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Protocols in ecological and environmental plant physiology


Functional Plant Biology publishes new and significant information on the functional biology of plants at all scales from the molecular through whole plant to community. More

Editor-in-Chief: Sergey Shabala


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Published online 04 May 2015
The decline in xylem flow to mango fruit at the end of its development is related to the appearance of embolism in the fruit pedicel 
Thibault Nordey, Mathieu Léchaudel and Michel Génard

Fruit water balance changes during the late growth stage in part due to xylem flow decrease. Our measurements on mango revealed that the decline in xylem flow was related to the decrease in the hydraulic conductivity of xylem vessels due to embolism. The xylem decrease in the later growth stage could affect fruit growth and fruit mineral composition.

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Published online 30 April 2015
Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance 
Walter Ajambang, Sintho W. Ardie, Hugo Volkaert, Georges F. Ngando-Ebongue and Sudarsono Sudarsono

In some cases, induction of male flower inflorescences in oil palm is difficult to accomplish. Investigation to explore part of the possible ways to induce male flower inflorescences from Pisifera oil palm and understanding the molecular processes associated with it have been investigated and answered. The findings may be important in the management of commercial oil palm production especially under changing climate conditions.

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Published online 17 April 2015
Temperature responses of photosynthesis and respiration in a sub-Antarctic megaherb from Heard Island 
Marcus Schortemeyer, John R. Evans, Dan Bruhn, Dana M. Bergstrom and Marilyn C. Ball

Climate warming may affect carbon gain and loss, with consequences for growth of cold climate species. Responses of photosynthesis and respiration to temperature were studied in Pringlea antiscorbutica R. Br. along an altitudinal gradient on sub-Antarctic Heard Island. The results showed greater importance of thermal acclimation of respiration than photosynthesis to maintenance of favourable carbon balances with increasing temperature range.

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Published online 16 April 2015
Dynamic carbon allocation into source and sink tissues determine within-plant differences in carbon isotope ratios 
Frederik Wegener, Wolfram Beyschlag and Christiane Werner

Plant organs of C3 plants differ in their C isotopic signature (δ13C) but the underlying mechanisms are still unclear. We induced different allocation strategies and found that the spatial δ13C variation within plants was strongly influenced by the life stage of the leaves. These results are important, as foliar δ13C is used in many fields of plant science (e.g. for estimating photosynthetic isotope fractionation).

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Published online 10 April 2015
In vivo epidermal UV-A absorbance is induced by sunlight and protects Soldanella alpina leaves from photoinhibition 
Constance Laureau, Sylvie Meyer, Xavier Baudin, Christophe Huignard and Peter Streb

High intensities of UV radiation and visible light are important stress factors affecting plants’ photosynthetic performance, particularly in the mountains. Protection from this stress is provided by UV-absorbing pigments in the epidermis of Soldanella alpina leaves and is induced by visible light. This UV shielding protects leaves from photodamage in their natural environment.

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Published online 10 April 2015
Photosynthetic characteristics and light energy conversions under different light environments in five tree species occupying dominant status at different stages of subtropical forest succession 
Qiang Zhang, Tai-Jie Zhang, Wah Soon Chow, Xin Xie, Yuan-Jun Chen and Chang-Lian Peng

How light drives the development of forest ecosystems is still not fully understood. The aim of this study is to reveal the mechanism driving subtropical forest succession along a light gradient. Our results indicate that photosynthetic capacity decreases along the successional axis and that late-successional species have more responsive energy dissipation capability to compensate for their inferior photosynthetic capacity.

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Published online 10 April 2015
Crosstalk among nitric oxide, calcium and reactive oxygen species during triterpenoid biosynthesis in Betula platyphylla 
Fansuo Zeng, Kun Liu, Sida Li and Yaguang Zhan

Crosstalk among NO, reactive oxygen species (ROS) and Ca2+ in tree species was not clear. The study showed that NO plays important roles in the synthesis and accumulation of triterpenoids in birch by regulating the intracellular ROS and Ca2+ signalling pathway. These results provide the theoretical basis and the technical support required for the use of triterpenoid biotechnology.

