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High-Resolution Kinematic Analysis of Root Gravitropic Bending Using RootPlot

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Plant Gravitropism

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2368))

Abstract

Root gravitropic bending is a complex growth process resulting from differential expansion of cells on the upper and lower sides of a gravistimulated root. In order to genetically dissect the molecular machinery underlying root bending, a thorough understanding of the kinetics and spatial distribution of the growth process is required. We have developed an experimental workflow that enables us to image growing roots at high spatiotemporal resolution and then convert XY-coordinates of root cellular markers into 3D representations of root growth profiles. Here, we present a detailed description of the setup for monitoring vertically oriented roots before and after gravistimulation. We also introduce our newly developed custom R-based program RootPlot, which calculates root velocity profiles from root XY-coordinate data obtained using a previously published image processing software. The raw velocity and derived relative elemental growth rate (REGR) curves are then fitted via LOWESS regression for assumption-free data analysis. The resulting smoothed growth profiles are plotted as heatmaps to visualize how different regions of the root contribute to the growth response over time. Additionally, RootPlot provides analysis of overall growth and bending rates based on root XY-coordinates.

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References

  1. Morgan DC, O’Brien T, Smith H (1980) Rapid photomodulation of stem extension in light-grown Sinapis alba L.: studies on kinetics, site of perception and photoreceptor. Planta 150:95–101. https://doi.org/10.1007/BF00582351

    Article  CAS  PubMed  Google Scholar 

  2. Cosgrove DJ (1985) Kinetic separation of phototropism from blue-light inhibition of stem elongation. Photochem Photobiol 42:745–751. https://doi.org/10.1111/j.1751-1097.1985.tb01642.x

    Article  CAS  PubMed  Google Scholar 

  3. Zieschang HE, Sievers A (1991) Graviresponse and the localization of its initiating cells in roots of Phleum pratense L. Planta 184:468–477. https://doi.org/10.1007/BF00197894

    Article  CAS  PubMed  Google Scholar 

  4. Ishikawa H, Hasenstein KH, Evans ML (1991) Computer-based video digitizer analysis of surface extension in maize roots: kinetics of growth rate changes during gravitropism. Planta 183:381–390. https://doi.org/10.1007/BF00197737

    Article  CAS  PubMed  Google Scholar 

  5. Orbovic V, Poff KL (1993) Growth distribution during phototropism of Arabidopsis thaliana seedlings. Plant Physiol 103:157–163. https://doi.org/10.1104/pp.103.1.157

    Article  PubMed  PubMed Central  Google Scholar 

  6. Massa GD, Gilroy S (2003) Touch modulates gravity sensing to regulate the growth of primary roots of Arabidopsis thaliana. Plant J 33:435–445. https://doi.org/10.1046/j.1365-313x.2003.01637.x

    Article  PubMed  Google Scholar 

  7. Galvan-Ampudia CS, Julkowska MM, Darwish E, Gandullo J, Korver RA, Brunoud G, Haring MA, Munnik T, Vernoux T, Testerink C (2013) Halotropism is a response of plant roots to avoid a saline environment. Curr Biol 23:2044–2050. https://doi.org/10.1016/j.cub.2013.08.042

    Article  CAS  PubMed  Google Scholar 

  8. Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM, Owen MR, Band LR, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat Plants 3:17057. https://doi.org/10.1038/nplants.2017.57

    Article  CAS  PubMed  Google Scholar 

  9. Bastien R, Guayasamin O, Douady S, Moulia B (2018) Coupled ultradian growth and curvature oscillations during gravitropic movement in disturbed wheat coleoptiles. PLoS One 13:e0194893. https://doi.org/10.1371/journal.pone.0194893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Jaffe MJ, Galston AW (1968) Physiology of tendrils. Annu Rev Plant Physiol 19:417–434

    Article  Google Scholar 

  11. van Doorn WG, van Meeteren U (2003) Flower opening and closure: a review. J Exp Bot 54:1801–1812. https://doi.org/10.1093/jxb/erg213

