GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light

Ahmad, 1993, HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor, Nature, 366, 162, 10.1038/366162a0 Ballare, 1999, Keeping up with the neighbours: phytochrome sensing and other signalling mechanisms, Trends Plant Sci., 4, 97, 10.1016/S1360-1385(99)01383-7 Ballare, 2012, Canopy light and plant health, Plant Physiol., 160, 145, 10.1104/pp.112.200733 Ballare, 2017, The shade-avoidance syndrome: multiple signals and ecological consequences, Plant Cell Environ., 40, 2530, 10.1111/pce.12914 Bellaloui, 2012, Effect of shade on seed protein, oil, fatty acids, and minerals in soybean lines varying in seed germinability in the early soybean production system, Am. J. Plant Sci., 3, 84, 10.4236/ajps.2012.31008 Board, 2001, Reduced lodging for soybean in low plant population is related to light quality, Crop Sci., 41, 379, 10.2135/cropsci2001.412379x Carriedo, 2016, Molecular control of crop shade avoidance, Curr. Opin. Plant Biol., 30, 151, 10.1016/j.pbi.2016.03.005 Casal, 2012, Shade avoidance, Arabidopsis Book, 10, e0157, 10.1199/tab.0157 Chen, 2012, Highly sensitive and quantitative profiling of acidic phytohormones using derivatization approach coupled with nano-LC-ESI-Q-TOF-MS analysis, J. Chromatogr. B, 905, 67, 10.1016/j.jchromb.2012.08.005 Cheong, 1998, STF1 is a novel TGACG-binding factor with a zinc-finger motif and a bZIP domain which heterodimerizes with GBF proteins, Plant J., 15, 199, 10.1046/j.1365-313X.1998.00197.x Cober, 2005, Genetic improvement rates of short-season soybean increase with plant population, Crop Sci., 45, 1029, 10.2135/cropsci2004.0232 de Wit, 2016, Integration of phytochrome and cryptochrome signals determines plant growth during competition for light, Curr. Biol., 26, 3320, 10.1016/j.cub.2016.10.031 Devlin, 1999, Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time, Plant Physiol., 119, 909, 10.1104/pp.119.3.909 Djakovic-Petrovic, 2007, DELLA protein function in growth responses to canopy signals, Plant J., 51, 117, 10.1111/j.1365-313X.2007.03122.x Earley, 2006, Gateway-compatible vectors for plant functional genomics and proteomics, Plant J., 45, 616, 10.1111/j.1365-313X.2005.02617.x Egli, 2005, Shade and temporal distribution of pod production and pod set in soybean, Crop Sci., 45, 1764, 10.2135/cropsci2004.0557 Finlayson, 2010, Phytochrome regulation of branching in Arabidopsis, Plant Physiol., 152, 1914, 10.1104/pp.109.148833 Fiorucci, 2017, Plant strategies for enhancing access to sunlight, Curr. Biol., 27, R931, 10.1016/j.cub.2017.05.085 Folta, 2003, Genomic and physiological studies of early cryptochrome 1 action demonstrate roles for auxin and gibberellin in the control of hypocotyl growth by blue light, Plant J., 36, 203, 10.1046/j.1365-313X.2003.01870.x Franklin, 2008, Shade avoidance, New Phytol., 179, 930, 10.1111/j.1469-8137.2008.02507.x Franklin, 2003, Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis, Plant Physiol., 131, 1340, 10.1104/pp.102.015487 Franklin, 2010, Phytochrome functions in Arabidopsis development, J. Exp. Bot., 61, 11, 10.1093/jxb/erp304 Fraser, 2016, Photoreceptor crosstalk in shade avoidance, Curr. Opin. Plant Biol., 33, 1, 10.1016/j.pbi.2016.03.008 Gong, 2015, Tolerance vs. avoidance: two strategies of soybean (Glycine max) seedlings in response to shade in intercropping, Photosynthetica, 53, 259, 10.1007/s11099-015-0103-8 Green-Tracewicz, 2011, Shade avoidance in soybean reduces branching and increases plant-to-plant variability in biomass and yield per plant, Weed Sci., 59, 43, 10.1614/WS-D-10-00081.1 Green-Tracewicz, 2012, Light quality and the critical period for weed control in soybean, Weed Sci., 60, 86, 10.1614/WS-D-11-00072.1 Halliday, 2009, Integration of light and auxin signaling, Cold Spring Harb. Perspect. Biol., 1, a001586, 10.1101/cshperspect.a001586 Hao, 2012, Interactions between HLH and bHLH factors modulate light-regulated plant development, Mol. Plant, 5, 688, 10.1093/mp/sss011 Hedden, 2003, The genes of the green revolution, Trends Genet., 19, 5, 10.1016/S0168-9525(02)00009-4 Hornitschek, 2009, Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers, EMBO J., 28, 3893, 10.1038/emboj.2009.306 Horvath, 2015, RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean, New Phytol., 207, 196, 10.1111/nph.13351 Hussain, 