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Published online 10 April 2015
The role of oxidative stress in determining the level of viability of black poplar (Populus nigra) seeds stored at different temperatures 
Ewa Marzena Kalemba, Jan Suszka and Ewelina Ratajczak

Black poplar (Populus nigra L.) is one of the most threatened tree species in Europe and they produce seeds characterised by short longevity. Oxidative stress increases during seed storage and injures seed tissues resulting in a loss of viability, particularly at temperatures higher than -10°C. Successful storage of seeds might be prolonged when specific low temperature is applied that minimises oxidative stress effects.

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Published online 26 March 2015
Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress 
Seyed Abdollah Hosseini, Javad Gharechahi, Manzar Heidari, Parisa Koobaz, Shapour Abdollahi, Mehdi Mirzaei, Babak Nakhoda and Ghasem Hosseini Salekdeh

According to a two-phase growth response concept, genotypes with differing susceptibility to salinity usually develop distinct responses when excess salt accumulates in their tissues. In this study, two rice genotypes (IR29 and FL478) were exposed to salt stress until they showed distinct growth. Their physiology and proteome responses were analysed. The sensitivity of IR29 to salinity may be due to its inability to exclude salt, compartmentalise excess ions or maintain its photosynthetic apparatus in a healthy state under salt stress.

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Published online 23 March 2015
Whole-plant respiration and its temperature sensitivity during progressive carbon starvation 
Martijn Slot and Kaoru Kitajima

Carbon release from plant respiration increases with temperature. Although it is thought that low sugar concentrations limit the rate of this increase, this has not been tested at the whole-plant level. When we sugar-starved Ardisia crenata plants, respiration decreased but, surprisingly, the sensitivity of respiration to warming increased. These results highlight the complexity of the controls over plant respiration, especially at the whole-plant level.

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Published online 20 March 2015
Impact of elevated atmospheric humidity on anatomical and hydraulic traits of xylem in hybrid aspen 
Anna Katarzyna Jasi?ska, Meeli Alber, Arvo Tullus, Märt Rahi and Arne Sellin

The Free Air Humidity Manipulation (FAHM) experiment offers unique possibilities to test trees’ acclimation capacity to increasing atmospheric humidity – a climate trend predicted for northern Europe. We investigated changes in wood anatomy and hydraulic conductivity in hybrid aspen; results showed moderate modifications in both the structure and functioning of xylem. Our results suggest that hybrid aspen is relatively insensitive to the changes in air humidity.

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Published online 17 March 2015
Leaf green-white variegation is advantageous under N deprivation in Pelargonium×hortorum 
Cyril Abadie, Marlène Lamothe, Caroline Mauve, Françoise Gilard and Guillaume Tcherkez

Growth and metabolism of green-white variegated and plain morphs of Pelargonium have been examined under nitrogen deficiency. Variegated plants performed better than non-variegated plants, owing to the remobilisation of nitrogenous compounds stored in leaf white areas. It is concluded that variegation is disadvantageous under non N-limited conditions due to the lower photosynthetic surface area, but is advantageous under nitrogen deprivation.

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Published online 06 March 2015
Novel chlorophylls and new directions in photosynthesis research 
Yaqiong Li and Min Chen

Chlorophylls d and f are red-shifted chlorophylls based on their significantly red-shifted absorption bands compared with chlorophyll a. Understanding the molecular mechanism of photosynthesis driven by red-shifted chlorophylls is of global importance and will contribute to cutting-edge photosynthetic research. The current research status in related to the red-shifted chlorophylls is reviewed in this review.

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Published online 24 February 2015
Towards a conceptual ABA ideotype in plant breeding for water limited environments 
Abraham Blum

ABA is a plant hormone produced in plants under drought stress. On one hand, it causes the plant to conserve its water status; on the other hand, it reduces growth and productivity. This opinion review examines the available data on ABA and attempts to resolve this conundrum by formulating an appropriate crop plant phenotypic ABA ideotype for breeders to pursue within different dryland stress environments.