    Article  PubMed  Google Scholar 

  12. Polko JK, Voesenek LA, Peeters AJ, Pierik R (2011) Petiole hyponasty: an ethylene-driven, adaptive response to changes in the environment. AoB Plants 2011:plr031. https://doi.org/10.1093/aobpla/plr031

    Article  PubMed  PubMed Central  Google Scholar 

  13. Brown AH (1993) Circumnutations: from Darwin to space flights. Plant Physiol 101:345–348. https://doi.org/10.1104/pp.101.2.345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bastien R, Meroz Y (2016) The kinematics of plant nutation reveals a simple relation between curvature and the orientation of differential growth. PLoS Comput Biol 12:e1005238. https://doi.org/10.1371/journal.pcbi.1005238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Sharp RE, Silk WK, Hsiao TC (1988) Growth of the maize primary root at low water potentials: I. Spatial distribution of expansive growth. Plant Physiol 87:50–57. https://doi.org/10.1104/pp.87.1.50

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ishikawa H, Evans ML (1993) The role of the distal elongation zone in the response of maize roots to auxin and gravity. Plant Physiol 102:1203–1210. https://doi.org/10.1104/pp.102.4.1203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Goodwin RH, Avers CJ (1956) Studies on roots. III. An analysis of root growth in Phleum pratense using photomicrographic records. Am J Bot 43:479–487

    Article  Google Scholar 

  18. Miller ND, Parks BM, Spalding EP (2007) Computer-vision analysis of seedling responses to light and gravity. Plant J 52:374–381. https://doi.org/10.1111/j.1365-313X.2007.03237.x

    Article  CAS  PubMed  Google Scholar 

  19. Chavarria-Krauser A, Nagel KA, Palme K, Schurr U, Walter A, Scharr H (2008) Spatio-temporal quantification of differential growth processes in root growth zones based on a novel combination of image sequence processing and refined concepts describing curvature production. New Phytol 177:811–821. https://doi.org/10.1111/j.1469-8137.2007.02299.x

    Article  PubMed  Google Scholar 

  20. Brooks TL, Miller ND, Spalding EP (2010) Plasticity of Arabidopsis root gravitropism throughout a multidimensional condition space quantified by automated image analysis. Plant Physiol 152:206–216. https://doi.org/10.1104/pp.109.145292

    Article  CAS  PubMed  Google Scholar 

  21. Shih HW, Miller ND, Dai C, Spalding EP, Monshausen GB (2014) The receptor-like kinase FERONIA is required for mechanical signal transduction in Arabidopsis seedlings. Curr Biol 24:1887–1892. https://doi.org/10.1016/j.cub.2014.06.064

    Article  CAS  PubMed  Google Scholar 

  22. Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H (2016) KymoRod: a method for automated kinematic analysis of rod-shaped plant organs. Plant J 88:468–475. https://doi.org/10.1111/tpj.13255

    Article  CAS  PubMed  Google Scholar 

  23. Shih HW, DePew CL, Miller ND, Monshausen GB (2015) The cyclic nucleotide-gated channel CNGC14 regulates root gravitropism in Arabidopsis thaliana. Curr Biol 25:3119–3125. https://doi.org/10.1016/j.cub.2015.10.025

    Article  CAS  PubMed  Google Scholar 

  24. Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Muller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCFTIR1/AFB-type Ca2+ signaling. Nat Commun 9:1174. https://doi.org/10.1038/s41467-018-03582-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by NSF grant MCB-1817934 to GBM. The authors thank Drs. Edgar Spalding and Nathan Miller for many helpful discussions and the use of the custom software Image Processing Toolkit v10.

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Correspondence to Gabriele B. Monshausen .

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Bhat, A., DePew, C.L., Monshausen, G.B. (2022). High-Resolution Kinematic Analysis of Root Gravitropic Bending Using RootPlot. In: Blancaflor, E.B. (eds) Plant Gravitropism. Methods in Molecular Biology, vol 2368. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1677-2_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1677-2_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1676-5

  • Online ISBN: 978-1-0716-1677-2

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