Abscisic acid regulates axillary bud outgrowth responses to the ratio of red to far-red light, Plant Physiol, 163, 1047, 10.1104/pp.113.221895
J Cagnola, 2012, Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato, Plant Physiol, 160, 1110, 10.1104/pp.112.201921
A Nagatani, 1991, Phytochrome B is not detectable in the <italic>hy3</italic> mutant of <italic>Arabidopsis</italic>, which Is deficient in responding to end-of-day far-red light treatments, Plant Cell Physiol, 32, 1119, 10.1093/oxfordjournals.pcp.a078177
JW Reed, 1993, Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout <italic>Arabidopsis</italic> development, Plant Cell, 5, 147, 10.1105/tpc.5.2.147
P Robson, 1993, Selected components of the shade-avoidance syndrome are displayed in a normal manner in mutants of <italic>Arabidopsis thaliana</italic> and <italic>Brassica rapa</italic> deficient in phytochrome B, Plant Physiol, 102, 1179, 10.1104/pp.102.4.1179
PF Devlin, 1999, Phytochrome D acts in the shade-avoidance syndrome in <italic>Arabidopsis</italic> by controlling elongation growth and flowering time, Plant Physiol, 119, 909, 10.1104/pp.119.3.909
AC Wollenberg, 2008, Acceleration of flowering during shade avoidance in <italic>Arabidopsis</italic> alters the balance between FLOWERING LOCUS C-mediated repression and photoperiodic induction of flowering, Plant Physiol, 148, 1681, 10.1104/pp.108.125468
SY Kim, 2008, Regulation of CONSTANS and FLOWERING LOCUS T expression in response to changing light quality, Plant Physiol, 148, 269, 10.1104/pp.108.122606
JM Jimenez-Gomez, 2010, Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis, PLoS Genet, 6, e1001100, 10.1371/journal.pgen.1001100
K Kanyuka, 2003, Mutations in the huge <italic>Arabidopsis</italic> gene <italic>BIG</italic> affect a range of hormone and light responses, Plant J, 35, 57, 10.1046/j.1365-313X.2003.01779.x
PD Cerdan, 2003, Regulation of flowering time by light quality, Nature, 423, 881, 10.1038/nature01636
KA Franklin, 2003, Phytochromes B, D, and E act redundantly to control multiple physiological responses in <italic>Arabidopsis</italic>, Plant Physiol, 131, 1340, 10.1104/pp.102.015487
F Robson, 2010, Jasmonate and phytochrome A signaling in <italic>Arabidopsis</italic> wound and shade responses are integrated through JAZ1 stability, Plant Cell, 22, 1143, 10.1105/tpc.109.067728
C Steindler, 1999, Shade avoidance responses are mediated by the ATHB-2 HD-zip protein, a negative regulator of gene expression, Development, 126, 4235, 10.1242/dev.126.19.4235
S Rolauffs, 2012, <italic>Arabidopsis</italic> COP1 and SPA genes are essential for plant elongation but not for acceleration of flowering time in response to a low red light to far-red light ratio, Plant Physiol, 160, 2015, 10.1104/pp.112.207233
KA Franklin, 2010, Phytochrome functions in <italic>Arabidopsis</italic> development, J Exp Bot, 61, 11, 10.1093/jxb/erp304
MM Neff, 1998, Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during <italic>Arabidopsis</italic> development, Plant Physiol, 118, 27, 10.1104/pp.118.1.27
JJ Casal, 1998, Conditional synergism between cryptochrome 1 and phytochrome B is shown by the analysis of <italic>phyA</italic>, <italic>phyB</italic>, and <italic>hy4</italic> simple, double, and triple mutants in <italic>Arabidopsis</italic>, Plant Physiol, 118, 19, 10.1104/pp.118.1.19
JJ Casal, 1995, Co-action between phytochrome B and HY4 in <italic>Arabidopsis thaliana</italic>, Planta, 197, 213, 10.1007/BF00202639
M Ahmad, 1997, The blue-light receptor cryptochrome 1 shows functional dependence on phytochrome A or phytochrome B in <italic>Arabidopsis thaliana</italic>, Plant J, 11, 421, 10.1046/j.1365-313X.1997.11030421.x
L Hennig, 1999, Functional interaction of cryptochrome 1 and phytochrome D, Plant J, 20, 289, 10.1046/j.1365-313X.1999.t01-1-00599.x
A Castillon, 2009, Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of <italic>Arabidopsis</italic> seedlings, Genetics, 182, 161, 10.1534/genetics.108.099887
T Usami, 2007, Roles for the N- and C-terminal domains of phytochrome B in interactions between phytochrome B and cryptochrome signaling cascades, Plant Cell Physiol, 48, 424, 10.1093/pcp/pcm012