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Published online 17 February 2015
Effects of different temperature regimes on flower development, microsporogenesis and fertility in bolting garlic (Allium sativum) 
Einat Shemesh Mayer, Tomer Ben-Michael, Sagie Kimhi, Itzhak Forer, Haim D. Rabinowitch and Rina Kamenetsky

Infertility prevents genetics research and conventional breeding in garlic. Recent achievement of fertility restoration enables extensive studies of garlic florogenesis and causes for male sterility. We report on temperature effects on flower development and pollen quality in fertile and male-sterile garlic, and on the vulnerable phases of pollen formation. It is concluded that under unstable climatic conditions, agro-management modifications will facilitate breeding and seed production in this important crop.

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blank image Functional Plant Biology
Volume 42 Number 5 2015
Plant Image Analysis

Subscriber Login

Descriptive Table of Contents 
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From image processing to computer vision: plant imaging grows up 
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Hannah Dee and Andrew French
pp. iii-v

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Image-based estimation of oat panicle development using local texture patterns 
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Roger Boyle, Fiona Corke and Catherine Howarth
pp. 433-443

High-throughput phenotyping facilities provide opportunities for plant development observation and monitoring on new scales, but also present new problems in automatic image analysis. This paper presents a solution to one such problem by automating the detection of flowering in oats. This demonstrates the applicability of state-of-the-art computer vision algorithms to phenotyping, which may well be of value in similar atlas-based measurement.


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Surface reconstruction of wheat leaf morphology from three-dimensional scanned data 
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Daryl M. Kempthorne, Ian W. Turner, John A. Belward, Scott W. McCue, Mark Barry, Joseph Young, Gary J. Dorr, Jim Hanan and Jerzy A. Zabkiewicz
pp. 444-451

Realistic virtual models of leaf surfaces are important for several applications in plant sciences, such as simulating agrichemical spray droplet motion on the leaf surface. Although there are effective approaches for reconstructing leaf surface from 3D scanned data, complications arise when dealing with wheat (Triticum aestivum) leaves, which tend to twist and bend. We present an algorithm that overcomes this topological difficulty, allowing significantly more leaf varieties to be modelled in this way.


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Automatic estimation of wheat grain morphometry from computed tomography data 
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Harry Strange, Reyer Zwiggelaar, Craig Sturrock, Sacha J. Mooney and John H. Doonan
pp. 452-459

Accurate and non-invasive measures of wheat grain morphometry can have impact on improvements in milling yield. An automated approach is presented to extract such measures from wheat CT data. The results show significant differences in measures between two disparate strains of wheat.


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On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images 
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Stefan Mairhofer, Craig Sturrock, Darren M. Wells, Malcolm J. Bennett, Sacha J. Mooney and Tony P. Pridmore
pp. 460-470

The evaluation of root system recovery methods for X-ray microcomputed tomography images is a challenging task. In this work, we aim to raise awareness of the evaluation problem and to propose experimental approaches that allow the performance of root extraction methods to be assessed. This should help users to better understand the strengths and limitations of each method and should allow a better comparison.


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Blobs and curves: object-based colocalisation for plant cells 
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Carl J. Nelson, Patrick Duckney, Timothy J. Hawkins, Michael J. Deeks, P. Philippe Laissue, Patrick J. Hussey and Boguslaw Obara
pp. 471-485

Quantifying the colocalisation of labels is a major application of fluorescent microscopy in plant biology. Pixel-based quantification of colocalisation, such as Pearson’s correlation coefficient, gives limited information for further analysis. We show how applying bioimage informatics tools to a commonplace experiment allows further quantifiable results to be extracted. We use our object-based colocalisation technique to extract distance information, show temporal changes and demonstrate the advantages and pitfalls of using bioimage informatics for plant science.


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Automated estimation of leaf area development in sweet pepper plants from image analysis 
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Graham W. Horgan, Yu Song, Chris A. Glasbey, Gerie W. A. M. van der Heijden, Gerrit Polder, J. Anja Dieleman, Marco C. A. M. Bink and Fred A. van Eeuwijk
pp. 486-492

The total area of the leaves on a plant is important in horticulture, but manually measuring it is tedious and destructive. Getting a computer to recognise and count leaves is difficult, so we have used statistical methods to relate leaf area to the variations in colour in an image. This has potential to be a big help for scientists developing and testing new crop cultivars.


