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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 25 May 2016
The influence of water stress on grapevine (Vitis vinifera L.) shoots in a cool, humid climate: growth, gas exchange and hydraulics 
Vinay Pagay, Vivian Zufferey and Alan N. Lakso

Seasonal soil moisture deficits are known to negatively affect growth and productivity of grapevines in semiarid climates; however, less is known about the effects of reduced moisture availability in cooler and wetter regions. Here, we characterise the physiological and hydraulic responses of grapevines to reduced soil water availability in a cool climate and show that these responses differ between grapevines as well as within grapevines at the level of individual shoots based on their size.

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Published online 23 May 2016
Understanding the regulation of iron nutrition: can it contribute to improving iron toxicity tolerance in rice? 
Geoffrey Onaga, Khady Nani Dramé and Abdelbagi M. Ismail

Molecular mechanisms underlying iron nutrition and regulation are not fully exploited for rice improvement against Fe-toxicity. It is vital to understand these mechanisms to unravel effective pathways for improving rice tolerance. A hypothetical genetic model for Fe toxicity tolerance in rice is presented, and key genes and proteins involved are discussed to provide future prospects for improved rice tolerance to Fe toxicity.

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Published online 18 May 2016
Integrated transcriptomics and metabolomics reveal induction of hierarchies of resistance genes in potato against late blight 
Kalenahalli N. Yogendra and Ajjamada C. Kushalappa

Potato production is threatened worldwide by late blight disease. A metabolo-transcriptomics approach revealed hierarchies of resistance genes triggered following pathogen invasion, including receptors, MAP kinases, phytohormones and transcription factor genes that regulated the downstream genes to biosynthesise phenylpropanoids, flavonoids, fatty acids and alkaloid metabolites to reinforce secondary cell walls, deterring pathogen advancement. These genes can be used in breeding following validation.

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Published online 17 May 2016
Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots 
Almudena Ferrández-Ayela, Ana Belén Sánchez-García, Cristina Martínez-Andújar, Zoltan Kevei, Miriam L. Gifford, Andrew J. Thompson, Francisco Pérez-Alfocea and José Manuel Pérez-Pérez

In nature and in the field, plants and crops are commonly exposed to different stresses. By screening public gene expression data, we identified several conserved stress-responsive genes in tomato roots that could be used as biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available.

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Published online 17 May 2016
Separating species and environmental determinants of leaf functional traits in temperate rainforest plants along a soil-development chronosequence 
Matthew H. Turnbull, Kevin L. Griffin, Nikolaos M. Fyllas, Jon Lloyd, Patrick Meir and Owen K. Atkin

In this research we measured ways in which rainforest trees and shrubs change their leaf function in response to massive changes in soil nutrient availability along a 120 000 year soil chronosequence in New Zealand. Leaf density/thickness and photosynthetic rates were most strongly affected by changes in species along the gradient, while leaf phosphorus and nitrogen content were most strongly influenced by changes in nutrient availability along the gradient. This work indicates that a large proportion of plant physiological response at the community level is based on changes in species, and not a direct response of individual species to environment per se – this should be considered when making predictions of responses of plants to short-term environmental change.

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Published online 16 May 2016
Insights into root structure and function of Bassia indica: water redistribution and element dispersion 
Oren Shelef, Paula Pongrac, Primož Pelicon, Primož Vavpeti?, Mitja Kelemen, Merav Seifan, Boris Rewald and Shimon Rachmilevitch

Root structure and function are related to environmental drivers. Investigating root system traits of the halophyte Bassia indica, we found that growth of horizontal roots towards salt is explained by a unique function: redistribution of water to allow efficient utility of nutrients in saline environment. These findings expand the current understanding of the strict connections between structure and function in roots.

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Published online 13 May 2016
Salt tolerance of the halophyte Limonium delicatulum is more associated with antioxidant enzyme activities than phenolic compounds 
Souid Aymen, Gabriele Morena, Longo Vincenzo, Pucci Laura, Bellani Lorenza, Smaoui Abderrazak, Abdelly Chedly and Ben Hamed Karim

Antioxidant responses are key elements in the successful adaptation of halophytes to saline habitats. This study evaluated the contribution of oxidative stress components towards salinity tolerance in the salt marsh halophyte Limonium delicatulum. Results showed that antioxidant enzymes are more linked to the plant tolerance than phenolic compounds. This suggests the possibility to manipulate both the content of phenols and antioxidant enzymes by increasing the salinity in the medium, to promote the medicinal uses of this halophyte.

