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Plant Phenotyping and Phenomics

© ©  Humplík et al. Plant Methods 201511:29Plant Methods is delighted to announce the launch of our special Thematic Series on Plant Phenotyping and Phenomics with the publication of three new methodology papers, all focusing on different solutions to the challenges of plant phenotyping.

Combined with three other recently published papers on the same topic, this collection is the starting point for what will be on on-going series of review papers and methodology papers on Plant Phenotyping and Phenomics that we will publish over the coming months. This collection includes a number of invited contributions from speakers at the 3rd International Plant Phenotyping Symposium: Phenotyping for Agricultural Sustainability (Chennai, India, 17-19th February 2014).

This thematic series covers all aspects of phenotyping and phenomics technologies as applied to plant research, including:
• Plant phenotyping technologies for the lab, greenhouse or field
• Plant growth analysis
• Novel sensors
• Image analysis
• Data management and integration
• Applications of modelling to plant phenotyping

Collection published: 6 November 2014
Last updated: 29 January 2016

Prof Brian Forde, Dr Mike Roberts, Prof Uli Schurr, co-edited by Prof. Uli Schurr and the Plant Methods Editorial Team.

  1. Content type: Research

    Recent advances in genome sequencing technologies have shifted the research bottleneck in plant sciences from genotyping to phenotyping. This shift has driven the development of phenomics, high-throughput non-...

    Authors: Pádraic J. Flood, Willem Kruijer, Sabine K. Schnabel, Rob van der Schoor, Henk Jalink, Jan F. H. Snel, Jeremy Harbinson and Mark G. M. Aarts

    Citation: Plant Methods 2016 12:14

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  2. Content type: Methodology

    Plant growth is a good indicator of crop performance and can be measured by different methods and on different spatial and temporal scales. In this study, we measured the canopy height growth of maize (Zea mays),...

    Authors: Michael Friedli, Norbert Kirchgessner, Christoph Grieder, Frank Liebisch, Michael Mannale and Achim Walter

    Citation: Plant Methods 2016 12:9

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  3. Content type: Commentary

    The importance of appropriate, accurate measurement and reporting of environmental parameters in plant sciences is a significant aspect of quality assurance for all researchers and their research. There is a c...

    Authors: A J Both, L Benjamin, J Franklin, G Holroyd, L D Incoll, M G Lefsrud and G Pitkin

    Citation: Plant Methods 2015 11:43

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  4. Content type: Methodology

    X-ray computed tomography (CT) has become a powerful tool for root phenotyping. Compared to rather classical, destructive methods, CT encompasses various advantages. In pot experiments the growth and developme...

    Authors: Johannes Pfeifer, Norbert Kirchgessner, Tino Colombi and Achim Walter

    Citation: Plant Methods 2015 11:41

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  5. Content type: Methodology

    Recent developments in unmanned aerial platforms (UAP) have provided research opportunities in assessing land allocation and crop physiological traits, including response to abiotic and biotic stresses. UAP-ba...

    Authors: M Zaman-Allah, O Vergara, J L Araus, A Tarekegne, C Magorokosho, P J Zarco-Tejada, A Hornero, A Hernández Albà, B Das, P Craufurd, M Olsen, B M Prasanna and J Cairns

    Citation: Plant Methods 2015 11:35

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  6. Content type: Methodology

    A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. This process has been used extensively in Arabidopsis to estimate circadian period in natural accessions a...

    Authors: Kathleen Greenham, Ping Lou, Sara E Remsen, Hany Farid and C Robertson McClung

    Citation: Plant Methods 2015 11:33

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  7. Content type: Review

    Over the last two decades, the development of high-throughput techniques has enabled us to probe the plant circadian clock, a key coordinator of vital biological processes, in ways previously impossible. With ...

    Authors: Andrew J Tindall, Jade Waller, Mark Greenwood, Peter D Gould, James Hartwell and Anthony Hall

    Citation: Plant Methods 2015 11:32

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  8. Content type: Review

    Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology studies. The self-constructed and commercial platforms established in the last few years, employ non-destructiv...

    Authors: Jan F Humplík, Dušan Lazár, Alexandra Husičková and Lukáš Spíchal

    Citation: Plant Methods 2015 11:29

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  9. Content type: Methodology

    The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized b...

