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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 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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Published online 13 February 2015
Interspecific variation in branch and leaf traits among three Syzygium tree species from different successional tropical forests 
Shi-Dan Zhu, Ya-Jun Chen, Kun-Fang Cao and Qing Ye

Understanding how functional traits are associated with habitats is of great importance in plant biology. Through investigating a suite of branch and leaf functional traits of three Syzygium tree species in different successional tropical forests, we demonstrate that traits related to photosynthesis and/or hydraulics, rather than to drought tolerance, are key factors underlying the response and adaptation of these congeneric species to different environments.

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Published online 12 February 2015
Histo-anatomical leaf variations related to depth in Posidonia oceanica 
Silvia Nicastro, Anna M. Innocenti and Nicodemo G. Passalacqua

Neptune seagrass, (P. oceanica) plays an important biological and ecological role in marine ecosystems. We studied the acclimation capacity of P. oceanica at different depth and light regimes, finding that the inner structure of leaf cells changes in a way similar to that shown by phytoplankton cells to low light conditions. This result could offer new opportunities for understanding seagrass adaptations to the marine ecosystem.

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Published online 12 February 2015
Nitrogen sharing and water source partitioning co-occur in estuarine wetlands 
Lili Wei, David A. Lockington, Shen Yu and Catherine E. Lovelock

Co-existence mechanisms of different plant species in an ecosystem are one of the mysteries of nature. This field investigation in a natural estuarine ecosystem used isotopic fingerprints of water and nutrients to understand co-existing plant species in resource sharing or partitioning. Facilitation and competition were found co-occurring between two different plant pairs for water and nutrient in the estuarine wetlands.

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Published online 27 January 2015
Image based phenotyping during winter: a powerful tool to assess wheat genetic variation in growth response to temperature 
Christoph Grieder, Andreas Hund and Achim Walter

Rates of plant growth and their reaction to main environmental factors such as temperature are difficult to determine under field conditions. By segmenting plant leaves from background in images taken from wheat plots, we were able to show significant variation among varieties for their response in canopy cover growth rates to changing temperatures. The developed approach is simple and fast and can be used to screen genetic mapping populations for growth response patterns to temperature and other environmental factors.

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Published online 27 January 2015
Roles of gibberellins and cytokinins in regulation of morphological and physiological traits in Polygonum cuspidatum responding to light and nitrogen availabilities 
Daisuke Sugiura, Koichiro Sawakami, Mikiko Kojima, Hitoshi Sakakibara, Ichiro Terashima and Masaki Tateno

The regulatory mechanisms of biomass allocation and the morphological and physiological traits of leaves in response to light and N availability are not fully understood. We found that both gibberellins and cytokinins are closely involved in the regulatory mechanisms in Polygonum cuspidatum. The results will help to further our understanding of plant morphogenesis in response to light and N availability.

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Published online 12 January 2015
Ethylene is involved in high air humidity promoted stomatal opening of tomato (Lycopersicon esculentum) leaves 
Louise E. Arve and Sissel Torre

Stomata movements are regulated by air humidity. The aim of this work was to study the role of ethylene and abscisic acid in air humidity stomatal responses. We show that both ethylene production and sensitivity play a role in high air humidity promoted stomatal opening and that high level of abscisic acid can inhibit the opening. The results indicate an interaction between ethylene and abscisic acid and provide novel insight into the role of plant hormones in air humidity regulated stomatal movements.

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Published online 12 December 2014
The variability in the xylem architecture of grapevine petiole and its contribution to hydraulic differences 
Uri Hochberg, Asfaw Degu, Tanya Gendler, Aaron Fait and Shimon Rachmilevitch

Grapevine (Vitis vinifera) is known for its cultivar variability in response to deficit irrigation. A 3 year study, comparing Shiraz and Cabernet Sauvignon petioles anatomy, showed that Shiraz had larger vessels diameter that resulted in higher hydraulic conductivity and transpiration rates. These traits lead to lower water potentials and vulnerability to cavitation. Our results provide a link between xylem anatomy and plant performances.