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Published online 19 April 2016
Halophytes as a source of salt tolerance genes and mechanisms: a case study for the Salt Lake area, Turkey 
Ceyda Ozfidan-Konakci, Baris Uzilday, Rengin Ozgur, Evren Yildiztugay, A. Hediye Sekmen and Ismail Turkan

Halophytes are salt tolerant plants that can live and reproduce at salt concentrations as high as sea water level. Salt Lake area in Turkey is rich in halophyte diversity and most of these species are endemics, which can be only found around Salt Lake area in the world. This review provides information on halophytes around Salt Lake and their tolerance mechanisms including research on model halophyte Eutrema parvulum (Schrenk) Al-Shehbaz & Warwick, which originates from Salt Lake, Turkey.

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Published online 06 April 2016
Dry seeds and environmental extremes: consequences for seed lifespan and germination 
Anne M. Visscher, Charlotte E. Seal, Rosemary J. Newton, Alba Latorre Frances and Hugh W. Pritchard

The focus of this review is the effects of extreme environmental conditions on dry seed lifespan and germination. We discuss dry seed survival of extreme temperatures, ultraviolet radiation and ultra-drying – conditions encountered in natural environments on Earth or in the vacuum of space. We indicate gaps in knowledge and also highlight the research that is needed to discover many of the mechanisms leading to extreme tolerance of dry seeds to these environmental conditions.

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Published online 03 March 2016
Enhancing salt tolerance in quinoa by halotolerant bacterial inoculation 
Aizheng Yang, Saqib Saleem Akhtar, Shahid Iqbal, Muhammad Amjad, Muhammad Naveed, Zahir Ahmad Zahir and Sven-Erik Jacobsen

Plant growth-promoting bacteria (PGPB) containing specific enzymes or hormones have been successful in ameliorating salinity stress in glycophytic plants, but halophytes have not previously been tested. We analysed the effects of PGPB on quinoa – regarded as a new global crop – under salt stress. Productivity of the salt tolerant species was improved by inoculating with PGPB in salt-affected soils.

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Published online 03 March 2016
Physiological factors determine the accumulation of D-glycero-D-ido-octulose (D-g-D-i-oct) in the desiccation tolerant resurrection plant Craterostigma plantagineum 
Qingwei Zhang and Dorothea Bartels

The eight carbon sugar octulose is correlated with desiccation tolerance in Craterostigma plantagineum: what happens when desiccation tolerance confronts senescence? During senescence carbohydrate and gene expression profiles change, which reflects a loss of desiccation tolerance. The synthesis of octulose is light-driven and octulose is involved in the antioxidant defence in C. plantagineum.

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Published online 16 February 2016
Salt stress responses in a geographically diverse collection of Eutrema/Thellungiella spp. accessions 
Yang Ping Lee, Christian Funk, Alexander Erban, Joachim Kopka, Karin I. Köhl, Ellen Zuther and Dirk K. Hincha

Salinity impairs plant growth but halophytes such as Eutrema salsugineum tolerate much higher salt concentrations than glycophytes such as Arabidopsis thaliana. We found natural variation in the salt tolerance of Eutrema accessions that was not correlated with compatible solute content. Metabolome and transcriptome analyses indicated metabolic pre-adaptation to salt stress in the halophyte and little overlap between salt-regulated genes in the two species.

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Published online 05 February 2016
Tripogon loliiformis elicits a rapid physiological and structural response to dehydration for desiccation tolerance 
Mohammad Reza Karbaschi, Brett Williams, Acram Taji and Sagadevan G. Mundree

This paper reports on investigations into the close relationship between the structural and physiological changes that occur during dehydration and rehydration of the resurrection grass Tripogon loliiformis. Results showed that T. loliiformis minimises dehydration-related damage through a rapid series of physiological and structural responses. Many of these changes enable the plant to regain full metabolic activity upon rehydration. These results provide powerful insights into the tolerance mechanisms of naturally resilient angiosperms and display great potential for the development of stress-tolerant crop plants.