T Usami, 2004, Cryptochromes and phytochromes synergistically regulate <italic>Arabidopsis</italic> root greening under blue light, Plant Cell Physiol, 45, 1798, 10.1093/pcp/pch205
G Meijer, 1965, The synergistic influence of a pre-irradiation on the photoinhibitton of gherkin seedlings, Photochem Photobiol, 4, 251, 10.1111/j.1751-1097.1965.tb05742.x
RM Hughes, 2012, Light-dependent, dark-promoted interaction between <italic>Arabidopsis</italic> cryptochrome 1 and phytochrome B proteins, J Biol Chem, 287, 22165, 10.1074/jbc.M112.360545
H Liu, 2011, The action mechanisms of plant cryptochromes, Trends Plant Sci, 16, 684, 10.1016/j.tplants.2011.09.002
CD Crocco, 2010, AtBBX21 and COP1 genetically interact in the regulation of shade avoidance, Plant J, 64, 551, 10.1111/j.1365-313X.2010.04360.x
H Guo, 1998, Regulation of flowering time by <italic>Arabidopsis</italic> photoreceptors, Science, 279, 1360, 10.1126/science.279.5355.1360
Z Zuo, 2011, Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis, Curr Biol, 21, 841, 10.1016/j.cub.2011.03.048
Y Liu, 2013, Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in <italic>Arabidopsis</italic>, PLoS Genet, 9, e1003861, 10.1371/journal.pgen.1003861
MM Keller, 2011, Cryptochrome 1 and phytochrome B control shade-avoidance responses in <italic>Arabidopsis</italic> via partially independent hormonal cascades, Plant J, 67, 195, 10.1111/j.1365-313X.2011.04598.x
DH Keuskamp, 2011, Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in <italic>Arabidopsis</italic> seedlings, Plant J, 67, 208, 10.1111/j.1365-313X.2011.04597.x
Y Ichihashi, 2010, The bHLH transcription factor SPATULA controls final leaf size in <italic>Arabidopsis thaliana</italic>, Plant Cell Physiol, 51, 252, 10.1093/pcp/pcp184
MC Reymond, 2012, A light-regulated genetic module was recruited to carpel development in <italic>Arabidopsis</italic> following a structural change to SPATULA, Plant Cell, 24, 2812, 10.1105/tpc.112.097915
P Leivar, 2012, Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in <italic>Arabidopsis</italic>, Plant Cell, 24, 1398, 10.1105/tpc.112.095711
J Soy, 2014, PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in <italic>Arabidopsis</italic> together with PIF3, PIF4, and PIF5, J Exp Bot, 65, 2925, 10.1093/jxb/ert465
E Huq, 2004, Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis, Science, 305, 1937, 10.1126/science.1099728
P Leivar, 2014, PIFs: Systems Integrators in Plant Development, The Plant Cell Online, 26, 56, 10.1105/tpc.113.120857
E Monte, 2004, The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development, Proc Natl Acad Sci U S A, 101, 16091, 10.1073/pnas.0407107101
Y Zhang, 2013, A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis, PLoS Genet, 9, e1003244, 10.1371/journal.pgen.1003244
K Nozue, 2011, Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in <italic>Arabidopsis</italic>, Plant Physiol, 156, 357, 10.1104/pp.111.172684
AK Spartz, 2014, SAUR inhibition of PP2C-D phosphatases activates plasma membrane H+-ATPases to promote cell expansion in <italic>Arabidopsis</italic>, Plant Cell, 26, 2129, 10.1105/tpc.114.126037
M de Wit, 2014, Auxin-mediated plant architectural changes in response to shade and high temperature, Physiol Plant, 151, 13, 10.1111/ppl.12099
K Mashiguchi, 2011, The main auxin biosynthesis pathway in <italic>Arabidopsis</italic>, Proc Natl Acad Sci U S A, 108, 18512, 10.1073/pnas.1108434108
C Won, 2011, Conversion of tryptophan to indole-3-acetic acid by <italic>TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS</italic> and <italic>YUCCA</italic>s in <italic>Arabidopsis</italic>, Proc Natl Acad Sci U S A, 108, 18518, 10.1073/pnas.1108436108
PJ Overvoorde, 2005, Functional genomic analysis of the <italic>AUXIN/INDOLE-3-ACETIC ACID</italic> gene family members in <italic>Arabidopsis thaliana</italic>, Plant Cell, 17, 3282, 10.1105/tpc.105.036723
M Delarue, 1998, <italic>Sur2</italic> mutations of <italic>Arabidopsis thaliana</italic> define a new locus involved in the control of auxin homeostasis, Plant J, 14, 603, 10.1046/j.1365-313X.1998.00163.x