    Authors: Matheus Kuska, Mirwaes Wahabzada, Marlene Leucker, Heinz-Wilhelm Dehne, Kristian Kersting, Erich-Christian Oerke, Ulrike Steiner and Anne-Katrin Mahlein

    Citation: Plant Methods 2015 11:28

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  10. Content type: Methodology

    Image analysis is increasingly used in plant phenotyping. Among the various imaging techniques that can be used in plant phenotyping, chlorophyll fluorescence imaging allows imaging of the impact of biotic or ...

    Authors: Céline Rousseau, Gilles Hunault, Sylvain Gaillard, Julie Bourbeillon, Gregory Montiel, Philippe Simier, Claire Campion, Marie-Agnès Jacques, Etienne Belin and Tristan Boureau

    Citation: Plant Methods 2015 11:24

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  11. Content type: Methodology

    Effects of abiotic and biotic stresses on plant photosynthetic performance lead to fitness and yield decrease. The maximum quantum efficiency of photosystem II (F v/F m) is a p...

    Authors: Justine Bresson, François Vasseur, Myriam Dauzat, Garance Koch, Christine Granier and Denis Vile

    Citation: Plant Methods 2015 11:23

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  12. Content type: Methodology

    Recently emerging approaches to high-throughput plant phenotyping have discovered their importance as tools in unravelling the complex questions of plant growth, development and response to the environment, bo...

    Authors: Jan F Humplík, Dušan Lazár, Tomáš Fürst, Alexandra Husičková, Miroslav Hýbl and Lukáš Spíchal

    Citation: Plant Methods 2015 11:20

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  13. Content type: Methodology

    Roots are vital to plants for soil exploration and uptake of water and nutrients. Root performance is critical for growth and yield of plants, in particular when resources are limited. Since roots develop in s...

    Authors: Ralf Metzner, Anja Eggert, Dagmar van Dusschoten, Daniel Pflugfelder, Stefan Gerth, Ulrich Schurr, Norman Uhlmann and Siegfried Jahnke

    Citation: Plant Methods 2015 11:17

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  14. Content type: Review

    Terahertz technology is still an evolving research field that attracts scientists with very different backgrounds working on a wide range of subjects. In the past two decades, it has been demonstrated that ter...

    Authors: Ralf Gente and Martin Koch

    Citation: Plant Methods 2015 11:15

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  15. Content type: Review

    Plant phenotyping refers to a quantitative description of the plant’s anatomical, ontogenetical, physiological and biochemical properties. Today, rapid developments are taking place in the field of non-destruc...

    Authors: Achim Walter, Frank Liebisch and Andreas Hund

    Citation: Plant Methods 2015 11:14

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  16. Content type: Methodology

    Water availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root system architecture has important functional implications for the timing ...

    Authors: Cecile AI Richard, Lee T Hickey, Susan Fletcher, Raeleen Jennings, Karine Chenu and Jack T Christopher

    Citation: Plant Methods 2015 11:13

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  17. Content type: Software

    Three-dimensional canopies form complex architectures with temporally and spatially changing leaf orientations. Variations in canopy structure are linked to canopy function and they occur within the scope of g...

    Authors: Mark Müller-Linow, Francisco Pinto-Espinosa, Hanno Scharr and Uwe Rascher

    Citation: Plant Methods 2015 11:11

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  18. Content type: Methodology

    Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language a...

    Authors: Anika Oellrich, Ramona L Walls, Ethalinda KS Cannon, Steven B Cannon, Laurel Cooper, Jack Gardiner, Georgios V Gkoutos, Lisa Harper, Mingze He, Robert Hoehndorf, Pankaj Jaiswal, Scott R Kalberer, John P Lloyd, David Meinke, Naama Menda, Laura Moore…

    Citation: Plant Methods 2015 11:10

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  19. Content type: Methodology

    Field-based high throughput phenotyping is a bottleneck for crop breeding research. We present a novel method for repeated remote phenotyping of maize genotypes using the Zeppelin NT aircraft as an experimenta...