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These articles have been peer reviewed and accepted for publication. They are still in production and have not been edited, so may differ from the final published form.

    FP14356  Accepted 29 April 2015
    Selectable marker-free co-expression of Nicotiana rustica CN and Nicotiana tabacum HAK1 genes improves resistance to tobacco mosaic virus in tobacco
    Lijun Qin, Dan Zhao, Yi Zhang, Degang Zhao

    FP15045  Accepted 27 April 2015
    Alkaloid production and capacity for methyljasmonate induction by hairy roots of two species in Tribe Anthocercideae, family Solanaceae.
    Suzanne Ryan, Kathleen DeBoer, John Hamill

    FP15068  Accepted 24 April 2015
    Photon flux density and temperature-dependent responses of photosynthesis and photosystem II performance of apple leaves grown in field conditions
    Dennis Greer

    FP15054  Accepted 24 April 2015
    Interactive effect of biochar and plant growth-promoting bacterial endophytes on ameliorating salinity stress in maize
    Saqib Akhtar, Mathias Andersen, Muhammad Naveed, Zahir Zahir, Fulai Liu

    FP14307  Accepted 24 April 2015
    Novel insights in Citrus sinensis non-host response denote photosynthesis decline, abiotic stress networks and secondary metabolism modifications
    Lucas Daurelio, María Tondo, María Romero, Paz Merelo, Adriana Cortadi, Manuel Talon, Francisco Tadeo, Elena Orellano

    FP15002  Accepted 21 April 2015
    Pilar Cendrero Mateo, A. Elizabete Carmo-Silva, Albert Porcar-Castell, Erik Hamerlynck, Shirley Papuga, Susan Moran

    FP15008  Accepted 20 April 2015
    Spatial heterogeneity in stomatal features during leaf elongation: an analysis using Rosa hybrida
    Dimitrios Fanourakis, Ep Heuvelink, Susana Carvalho

    FP15052  Accepted 16 April 2015
    Variation potential induces decreased photosystem I damage and increased photosystem II damage under high external temperature in pea
    Vladimir Sukhov, Lyubov Surova, Oksana Sherstneva, Albina Bushueva, Vladimir Vodeneev

    FP14294  Accepted 15 April 2015
    A possible link between hydraulic properties and leaf habits in Hevea brasiliensis
    Wen Chen, Kun-Fang Cao

    FP15021  Accepted 13 April 2015
    Cryptic crassulacean acid metabolism (CAM) in Jatropha curcas L.
    Klaus Winter, Joseph Holtum

    FP14127  Accepted 13 April 2015
    Sapwood allocation in tropical trees: a test of hypotheses
    Peter Schippers, Mart Vlam, Pieter Zuidema, Frank Sterck

    FP15057  Accepted 11 April 2015
    Heterogeneity of photosynthesis within leaves is associated with alteration of leaf structural features and leaf N content per leaf area in rice
    Dongliang Xiong, Tingting Yu, Xi Liu, Yong Li, Shaobing Peng, Jianliang Huang

    FP15026  Accepted 02 April 2015
    Genetic Suppression of Plant Development and Chloroplast Biogenesis by SCO3 and PhyB Pathways
    Diep Ganguly, Peter Crisp, Klaus Harter, Barry Pogson, Veronica Albrecht-Borth


The Most Read ranking is based on the number of downloads from the CSIRO PUBLISHING website of articles published in the previous 12 months. Usage statistics are updated daily.