2019, Shade effect on carbohydrates dynamics and stem strength of soybean genotypes, Environ. Exp. Bot., 162, 374, 10.1016/j.envexpbot.2019.03.011 Jiang, 2020, Gibberellins modulate shade-induced soybean hypocotyl elongation downstream of the mutual promotion of auxin and brassinosteroids, Plant Physiol. Biochem., 150, 209, 10.1016/j.plaphy.2020.02.042 Kaneko, 2003, Where do gibberellin biosynthesis and gibberellin signaling occur in rice plants?, Plant J., 35, 104, 10.1046/j.1365-313X.2003.01780.x Keller, 2011, Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades, Plant J., 67, 195, 10.1111/j.1365-313X.2011.04598.x Keuskamp, 2011, Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings, Plant J., 67, 208, 10.1111/j.1365-313X.2011.04597.x Lee, 2019, Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV, Theor. Appl. Genet., 132, 1639, 10.1007/s00122-019-03304-5 Leeflang, 1999, Are stoloniferous plants able to avoid neighbours in response to low R:FR ratios in reflected light?, Plant Ecol., 141, 59, 10.1023/A:1009897031525 Leivar, 2008, The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels, Plant Cell, 20, 337, 10.1105/tpc.107.052142 Leivar, 2011, PIFs: pivotal components in a cellular signaling hub, Trends Plant Sci., 16, 19, 10.1016/j.tplants.2010.08.003 Li, 2012, Linking photoreceptor excitation to changes in plant architecture, Gene Dev., 26, 785, 10.1101/gad.187849.112 Li, 2020, A domestication-associated gene GmPRR3b regulates the circadian clock and flowering time in soybean, Mol. Plant Libenson, 2002, Low red to far-red ratios reaching the stem reduce grain yield in sunflower, Crop Sci., 42, 1180, 10.2135/cropsci2002.1180 Lin, 2005, The cryptochromes, Genome Biol., 6, 220, 10.1186/gb-2005-6-5-220 Lin, 1996, Arabidopsis cryptochrome 1 is a soluble protein mediating blue light-dependent regulation of plant growth and development, Plant J., 10, 893, 10.1046/j.1365-313X.1996.10050893.x Liu, 2008, Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene, Genetics, 180, 995, 10.1534/genetics.108.092742 Liu, 2011, Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light, Gene Dev., 25, 1029, 10.1101/gad.2025011 Liu, 2011, The action mechanisms of plant cryptochromes, Trends Plant Sci., 16, 684, 10.1016/j.tplants.2011.09.002 Liu, 2017, Selection of soybean elite cultivars based on phenotypic and genomic characters related to lodging tolerance, Plant Breed., 136, 526, 10.1111/pbr.12495 Liu, 2018, Shortened basal internodes encodes a gibberellin 2-oxidase and contributes to lodging resistance in rice, Mol. Plant, 11, 288, 10.1016/j.molp.2017.12.004 Liu, 2020, Toward a 'green revolution' for soybean, Mol. Plant 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 Meng, 2013, Blue light-dependent interaction between cryptochrome2 and CIB1 regulates transcription and leaf senescence in soybean, Plant Cell, 25, 4405, 10.1105/tpc.113.116590 Morales, 2013, Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway, Funct. Plant Biol., 40, 1029, 10.1071/FP12296 Morgan, 1979, A systematic relationship between phytochrome-controlled development and species habitat, for plants grown in simulated natural radiation, Planta, 145, 253, 10.1007/BF00454449 Murphy, 2017, Identity recognition in response to different levels of genetic relatedness in commercial soya bean, R. Soc. Open Sci., 4, 160879, 10.1098/rsos.160879 Muth, 2002, Tree seedling canopy responses to conflicting photosensory cues, Oecologia, 132, 197, 10.1007/s00442-002-0957-x Naito, 2015, CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites, Bioinformatics, 31, 1120, 10.1093/bioinformatics/btu743 Noor, 1980, Influence of induced lodging on pod distribution and seed yield in soybeans, Agron. J., 72, 904, 10.2134/agronj1980.00021962007200060010x Ohara, 1994, Some ecological and demographic characteristics of two growth forms of wild soybean (Glycine soja), Can. J. Bot., 72, 486, 10.1139/b94-065 Pantazopoulou, 2017, Neighbor detection at the leaf tip adaptively regulates upward leaf movement through spatial auxin dynamics, Proc. Natl. Acad. Sci. U S A, 114, 7450, 10.1073/pnas.1702275114 Pausch, 1991, Growth and photosynthesis of soybean (Glycine max (L.) Merr.) in simulated vegetation shade: influence of the ratio of red to far-red radiation, Plant Cell Environ., 14, 647, 10.1111/j.1365-3040.1991.tb01537.x