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Published online 09 December 2014
Sufficient leaf transpiration and nonstructural carbohydrates are beneficial for high-temperature tolerance in three rice (Oryza sativa) cultivars and two nitrogen treatments 
Dongliang Xiong, Tingting Yu, Xiaoxia Ling, Shah Fahad, Shaobing Peng, Yong Li and Jianliang Huang

Extreme high temperature can threaten rice (Oryza sativa L.) production by decreasing its seed setting percentage; however, sufficient nitrogen can alleviate this detrimental effect. Heat-tolerant cultivars show high leaf transpiration and nonstructural carbohydrates, and sufficient nitrogen can improve them. This suggests that sufficient leaf transpiration and nonstructural carbohydrates are beneficial for high-temperature tolerance in three rice cultivars and two N treatments.

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Published online 09 December 2014
Plant hydraulic conductance adapts to shoot number but limits shoot vigour in grapevines 
Markus Keller, Laura S. Deyermond and Bhaskar R. Bondada

This study sought to provide a biophysical basis for the common observation that shoot vigour in grapevines declines as the number of shoots per plant increases. We found that the plant’s capacity to supply water to its canopy adapts to the shoot number; however, limited adaptation, rather than competition with fruit growth, may constrain shoot growth and fruit growth. These findings may be used to optimise cultural practices that balance shoot and fruit growth for maximum quality.

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Published online 02 December 2014
Hydrogen peroxide promotes programmed cell death and salicylic acid accumulation during the induced production of sesquiterpenes in cultured cell suspensions of Aquilaria sinensis 
Juan Liu, Yanhong Xu, Zheng Zhang and Jianhe Wei

We investigated the formation of agarwood, a substance believed to have interesting medicinal properties and that is produced only by certain plants when they are responding to an injury or infection. We evaluated the effects of hydrogen peroxide on cells of the plant Aquilaria sinensis; as we expected, the plant cells responded to this damaging chemical with specific changes in gene expression and the production of compounds known to be linked with toxicity and programmed cell death. Our results indicate that exposure to a reactive oxygen species, such as hydrogen peroxide, produces multiple cellular responses that culminate in an effective defensive reaction on the part of the plant (i.e. production of agarwood).

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Published online 02 December 2014
On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images 
Stefan Mairhofer, Craig Sturrock, Darren M. Wells, Malcolm J. Bennett, Sacha J. Mooney and Tony P. Pridmore

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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Published online 26 November 2014
Image-based estimation of oat panicle development using local texture patterns 
Roger Boyle, Fiona Corke and Catherine Howarth

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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Published online 05 November 2014
Automatic estimation of wheat grain morphometry from computed tomography data 
Harry Strange, Reyer Zwiggelaar, Craig Sturrock, Sacha J. Mooney and John H. Doonan

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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Published online 23 September 2014
Surface reconstruction of wheat leaf morphology from three-dimensional scanned data 
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

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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Published online 22 September 2014
Blobs and curves: object-based colocalisation for plant cells 
Carl J. Nelson, Patrick Duckney, Timothy J. Hawkins, Michael J. Deeks, P. Philippe Laissue, Patrick J. Hussey and Boguslaw Obara

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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Published online 19 August 2014
Automated estimation of leaf area development in sweet pepper plants from image analysis 
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

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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Volume 42 Number 3 2015

Subscriber Login

Descriptive Table of Contents 
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Functional Plant Biology in 2015: new features and incentives for authors 
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Sergey Shabala
pp. v-vi

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The structure and activity of nodulation-suppressing CLE peptide hormones of legumes 
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April H. Hastwell , Peter M. Gresshoff and Brett J. Ferguson
pp. 229-238

CLE peptides are critical regulators of plant development, and include members that control legume nodule numbers in symbiosis with nitrogen-fixing rhizobia bacteria. These peptides are essential for the host plant to maintain a balance between acquiring nitrogen and expending energy forming and maintaining nodules. The structure and function of all known nodulation-suppressing CLE peptides is the focus of this review.