    Authors: Frank Liebisch, Norbert Kirchgessner, David Schneider, Achim Walter and Andreas Hund

    Citation: Plant Methods 2015 11:9

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  20. Content type: Methodology

    The water status in plant leaves is a good indicator for the water status in the whole plant revealing stress if the water supply is reduced. The analysis of dynamic aspects of water availability in plant tiss...

    Authors: Said Dadshani, Andriy Kurakin, Shukhrat Amanov, Benedikt Hein, Heinz Rongen, Steve Cranstone, Ulrich Blievernicht, Elmar Menzel, Jens Léon, Norbert Klein and Agim Ballvora

    Citation: Plant Methods 2015 11:8

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  21. Content type: Review

    We review a set of recent multiscale imaging techniques, producing high-resolution images of interest for plant sciences. These techniques are promising because they match the multiscale structure of plants. H...

    Authors: David Rousseau, Yann Chéné, Etienne Belin, Georges Semaan, Ghassen Trigui, Karima Boudehri, Florence Franconi and François Chapeau-Blondeau

    Citation: Plant Methods 2015 11:6

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  22. Content type: Methodology

    Piercing-sucking insects are major vectors of plant viruses causing significant yield losses in crops. Functional genomics of plant resistance to these insects would greatly benefit from the availability of hi...

    Authors: Karen J Kloth, Cindy JM ten Broeke, Manus PM Thoen, Marianne Hanhart-van den Brink, Gerrie L Wiegers, Olga E Krips, Lucas PJJ Noldus, Marcel Dicke and Maarten A Jongsma

    Citation: Plant Methods 2015 11:4

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  23. Content type: Methodology

    Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system architectu...

    Authors: Laura Mathieu, Guillaume Lobet, Pierre Tocquin and Claire Périlleux

    Citation: Plant Methods 2015 11:3

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  24. Content type: Methodology

    Combined assessment of leaf reflectance and transmittance is currently limited to spot (point) measurements. This study introduces a tailor-made hyperspectral absorption-reflectance-transmittance imaging (Hype...

    Authors: Sergej Bergsträsser, Dimitrios Fanourakis, Simone Schmittgen, Maria Pilar Cendrero-Mateo, Marcus Jansen, Hanno Scharr and Uwe Rascher

    Citation: Plant Methods 2015 11:1

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  25. Content type: Methodology

    In grasses, leaf growth is often monitored to gain insights in growth processes, biomass accumulation, regrowth after cutting, etc. To study the growth dynamics of the grass leaf, its length is measured at reg...

    Authors: Wannes Voorend, Peter Lootens, Hilde Nelissen, Isabel Roldán-Ruiz, Dirk Inzé and Hilde Muylle

    Citation: Plant Methods 2014 10:37

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  26. Content type: Methodology

    The color of crop leaves is closely correlated with nitrogen (N) status and can be quantified easily with a digital still color camera and image processing software. The establishment of the relationship betwe...

    Authors: Yuan Wang, Dejian Wang, Peihua Shi and Kenji Omasa

    Citation: Plant Methods 2014 10:36

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  27. Content type: Methodology

    Measuring grain characteristics is an integral component of cereal breeding and research into genetic control of seed development. Measures such as thousand grain weight are fast, but do not give an indication...

    Authors: Alex P Whan, Alison B Smith, Colin R Cavanagh, Jean-Philippe F Ral, Lindsay M Shaw, Crispin A Howitt and Leanne Bischof

    Citation: Plant Methods 2014 10:23

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  28. Content type: Methodology

    A quantitative characterization of root system architecture is currently being attempted for various reasons. Non-destructive, rapid analyses of root system architecture are difficult to perform due to the hid...

    Authors: Chantal Le Marié, Norbert Kirchgessner, Daniela Marschall, Achim Walter and Andreas Hund

    Citation: Plant Methods 2014 10:13

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  29. Content type: Methodology

    Light curtain arrays (LC), a recently introduced phenotyping method, yield a binary data matrix from which a shoot silhouette is reconstructed. We addressed the accuracy and applicability of LC in assessing le...

    Authors: Dimitrios Fanourakis, Christoph Briese, Johannes FJ Max, Silke Kleinen, Alexander Putz, Fabio Fiorani, Andreas Ulbrich and Ulrich Schurr

    Citation: Plant Methods 2014 10:9

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