Root Gravitropism: Quantification, Challenges, and Solutions

Part of the Methods in Molecular Biology book series (MIMB, volume 1761)


Better understanding of root traits such as root angle and root gravitropism will be crucial for development of crops with improved resource use efficiency. This chapter describes a high-throughput, automated image analysis method to trace Arabidopsis (Arabidopsis thaliana) seedling roots grown on agar plates. The method combines a “particle-filtering algorithm with a graph-based method” to trace the center line of a root and can be adopted for the analysis of several root parameters such as length, curvature, and stimulus from original root traces.

Key words

Root gravitropism RootTrace Image analysis Arabidopsis 



We acknowledge support from the Biological and Biotechnological Science Research Council (BBSRC), European Research Council (ERC), Royal Society, and Newton International and Advanced Fellowship awards.


  1. 1.
    Lynch JP (2011) Root phenes for enhanced soil exploration and phosphorus acquisition: tools for future crops. Plant Physiol 156(3):1041–1049. Scholar
  2. 2.
    Sato EM, Hijazi H, Bennett MJ, Vissenberg K, Swarup R (2015) New insights into root gravitropic signalling. J Exp Bot 66(8):2155–2165. Scholar
  3. 3.
    Swarup R, Bennett MJ (2009) Root gravitropism. Annu Plant Rev 37:157–174Google Scholar
  4. 4.
    Swarup R, Wells D, Bennett MJ (2013) Root gravitropism. In: Eshel A, Beeckman T (eds) The hidden half. CRC Press, Boca Raton, pp 19–34. IV edition:19–34Google Scholar
  5. 5.
    Blancaflor EB, Fasano JM, Gilroy S (1998) Mapping the functional roles of cap cells in the response of Arabidopsis primary roots to gravity. Plant Physiol 116(1):213–222CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Swarup R, Bennett MJ (2014) Auxin transport: providing plants with a new sense of direction. Biochemist 36:12–16Google Scholar
  7. 7.
    Swarup R, Kramer EM, Perry P, Knox K, Leyser HM, Haseloff J, Beemster GT, Bhalerao R, Bennett MJ (2005) Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal. Nat Cell Biol 7(11):1057–1065. Scholar
  8. 8.
    Boonsirichai K, Sedbrook JC, Chen R, Gilroy S, Masson PH (2003) ALTERED RESPONSE TO GRAVITY is a peripheral membrane protein that modulates gravity-induced cytoplasmic alkalinization and lateral auxin transport in plant statocytes. Plant Cell 15(11):2612–2625CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Ottenschlager I, Wolff P, Wolverton C, Bhalerao RP, Sandberg G, Ishikawa H, Evans M, Palme K (2003) Gravity-regulated differential auxin transport from columella to lateral root cap cells. Proc Natl Acad Sci U S A 100(5):2987–2991. Scholar
  10. 10.
    Rashotte AM, DeLong A, Muday GK (2001) Genetic and chemical reductions in protein phosphatase activity alter auxin transport, gravity response, and lateral root growth. Plant Cell 13(7):1683–1697CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Knight TA (1806) On the direction of the radicle and germen during the vegetation of seeds. Philos Trans R Soc Lond 96:99–108CrossRefGoogle Scholar
  12. 12.
    Swarup R, Peret B (2012) AUX/LAX family of auxin influx carriers-an overview. Front Plant Sci 3:225. Scholar
  13. 13.
    Basu P, Pal A, Lynch JP, Brown KM (2007) A novel image-analysis technique for kinematic study of growth and curvature. Plant Physiol 145(2):305–316. Scholar
  14. 14.
    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(3):811–821. Scholar
  15. 15.
    Qi X, Qi J, Wu Y (2007) RootLM: a simple color image analysis program for length measurement of primary roots in Arabidopsis. Plant Root 1:10–16CrossRefGoogle Scholar
  16. 16.
    French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T (2009) High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol 150(4):1784–1795CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Pound MP, French AP, Atkinson JA, Wells DM, Bennett MJ, Pridmore T (2013) RootNav: navigating images of complex root architectures. Plant Physiol 162(4):1802–1814CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15(3):473–497CrossRefGoogle Scholar
  19. 19.
    Wells DM, French AP, Naeem A, Ishaq O, Traini R, Hijazi H, Bennett MJ, Pridmore TP (2012) Recovering the dynamics of root growth and development using novel image acquisition and analysis methods. Philos Trans R Soc Lond B Biol Sci 367(1595):1517–1524CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Swarup R, Kargul J, Marchant A, Zadik D, Rahman A, Mills R, Yemm A, May S, Williams L, Millner P, Tsurumi S, Moore I, Napier R, Kerr ID, Bennett MJ (2004) Structure-function analysis of the presumptive Arabidopsis auxin permease AUX1. Plant Cell 16(11):3069–3083. Scholar

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© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Centre for Plant Integrative Biology, School of BiosciencesUniversity of NottinghamLoughboroughUK

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