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Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source 
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Huaiyu Yang , Jenny von der Fecht-Bartenbach , Jiří Friml , Jan U. Lohmann , Benjamin Neuhäuser and Uwe Ludewig
pp. 239-251

Ammonium and NO3 are the major nitrogen sources of plants. Although NH4+ is preferred, plant growth is suppressed at higher concentrations. Here, the transcriptomes of seedlings grown on (NH4)2SO4, KNO3 or NH4NO3 were compared. A major difference in auxin-regulated genes was observed and the importance of auxin was confirmed using mutants in the auxin pathway.

    | Supplementary Material (5 MB)

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Linking osmotic adjustment and stomatal characteristics with salinity stress tolerance in contrasting barley accessions 
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Min Zhu , Meixue Zhou , Lana Shabala and Sergey Shabala
pp. 252-263

Soil salinisation is a global issue that affects plant growth and limits agricultural production, and a comprehensive understanding of the mechanism of salt tolerance is essential for breeding salt-tolerant genotypes. Our results indicate that higher stomatal density and a predominant use of inorganic osmolytes are critical for the osmotic adjustment when barley exposed to salinity stress. These findings offer breeders new phenotyping methods for screening salt-tolerant genotypes, and provide a new insight into mechanisms of salt tolerance in this species.

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Water relations of an invasive halophyte (Spartina patens): osmoregulation and ionic effects on xylem hydraulics 
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Valentino Casolo , Martina Tomasella , Valentina De Col , Enrico Braidot , Tadeja Savi and Andrea Nardini
pp. 264-273

Invasive plants pose serious risks for conservation of coastal habitats. Spartina patens revealed physiological mechanisms based on salt uptake and accumulation, and ability to control the capacity of the plant to transport water, thus allowing colonisation of both dunes and marshes. Studies are needed to investigate the eventual occurrence of similar mechanisms in native species outcompeted by alien ones.


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Isolation and functional characterisation of CDPKs gene from Arachis hypogaea under salt stress 
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Yan Li , Feng Fang , Feng Guo , Jing-Jing Meng , Xin-Guo Li , Guang-Min Xia and Shu-Bo Wan
pp. 274-283

Calcium-dependent protein kinase (CDPK) is an important member of Ca2+-signal transduction pathway for plants to resist environmental stress. We cloned a peanut CDPK gene to analyse its function. The over-expressing AhCDPK improved resistance of tobacco to salt stress. Our results will help improve peanut salt resistance and further expand its cultivation in saline-alkali soils.

    | Supplementary Material (958 KB)

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Metabolomics deciphers quantitative resistance mechanisms in diploid potato clones against late blight 
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Kalenahalli N. Yogendra , Ajjamada C. Kushalappa , Felipe Sarmiento , Ernesto Rodriguez and Teresa Mosquera
pp. 284-298

Potato production is threatened worldwide by late blight disease, which destroys crops and lays a heavy financial burden on producers. Diploid potatoes with high disease resistance were analysed for the first time to identify the resistance related metabolites and associated genes responsible for impeding the pathogen. Phenylpropanoids, flavonoids, fatty acids and alkaloids induced reinforcement of secondary cell walls deterring pathogen advancement, and the genes involved can be used in breeding following validation.

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Intraspecific variation in leaf growth of wheat (Triticum aestivum) under Australian Grain Free Air CO2 Enrichment (AGFACE): is it regulated through carbon and/or nitrogen supply? 
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Chamindathee L. Thilakarathne , Sabine Tausz-Posch , Karen Cane , Robert M. Norton , Glenn J. Fitzgerald , Michael Tausz and Saman Seneweera
pp. 299-308

Increased plant growth and yield response to elevated [CO2] is closely associated with leaf area expansion. The main aim of this study was to investigate the mechanism of leaf area expansion and its genetic plasticity. Our results suggest that carbon supplies to growing leaves are cultivar dependent, and well correlated with leaf area expansion and whole-plant growth.


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Seasonal changes in the photosynthetic response to CO2 and temperature in apple (Malus domestica cv. ‘Red Gala’) leaves during a growing season with a high temperature event 
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Dennis H. Greer
pp. 309-324

Extreme summer temperatures are increasingly frequent and are known to cause a loss in crop productivity. The aim was to test the photosynthetic performance of economically important Malus domestica (apple) trees under these conditions and discovered that extreme heat compromised the photosynthetic process but recovery occurred when the temperatures subsided. These results provide a basis for comprehending the impact of climate change.


