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Transcriptomic and proteomic analyses of far-red light effects in inducing shoot elongation in the presence or absence of paclobutrazol in Chinese pine

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Abstract

In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.

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References

  • Abbasi BH, Stiles AR, Saxena PK, Liu C (2012) Gibberellic acid increases secondary metabolite production in Echinacea purpurea hairy roots. Appl Biochem Biotechnol 168:2057–2066

    Article  CAS  PubMed  Google Scholar 

  • Alosi MC, Neale DB (1992) Light- and phytochrome-mediated gene expression in Douglas-fir seedlings. Physiol Plant 86:71–76

    Article  CAS  Google Scholar 

  • Arana MV, Sanchez-Lamas M, Strasser B, Ibarra SE, Cerdan PD, Botto JF, Sanchez RA (2014) Functional diversity of phytochrome family in the control of light and gibberellin-mediated germination in Arabidopsis. Plant Cell Environ 37:2014–2023

    Article  CAS  PubMed  Google Scholar 

  • Ballare CL, Pierik R (2017) The shade-avoidance syndrome: multiple signals and ecological consequences. Plant Cell Environ 40:2530–2543

    Article  CAS  PubMed  Google Scholar 

  • Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34:525–527

    Article  CAS  PubMed  Google Scholar 

  • Burgin MJ, Casal JJ, Whitelam GC, Sanchez RA (1999) A light-regulated pool of phytochrome and rudimentary high-irradiance responses under far-red light in Pinus elliottii and Pseudotsuga menziesii. J Exp Bot 335:831–836

    Article  Google Scholar 

  • Cagnola JI, Ploschuk E, Benech-Arnold T, Finlayson SA, Casal JJ (2012) Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato. Plant Physiol 160:1110–1119

    Article  PubMed  PubMed Central  Google Scholar 

  • De La Rosa TM, Aphalo PJ, Lehto T (1998) Effects of far-red light on the growth, mycorrhizas and mineral nutrition of Scots pine seedlings. Plant Soil 201:17–25

    Article  Google Scholar 

  • Ding Z, Zhang Y, Xiao Y, Liu F, Wang M, Zhu X, Liu P, Sun Q, Wang W, Peng M, Brutnell T, Li P (2016) Transcriptome response of cassava leaves under natural shade. Sci Rep 6:31673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Djakovic-Petrovic T, de Wit M, Voesenek LA, Pierik R (2007) DELLA protein function in growth responses to canopy signals. Plant J 51:117–126

    Article  CAS  PubMed  Google Scholar 

  • Falcioni R, Moriwaki T, Perez-Llorca M, Munné-Bosch S, Gibin MS, Sato F, Pelozo A, Pattaro MC, Giacomelli ME, Rüggeberg M, Antunes WC (2020) Cell wall structure and composition is affected by light quality in tomato seedlings. J Photochem Photobiol B 203:111745

    Article  CAS  PubMed  Google Scholar 

  • Fan D, Zhang S, Yan H, Wu Q, Xu X, Wang X (2018) Do karst woody plants control xylem tension to avoid substantial xylem cavitation in the wet season? For Ecosyst 5:40

    Article  Google Scholar 

  • Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, Schäfer E, Fu X, Fan L, Deng XW (2008) Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451:475–479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernbach E, Mohr H (1990) Coaction of blue/ultraviolet-A light and light absorbed by phytochrome in controlling growth of pine (Pinus sylvestris L.) seedlings. Planta 180:212–216

    Article  CAS  PubMed  Google Scholar 

  • Guo H, Wang Y, Liu H, Hu P, Jia Y, Zhang C, Wang Y, Gu S, Yang C, Wang C (2015) Exogenous GA3 application enhances xylem development and induces the expression of secondary wall biosynthesis related genes in Betula platyphylla. Int J Mol Sci 16:22960–22975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harberd NP, Belfield E, Yasumura Y (2009) The angiosperm gibberellin-GID1-DELLA growth regulatory mechanism: how an “inhibitor of an inhibitor” enables flexible response to fluctuating environments. Plant Cell 21:1328–1339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hildebrandt TM, Nunes AN, Araújo WL, Braun H (2015) Amino acid catabolism in plants. Mol Plant 8:1563–1579

    Article  CAS  PubMed  Google Scholar 

  • Hisamatsu T, King RW, Helliwell CA, Koshioka M (2005) The involvement of gibberellin 20-oxidase genes in phytochrome-regulated petiole elongation of Arabidopsis. Plant Physiol 138:1106–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu XG, Liu H, Jin YQ, Sun YQ, Li Y, Zhao W, El-Kassaby YA, Wang XR, Mao JF (2016) De Novo transcriptome assembly and characterization for the widespread and stress-tolerant conifer Platycladus orientalis. PloS One 11:e148985

    Google Scholar 

  • Huang Y, Yin Y, Sanuki A, Fukuda N, Ezura H, Matsukura C (2015) Phosphoenolpyruvate carboxykinase (PEPCK) deficiency affects the germination, growth and fruit sugar content in tomato (Solanum lycopersicum L.). Plant Physiol Biochem 96:417–425

    Article  CAS  PubMed  Google Scholar 

  • Jaakola L, Hohtola A (2010) Effect of latitude on flavonoid biosynthesis in plants. Plant Cell Environ 33:1239–1247