KA Franklin, 2011, Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature, Proc Natl Acad Sci U S A, 108, 20231, 10.1073/pnas.1110682108
JL Nemhauser, 2000, Auxin and ETTIN in <italic>Arabidopsis</italic> gynoecium morphogenesis, Development, 127, 3877, 10.1242/dev.127.18.3877
J Foreman, 2011, Shedding light on flower development: phytochrome B regulates gynoecium formation in association with the transcription factor <italic>SPATULA</italic>, Plant Signal Behav, 6, 471, 10.4161/psb.6.4.14496
AE Valdes, 2011, <italic>Arabidopsis thaliana TERMINAL FLOWER2</italic> is involved in light-controlled signalling during seedling photomorphogenesis, Plant Cell Environ, 35, 1013, 10.1111/j.1365-3040.2011.02468.x
C Wasternack, 2013, Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany, Ann Bot, 111, 1021, 10.1093/aob/mct067
I Cerrudo, 2012, Low red/far-red ratios reduce <italic>Arabidopsis</italic> resistance to <italic>Botrytis cinerea</italic> and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism, Plant Physiol, 158, 2042, 10.1104/pp.112.193359
EW Chehab, 2011, Intronic T-DNA insertion renders <italic>Arabidopsis opr3</italic> a conditional jasmonic acid-producing mutant, Plant Physiol, 156, 770, 10.1104/pp.111.174169
P Fernandez-Calvo, 2011, The <italic>Arabidopsis</italic> 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, 701, 10.1105/tpc.110.080788
V Cevik, 2012, MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in <italic>Arabidopsis</italic>, Plant Physiol, 160, 541, 10.1104/pp.112.202697
R Chen, 2012, The <italic>Arabidopsis</italic> mediator subunit MED25 differentially regulates jasmonate and abscisic acid signaling through interacting with the MYC2 and ABI5 transcription factors, Plant Cell, 24, 2898, 10.1105/tpc.112.098277
C Klose, 2012, The mediator complex subunit PFT1 interferes with COP1 and HY5 in the regulation of <italic>Arabidopsis</italic> light signaling, Plant Physiol, 160, 289, 10.1104/pp.112.197319
X Hou, 2010, DELLAs modulate jasmonate signaling via competitive binding to JAZs, Dev Cell, 19, 884, 10.1016/j.devcel.2010.10.024
J Chen, 2013, Inhibition of arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner, J Plant Res, 126, 161, 10.1007/s10265-012-0509-3
D-L Yang, 2012, Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascad, Proc Natl Acad Sci U S A, 109, E1192, 10.1073/pnas.1201616109
S Noir, 2013, Jasmonate controls leaf growth by repressing cell proliferation and the onset of endoreduplication while maintaining a potential stand-by mode, Plant Physiol, 161, 1930, 10.1104/pp.113.214908
I Rieu, 2008, The gibberellin biosynthetic genes <italic>AtGA20ox1</italic> and <italic>AtGA20ox2</italic> act, partially redundantly, to promote growth and development throughout the <italic>Arabidopsis</italic> life cycle, Plant J, 53, 488, 10.1111/j.1365-313X.2007.03356.x
P Achard, 2006, Integration of plant responses to environmentally activated phytohormonal signals, Science, 311, 91, 10.1126/science.1118642
PY Hsu, 2013, Accurate timekeeping is controlled by a cycling activator in <italic>Arabidopsis</italic>, eLife, 2, e00473, 10.7554/eLife.00473
M Takase, 2013, The unique function of the Arabidopsis circadian clock gene PRR5 in the regulation of shade avoidance response, Plant Signal Behav, 8, e23534, 10.4161/psb.23534
D Schachtman, 1992, Expression of an inward-rectifying potassium channel by the <italic>Arabidopsis</italic> KAT1 cDNA, Science, 258, 1654, 10.1126/science.8966547
RL Nakamura, 1995, Expression of an <italic>Arabidopsis</italic> potassium channel gene in guard cells, Plant Physiol, 109, 371, 10.1104/pp.109.2.371
J-U Sutter, 2007, Abscisic acid triggers the endocytosis of the <italic>Arabidopsis</italic> KAT1 K+ channel and its recycling to the plasma membrane, Current Biol, 17, 1396, 10.1016/j.cub.2007.07.020
C Eisenach, 2011, The trafficking protein SYP121 of <italic>Arabidopsis</italic> connects programmed stomatal closure and K+ channel activity with vegetative growth, Plant J, 69, 241, 10.1111/j.1365-313X.2011.04786.x
S Abel, 1995, The PS-IAA4/5-like family of early auxin-inducible mRNAs in <italic>Arabidopsis thaliana</italic>, J Mol Biol, 251, 533, 10.1006/jmbi.1995.0454