Rank Paper Details
1. Published 13 February 2015
The structure and activity of nodulation-suppressing CLE peptide hormones of legumes

April H. Hastwell, Peter M. Gresshoff and Brett J. Ferguson

2. Published 30 September 2014
Genomics for drought resistance – getting down to earth

Abraham Blum

3. Published 14 August 2014
Crop yield components – photoassimilate supply- or utilisation limited-organ development?

John W. Patrick and Kim Colyvas

4. Published 7 May 2014
Variation in mesophyll conductance among Australian wheat genotypes

Eisrat Jahan, Jeffrey S. Amthor, Graham D. Farquhar, Richard Trethowan and Margaret M. Barbour

5. Published 30 September 2014
Mucilage exudation facilitates root water uptake in dry soils

Mutez A. Ahmed, Eva Kroener, Maire Holz, Mohsen Zarebanadkouki and Andrea Carminati

6. Published 14 July 2014
Photosynthesis–nitrogen relationships in tropical forest tree species as affected by soil phosphorus availability: a controlled environment study

Keith J. Bloomfield, Graham D. Farquhar and Jon Lloyd

7. Published 30 September 2014
Strategies to increase the yield and yield stability of crops under drought – are we making progress?

Neil C. Turner, Abraham Blum, Mehmet Cakir, Pasquale Steduto, Roberto Tuberosa and Neil Young

8. Published 14 August 2014
When smaller is better: leaf hydraulic conductance and drought vulnerability correlate to leaf size and venation density across four Coffea arabica genotypes

Andrea Nardini, Eele Õunapuu-Pikas and Tadeja Savi

9. Published 30 September 2014
Two potato (Solanum tuberosum) varieties differ in drought tolerance due to differences in root growth at depth

Jaime Puértolas, Carlos Ballester, E. David Elphinstone and Ian C. Dodd

10. Published 14 August 2014
Review on shape formation in epidermal pavement cells of the Arabidopsis leaf

Eveline Jacques, Jean-Pierre Verbelen and Kris Vissenberg

11. Published 7 May 2014
Spring barley shows dynamic compensatory root and shoot growth responses when exposed to localised soil compaction and fertilisation

Johannes Pfeifer, Marc Faget, Achim Walter, Stephan Blossfeld, Fabio Fiorani, Ulrich Schurr and Kerstin A. Nagel

12. Published 30 September 2014
Partial root zone drying exerts different physiological responses on field-grown grapevine (Vitis vinifera cv. Monastrell) in comparison to regulated deficit irrigation

Pascual Romero, Juan Gabriel Pérez-Pérez, Francisco M. del Amor, Adrián Martinez-Cutillas, Ian C. Dodd and Pablo Botía

13. Published 7 May 2014
Environmental stress activation of plant long-terminal repeat retrotransposons

Ahmed M. Alzohairy, Jamal S. M. Sabir, Gábor Gyulai, Rania A. A. Younis, Robert K. Jansen and Ahmed Bahieldin

14. Published 7 January 2015
High night temperature induces contrasting responses for spikelet fertility, spikelet tissue temperature, flowering characteristics and grain quality in rice

Onoriode Coast, Richard H. Ellis, Alistair J. Murdoch, Cherryl Quiñones and Krishna S. V. Jagadish

15. Published 30 September 2014
Individual and combined effects of transient drought and heat stress on carbon assimilation and seed filling in chickpea

Rashmi Awasthi, Neeru Kaushal, Vincent Vadez, Neil C. Turner, Jens Berger, Kadambot H. M. Siddique and Harsh Nayyar

16. Published 30 September 2014
Physiological basis of salt stress tolerance in rice expressing the antiapoptotic gene SfIAP

Thi My Linh Hoang, Brett Williams, Harjeet Khanna, James Dale and Sagadevan G. Mundree

17. Published 14 August 2014
Responses of rice to Fe2+ in aerated and stagnant conditions: growth, root porosity and radial oxygen loss barrier

Jenjira Mongon, Dennis Konnerup, Timothy D. Colmer and Benjavan Rerkasem

18. Published 30 September 2014
Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

John T. Christopher, Mathieu Veyradier, Andrew K. Borrell, Greg Harvey, Susan Fletcher and Karine Chenu

19. Published 30 September 2014
Quantitative trait locus mapping of the transpiration ratio related to preflowering drought tolerance in sorghum (Sorghum bicolor)

Mohankumar H. Kapanigowda, William A. Payne, William L. Rooney, John E. Mullet and Maria Balota

20. Published 17 June 2014
Seed storage albumins: biosynthesis, trafficking and structures

Joshua S. Mylne, Ikuko Hara-Nishimura and K. Johan Rosengren

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