    CAS  PubMed  Google Scholar 

  • Jing Y, Lin R (2020) Transcriptional regulatory network of the light signaling pathways. New Phytol 227:683–697

    Article  CAS  PubMed  Google Scholar 

  • Keuskamp DH, Sasidharan R, Vos I, Peeters AJM, Voesenek LACJ, Pierik R (2011) Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings. Plant J 67:208–217

    Article  CAS  PubMed  Google Scholar 

  • Kozuka T, Kobayashi J, Horiguchi G, Demura T, Sakakibara H, Tsukaya H, Nagatani A (2010) Involvement of auxin and brassinosteroid in the regulation of petiole elongation under the shade. Plant Physiol 153:1608–1618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lewandowska M, Keyl A, Feussner I (2020) Wax biosynthesis in response to danger: its regulation upon abiotic and biotic stress. New Phytol 227:698–713

    Article  CAS  PubMed  Google Scholar 

  • Li W, Liu S, Ma J, Liu H, Han F, Li Y, Niu S (2020) Gibberellin signaling is required for far-red light-induced shoot elongation in Pinus tabuliformis seedlings. Plant Physiol 182:658–668

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Cohen JD, Gardner G (2011) Low-fluence red light increases the transport and biosynthesis of auxin. Plant Physiol 157:891–904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo X, Cao D, Li H, Zhao D, Xue H, Niu J, Chen L, Zhang F, Cao S (2018) Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour. Sci Rep 8:12362

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mukai Y, Tazaki K, Fujii T, Yamamoto N (1992) Light-independent expression of three photosynthetic genes, cab, rbcS and rbcL, in coniferous plants. Plant Cell Environ 33:859–866

    CAS  Google Scholar 

  • Ouyang F, Mao JF, Wang J, Zhang S, Li Y (2015) Transcriptome analysis reveals that red and blue light regulate growth and phytohormone metabolism in Norway Spruce [Picea abies (L.) Karst]. PloS One 10:e127896

    Google Scholar 

  • Pimentel H, Bray NL, Puente S, Melsted P, Pachter L (2017) Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods 14:687–690

    Article  CAS  PubMed  Google Scholar 

  • Quail PH (2002) Phytochrome photosensory signalling networks. Nat Rev Mol Cell Biol 3:85–93

    Article  CAS  PubMed  Google Scholar 

  • Ranade SS, Delhomme N, García-Gil MR (2019) Transcriptome analysis of shade avoidance and shade tolerance in conifers. Planta 250:299–318

    Article  CAS  PubMed  Google Scholar 

  • Sasidharan R, Chinnappa CC, Voesenek LACJ, Pierik R (2008) The regulation of cell wall extensibility during shade avoidance: a study using two contrasting ecotypes of Stellaria longipes. Plant Physiol 148:1557–1569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sasidharan R, Pierik R (2010) Cell wall modification involving XTHs controls phytochrome-mediated petiole elongation in Arabidopsis thaliana. Plant Signaling Behav 5:1491–1492

    Article  CAS  Google Scholar 

  • Voelckel C, Gruenheit N, Lockhart P (2017) Evolutionary transcriptomics and proteomics: insight into plant adaptation. Trends Plant Sci 22:462–471

    Article  CAS  PubMed  Google Scholar 

  • Wang G, Que F, Xu Z, Wang F, Xiong A (2017) Exogenous gibberellin enhances secondary xylem development and lignification in carrot taproot. Protoplasma 254:839–848

    Article  CAS  PubMed  Google Scholar 

  • Wille W, Pipper CB, Rosenqvist E, Andersen SB, Weiner J (2017) Reducing shade avoidance responses in a cereal crop. AoB Plants 9:plx039

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yamauchi Y, Takeda-Kamiya N, Hanada A, Ogawa M, Kuwahara A, Seo M, Kamiya Y, Yamaguchi S (2007) Contribution of gibberellin deactivation by AtGA2ox2 to the suppression of germination of dark-imbibed Arabidopsis thaliana seeds. Trends Plant Sci 48:555–561

    CAS  Google Scholar 

  • Yang C, Li L (2017) Hormonal regulation in shade avoidance. Front Plant Sci 8:1527

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhen S, van Iersel MW (2017) Far-red light is needed for efficient photochemistry and photosynthesis. J Plant Physiol 209:115–122

    Article  CAS  PubMed  Google Scholar 

Download references

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Authors and Affiliations

  1. National Engineering Laboratory for Forest Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Yingtian Guo, Shihui Niu & Wei Li

  2. Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada

    Yousry A. El-Kassaby

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  1. Yingtian Guo
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  2. Shihui Niu
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  3. Yousry A. El-Kassaby
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  4. Wei Li
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Correspondence to Wei Li.

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Project finding: This work was supported by the National Natural Science Foundation of China (31770713), and Biosafety and Genetic Resources Management Project of State Forestry and Grassland Administration (KJZXSA202030).

The online version is available at www.springerlink.com.

Corresponding editor: Yanbo Hu.

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Guo, Y., Niu, S., El-Kassaby, Y.A. et al. Transcriptomic and proteomic analyses of far-red light effects in inducing shoot elongation in the presence or absence of paclobutrazol in Chinese pine. J. For. Res. 33, 1033–1043 (2022). https://doi.org/10.1007/s11676-021-01406-9

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  • DOI: https://doi.org/10.1007/s11676-021-01406-9

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