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How different pruning severities alter shoot structure: a modelling approach in young ‘Nonpareil’ almond trees 
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Claudia Negrón , Loreto Contador , Bruce D. Lampinen , Samuel G. Metcalf , Yann Guédon , Evelyne Costes and Theodore M. DeJong
pp. 325-335

Pruning clearly influences subsequent growth and structure of trees; however, systematic studies on shoot structural responses to pruning severity have been difficult due to shoot structural complexity. This research used a statistical modelling approach to characterise shoot structural responses to pruning severity in ‘Nonpareil’ almond trees. Shoot responses to pruning were relatively consistent and predictable among similar shoot types within pruning treatments while pruning severity increased shoot structural complexity.


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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.

    FP14240  Accepted 02 March 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, Peter Streb

    FP14343  Accepted 28 February 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 Ardie, Hugo Volkaert, George Ngando-Ebongue, S. Sudarsono

    FP14329  Accepted 24 February 2015
    Whole-plant respiration and its temperature sensitivity during progressive carbon starvation
    Martijn Slot, Kaoru Kitajima

    FP14224  Accepted 17 February 2015
    Impact of elevated atmospheric humidity on anatomical and hydraulic traits of xylem in hybrid aspen
    Anna Jasinska, Meeli Alber, Arvo Tullus, Märt Rahi, Arne Sellin

    FP14134  Accepted 12 February 2015
    Temperature responses of photosynthesis and respiration by a sub-Antarctic megaherb from Heard Island
    Marcus Schortemeyer, John Evans, Dan Bruhn, Dana Bergstrom, Marilyn Ball

    FP14250  Accepted 09 February 2015
    Leaf green-white variegation is advantageous under N deprivation in Pelargonium × hortorum
    Cyril Abadie, Marlene Lamothe, Caroline Mauve, Francoise Gilard, Guillaume Tcherkez

    FP14274  Accepted 07 February 2015
    Comparative proteomic and physiological characterization of two closely related rice genotypes with contrasting responses to salt stress
    Seyed Abdollah Hosseini, Javad Gharechahi, Manzar Heidari, Parisa Koobaz, Shapour Heidari, Mehdi Mirzaei, Babak Nakhoda, Ghasem Hosseini Salekdeh

    FP14350  Accepted 06 February 2015
    GOLDACRE REVIEW = Novel chlorophylls and new directions in photosynthesis research
    Yaqiong Li, Min Chen


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 8 April 2014
Drought resistance and soil water extraction of a perennial C4 grass: contributions of root and rhizome traits

Yi Zhou, Christopher J. Lambrides and Shu Fukai

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

John W. Patrick and Kim Colyvas

5. 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

6. Published 14 March 2014
Awn primordium to tipping is the most decisive developmental phase for spikelet survival in barley

Ahmad M. Alqudah and Thorsten Schnurbusch

7. 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

8. 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

9. 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

10. 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

11. Published 17 June 2014
Physiological, proteomic and transcriptional responses of wheat to combination of drought or waterlogging with late spring low temperature

Xiangnan Li, Jian Cai, Fulai Liu, Tingbo Dai, Weixing Cao and Dong Jiang

12. Published 14 March 2014
Differential physiological responses of different rice (Oryza sativa) cultivars to elevated night temperature during vegetative growth

Ulrike Glaubitz, Xia Li, Karin I. Köhl, Joost T. van Dongen, Dirk K. Hincha and Ellen Zuther

13. 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

14. Published 8 April 2014
Vapour pressure deficit aids the interpretation of cotton canopy temperature response to water deficit

Warren C. Conaty, James R. Mahan, James E. Neilsen and Greg A. Constable

15. 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

16. Published 8 April 2014
Soil water availability influences the temperature response of photosynthesis and respiration in a grass and a woody shrub

Tony Joseph, David Whitehead and Matthew H. Turnbull

17. Published 8 April 2014
More fertile florets and grains per spike can be achieved at higher temperature in wheat lines with high spike biomass and sugar content at booting

M. Fernanda Dreccer, Kimberley B. Wockner, Jairo A. Palta, C. Lynne McIntyre, M. Gabriela Borgognone, Maryse Bourgault, Matthew Reynolds and Daniel J. Miralles

18. Published 7 May 2014
Stomatal pore size and density in mangrove leaves and artificial leaves: effects on leaf water isotopic enrichment during transpiration

Leonel da Silveira Lobo Sternberg and Lynn M. Manganiello

19. 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

20. 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

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