High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool

French, A. P.; Úbeda-Tomás, Susana; Holman, Tara J.; Bennett, Malcolm J.; Pridmore, Tony

doi:10.1104/pp.109.140558

Cited by 186 publications

(154 citation statements)

References 37 publications

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“…Five-day-old DII-VENUS seedlings were grown as described previously (35) and treated with the indicated concentration of IAA. Immediately following treatment, the seedlings were scanned every 2 min for 2 h. The fluorescence intensity of nuclei was extracted at each time point using Fiji software (http://pacific.mpi-cbg.de) and the values were analyzed using Microsoft Excel.…”

Section: Methodsmentioning

confidence: 99%

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

Band

Wells²,

Larrieu³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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302

275

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Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAAbased reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 908 gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 408 to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.environmental sensing | systems biology R oot gravitropism has fascinated researchers since Knight (1) and Darwin (2). More recently, reorientation of Arabidopsis seedlings has been shown to trigger the asymmetric release of the growth regulator auxin from gravity-sensing columella cells at the root apex (Fig. 1A) (3-5). The resulting lateral auxin gradient is hypothesized to drive a differential growth response, where cell expansion on the lower side of the elongation zone is reduced relative to the upper side, causing the root to bend downward (6-8). Despite representing one of the oldest hypotheses in plant biology, key questions about auxin-regulated root gravitropism remain to be experimentally determined. How rapidly does the lateral auxin gradient form? Is this timescale consistent with the theory that auxin redistribution drives root bending? How long does the lateral auxin gradient persist? What triggers auxin redistribution to return to equal levels?Our understanding of gravity-induced auxin redistribution has been limited by the tools available to monitor auxin concentrations at high spatiotemporal resolution. Currently, the most widely used tools to follow auxin distribution in tissues are auxin-inducible reporters such as DR5::GFP (3, 4). However, as an output of the auxin response pathway (Fig. 1B), the activity of the DR5 reporter does not directly relate to endogenous auxin abundance, but also depends on additional parameters including local auxin signaling capacities and rates of transcription and translation (Fig. 1B). In practice, these intermediate processes confer a time delay of ∼1.5-2 h between changes in auxin abundance and DR5 reporter activity (9, 4), making it difficult to quantify the speed and magnitude of fold changes in auxin distribution during a root gravitropic response.Auxi...

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Section: Methodsmentioning

confidence: 99%

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

Band

Wells²,

Larrieu³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

302

275

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“…These include growth on moistened germination paper rolls or pouches, sand rhizotrons, rhizoboxes, in compost followed by washing, soil columns and gelbased systems where phenotypic effects can be imaged using flatbed scanners, digital cameras, lasers, or even x-ray computed tomography (CT) (Hetz et al, 1996;Whiting et al, 2000;Bengough et al, 2004;Fang et al, 2009;French et al, 2009;Gregory et al, 2009;Hammond et al, 2009;Iyer-Pascuzzi et al, 2010;Trachsel et al, 2010;Tracy et al, 2010Tracy et al, , 2011Chapman et al, 2011;Lobet et al, 2011;Lucas et al, 2011). Magnetic resonance imaging (for noninvasive analysis of root structures) and positron emission tomography (for analysis of carbon transport and accumulation) can be combined to study the dynamics of structure-function relationships of roots in real soils in a noninvasive manner .…”

Section: How To Image Root Systems?mentioning

confidence: 99%

Analyzing Lateral Root Development: How to Move Forward

et al. 2012

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Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.Root system architecture is a key determinant of nutrient and water use efficiency and describes, on a macro scale, the organization of the primary root and root-and stemderived branches where they are present in monocots and dicots (Hochholdinger et al., 2004;De Smet et al., 2006;Hochholdinger and Zimmermann, 2008;Pé ret et al., 2009;Coudert et al., 2010

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“…These impediments also preclude use of the recently developed 'structure tensor' methods for automated determination of velocity fields (optical flow) (Schmundt et al, 1998;Walter et al, 2002;Palaniappan et al, 2004;French et al, 2009), which depend upon a high density of natural features along a continuously visible, expanding surface.…”

Section: Introductionmentioning

confidence: 99%

Developmentally equivalent tissue sampling based on growth kinematic profiling of Arabidopsis inflorescence stems

Hall

Ellis

2012

New Phytologist

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Summary• Directional growth in Arabidopsis thaliana during bolting of the inflorescence stem makes this an attractive system for study of the underlying processes of tissue elongation and cell wall extension. Analysis of local molecular events accompanying Arabidopsis inflorescence stem elongation is hampered by difficulties in isolating developmentally matched tissue samples from different plants.• Here, we present a novel sampling approach in which specific developmental stages along the developing stem are defined nonintrusively in terms of their relative elemental growth rate by use of time-lapse imagery and subsequent derivation of growth kinematic profiles for individual plants.• Growth kinematic profiling reveals that key developmental transitions such as the point of maximum elongation rate and the point of cessation of elongation occur over broad and overlapping ranges across individuals within a population of the Columbia (Col-0) ecotype. The position of these transitions is only weakly correlated with overall plant height, which undermines the common assumption that physically similar plants have closely matched growth profiles.• This kinematic profiling approach provides high-resolution growth phenotyping of the developing stem and thereby enables the harvest, pooling and analysis of developmentally matched tissue samples from multiple Arabidopsis plants.

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High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool

Cited by 186 publications

References 37 publications

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

Analyzing Lateral Root Development: How to Move Forward

Developmentally equivalent tissue sampling based on growth kinematic profiling of Arabidopsis inflorescence stems

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