K Philippar, 2004, Auxin activates <italic>KAT1</italic> and <italic>KAT2</italic>, two K+-channel genes expressed in seedlings of <italic>Arabidopsis thaliana</italic>, Plant J, 37, 815, 10.1111/j.1365-313X.2003.02006.x
J Putterill, 1995, The CONSTANS gene of <italic>Arabidopsis</italic> promotes flowering and encodes a protein showing similarities to zinc finger transcription factors, Cell, 80, 847, 10.1016/0092-8674(95)90288-0
DH Park, 1999, Control of circadian rhythms and photoperiodic flowering by the <italic>Arabidopsis GIGANTEA</italic> gene, Science, 285, 1579, 10.1126/science.285.5433.1579
S Fowler, 1999, <italic>GIGANTEA</italic>: a circadian clock-controlled gene that regulates photoperiodic flowering in <italic>Arabidopsis</italic> and encodes a protein with several possible membrane-spanning domains, EMBO J, 18, 4679, 10.1093/emboj/18.17.4679
YH Song, 2013, Flowering time regulation: photoperiod- and temperature-sensing in leaves, Trends Plant Sci, 18, 575, 10.1016/j.tplants.2013.05.003
M Holm, 2002, Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in <italic>Arabidopsis</italic>, Genes Dev, 16, 1247, 10.1101/gad.969702
SV Kumar, 2012, Transcription factor PIF4 controls the thermosensory activation of flowering, Nature, 484, 242, 10.1038/nature10928
R Rawat, 2011, REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the <italic>Arabidopsis</italic> circadian clock, PLoS Genet, 7, e1001350, 10.1371/journal.pgen.1001350
AC Leopold, 1958, Auxin uses in the control of flowering and fruiting, Annu Rev Plant Physiol, 9, 281, 10.1146/annurev.pp.09.060158.001433
SN Gangappa, 2010, MYC2, a bHLH transcription factor, modulates the adult phenotype of SPA1, Plant Signal Behav, 5, 1650, 10.4161/psb.5.12.13981
S Makkena, 2013, The bHLH transcription factor SPATULA is a key regulator of organ size in <italic>Arabidopsis thaliana</italic>, Plant Signal Behav, 8, e24140, 10.4161/psb.24140
N Cifuentes-Esquivel, 2013, The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in <italic>Arabidopsis</italic> seedlings, Plant J, 75, 989, 10.1111/tpj.12264
DM Friedrichsen, 2002, Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth, Genetics, 162, 1445, 10.1093/genetics/162.3.1445
DL Filiault, 2012, A genome-wide association study identifies variants underlying the <italic>Arabidopsis thaliana</italic> shade avoidance response, PLoS Genet, 8, e1002589, 10.1371/journal.pgen.1002589
R Kumar, 2012, A high-throughput method for Illumina RNA-Seq library preparation, Front Plant Sci, 3, 202, 10.3389/fpls.2012.00202
K Nozue, 2007, Rhythmic growth explained by coincidence between internal and external cues, Nature, 448, 358, 10.1038/nature05946
MD Abramoff, 2004, Image processing with ImageJ, Biophotonics International, 11, 36
C Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120
MD Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616
2005, R Foundation for Statistical Computing
MD Young, 2010, Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol, 11, R14, 10.1186/gb-2010-11-2-r14
JL Nemhauser, 2006, Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses, Cell, 126, 467, 10.1016/j.cell.2006.05.050
R Zentella, 2007, Global analysis of DELLA direct targets in early gibberellin signaling in <italic>Arabidopsis</italic>, Plant Cell, 19, 3037, 10.1105/tpc.107.054999
S Carbon, 2009, AmiGO: online access to ontology and annotation data, Bioinformatics, 25, 288, 10.1093/bioinformatics/btn615
Bates D, Maechler M, Bolker B, Walker S (2014) lme4: Linear mixed-effects models using Eigen and S4. <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://CRAN.R-project.org/package=lme4" xlink:type="simple">http://CRAN.R-project.org/package=lme4</ext-link>.
Kuznetsova A, Brockhoff PB, Christensen RHB (2014) lmerTest: Tests for random and fixed effects for linear mixed effect models (lmer objects of lme4 package). <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://CRAN.R-project.org/package=lmerTest" xlink:type="simple">http://CRAN.R-project.org/package=lmerTest</ext-link>.
Y Benjamini, 1995, Controlling the false discovery rate—a practical and powerful approach to multiple testing, J Roy Statist Soc Ser B, 57, 289, 10.1111/j.2517-6161.1995.tb02031.x