Pedersen, 2004, Response of soybean yield components to management system and planting date, Agron. J., 96, 1372, 10.2134/agronj2004.1372 Pedmale, 2016, Cryptochromes interact directly with PIFs to control plant growth in limiting blue light, Cell, 164, 233, 10.1016/j.cell.2015.12.018 Peng, 1999, Green revolution' genes encode mutant gibberellin response modulators, Nature, 400, 256, 10.1038/22307 Pierik, 2014, Shade avoidance: phytochrome signalling and other aboveground neighbour detection cues, J. Exp. Bot., 65, 2815, 10.1093/jxb/ert389 Pierik, 2009, Auxin and ethylene regulate elongation responses to neighbor proximity signals independent of gibberellin and della proteins in Arabidopsis, Plant Physiol., 149, 1701, 10.1104/pp.108.133496 Ray, 2013, Yield trends are insufficient to double global crop production by 2050, PLoS One, 8, e66428, 10.1371/journal.pone.0066428 Ray, 2012, Recent patterns of crop yield growth and stagnation, Nat. Commun., 3, 1293, 10.1038/ncomms2296 Runkle, 2001, Specific functions of red, far red, and blue light in flowering and stem extension of long-day plants, J. Am. Soc. Hortic. Sci., 126, 275, 10.21273/JASHS.126.3.275 Sasidharan, 2008, The regulation of cell wall extensibility during shade avoidance: a study using two contrasting ecotypes of Stellaria longipes, Plant Physiol., 148, 1557, 10.1104/pp.108.125518 Sasaki, 2002, Green revolution: a mutant gibberellin-synthesis gene in rice, Nature, 416, 701, 10.1038/416701a Schmutz, 2010, Genome sequence of the palaeopolyploid soybean, Nature, 463, 178, 10.1038/nature08670 Sellaro, 2010, Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis, Plant Physiol., 154, 401, 10.1104/pp.110.160820 Sessa, 2005, A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis, Gene Dev., 19, 2811, 10.1101/gad.364005 Shin, 2016, Isolation of three B-box zinc finger proteins that interact with STF1 and COP1 defines a HY5/COP1 interaction network involved in light control of development in soybean, Biochem. Biophys. Res. Commun., 478, 1080, 10.1016/j.bbrc.2016.08.069 Silverstone, 1997, Developmental regulation of the gibberellin biosynthetic gene GA1 in Arabidopsis thaliana, Plant J., 12, 9, 10.1046/j.1365-313X.1997.12010009.x Song, 2008, DNA-binding study identifies C-box and hybrid C/G-box or C/A-box motifs as high-affinity binding sites for STF1 and LONG HYPOCOTYL5 proteins, Plant Physiol., 146, 1862, 10.1104/pp.107.113217 Sun, 2015, Targeted mutagenesis in soybean using the CRISPR-Cas9 system, Sci. Rep., 5, 1 Vandenbussche, 2005, Reaching out of the shade, Curr. Opin. Plant Biol., 8, 462, 10.1016/j.pbi.2005.07.007 Vanstraelen, 2012, Hormonal interactions in the regulation of plant development, Annu. Rev. Cell Dev. Biol., 28, 463, 10.1146/annurev-cellbio-101011-155741 Wang, 2016, Regulatory modules controlling early shade avoidance response in maize seedlings, BMC Genomics, 17, 269, 10.1186/s12864-016-2593-6 Wang, 2020, Mechanisms of cryptochrome-mediated photoresponses in plants, Annu. Rev. Plant Biol., 71, 10.1146/annurev-arplant-050718-100300 Wang, 2015, Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis, Plant Cell, 27, 323, 10.1105/tpc.114.135103 Weissgerber, 2015, Beyond bar and line graphs: time for a new data presentation paradigm, PLoS Biol., 13, e1002128, 10.1371/journal.pbio.1002128 Weller, 2009, Light regulation of gibberellin biosynthesis in pea is mediated through the COP1/HY5 pathway, Plant Cell, 21, 800, 10.1105/tpc.108.063628 Wu, 2017, Shade inhibits leaf size by controlling cell proliferation and enlargement in soybean, Sci. Rep., 7, 9259, 10.1038/s41598-017-10026-5 Yang, 2014, Growth of soybean seedlings in relay strip intercropping systems in relation to light quantity and red:far-red ratio, Field Crop Res., 155, 245, 10.1016/j.fcr.2013.08.011 Zhang, 2008, Association of the circadian rhythmic expression of GmCRY1a with a latitudinal cline in photoperiodic flowering of soybean, Proc. Natl. Acad. Sci. U S A, 105, 21028, 10.1073/pnas.0810585105 Zhang, 1999, The use of glufosinate as a selective agent in Agrobacterium-mediated transformation of soybean, Plant Cell Tissue Organ Cult., 56, 37, 10.1023/A:1006298622969 Zhao, 2007, A study of gibberellin homeostasis and cryptochrome-mediated blue light inhibition of hypocotyl elongation, Plant Physiol., 145, 106, 10.1104/pp.107.099838