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Published online 01 February 2016
Differences in LEA-like 11-24 gene expression in desiccation tolerant and sensitive species of Linderniaceae are due to variations in gene promoter sequences 
Saeedeh Ataei, Verena Braun, Dinakar Challabathula and Dorothea Bartels

The aim of this study was to develop an understanding of the molecular basis for differential gene expression in desiccation-tolerant and non-desiccation tolerant plants. Although the genetic information for the stress protective LEA-like protein is contained in closely related plants, the encoded transcript accumulates to higher levels in the desiccation tolerant plants than in the non-tolerant plants. The analysis identified specific promoter response elements that are responsible for the differential expression.

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Published online 12 January 2016
Molecular and biochemical characterisation of a novel type II peroxiredoxin (XvPrx2) from the resurrection plant Xerophyta viscosa 
Kershini Govender, Jennifer A. Thomson, Sagadevan Mundree, Abdelaleim Ismail ElSayed and Mohammed Suhail Rafudeen

Plant peroxiredoxins are remarkable enzymes that can detoxify reactive oxygen species (ROS) and undergo structural changes to provide chaperone activity. This study characterised a novel peroxiredoxin from the resurrection plant Xerophyta viscosa, which was associated with abiotic stress where the enzyme could protect DNA from damage and detoxify ROS. These results emphasise the importance of peroxiredoxins in tolerance mechanisms against environmental stress.

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Volume 43 Number 6 2016

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Descriptive Table of Contents 
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Photosynthesis, light energy partitioning, and photoprotection in the shade-demanding species Panax notoginseng under high and low level of growth irradiance 
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Jun-Wen Chen , Shuang-Bian Kuang , Guang-Qiang Long , Sheng-Chao Yang , Zhen-Gui Meng , Long-Gen Li , Zhong-Jian Chen and Guang-Hui Zhang
pp. 479-491

Ecologists have extensively studied the photoprotection of the shade-demanding species from high light with one objective being to elucidate photoprotective mechanisms of a typically shade-demanding species Panax notoginseng. In high-light-grown plants irradiated by high light, more electrons are consumed by non-net carboxylative processes that activate the component of nonphotochemical quenching. The present study shows an interesting aspect of photosynthesis and photoprotection in a shade-demanding species.


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Barrier against water loss: relationship between epicuticular wax composition, gene expression and leaf water retention capacity in banana 
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Megha H. Sampangi-Ramaiah , Kundapura V. Ravishankar , Shivashankar K. Seetharamaiah , Tapas K. Roy , Laxman R. Hunashikatti , Ajitha Rekha and Pandurangaiah Shilpa
pp. 492-501

This study examines the quantitative and qualitative composition of cuticular wax and their relationship with leaf water retention in banana. The role of total cuticular wax content, wax compounds and their relationship with leaf water retention, followed by gene expression analysis are reported. The results shows that both cuticular wax content and composition plays an important role in maintaining leaf water content.

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Hybrid variation for root system efficiency in maize: potential links to drought adaptation 
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Erik J. van Oosterom , Zongjian Yang , Fenglu Zhang , Kurt S. Deifel , Mark Cooper , Carlos D. Messina and Graeme L. Hammer
pp. 502-511

Root traits may enhance drought adaptation in maize. Root system efficiency (RSE) is defined here as a measure of canopy conductance per unit of investment in root biomass. The significant genotypic differences in RSE found in this study allow the design of breeding strategies to exploit this trait.


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Phosphatidic acid synthesis, octadecanoic pathway and fatty acids content as lipid markers of exogeneous salicylic acid-induced elicitation in wheat 
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Christine Tayeh , Béatrice Randoux , Frédéric Laruelle , Natacha Bourdon and Philippe Reignault
pp. 512-522

Salicylic acid (SA) induces plant defences and renders wheat resistant to the fungal pathogen responsible for the powdery mildew disease. It has been delivered here directly inside wheat leaf tissues in order to test its effect on the treated cells. Lipid metabolism is affected to a great extent by such a treatment and is proposed to be, at least in wheat, a useful marker of the induction of defences by SA, as a potential alternative to fungicides.

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Changes in photosynthesis and carbohydrate metabolism in sugarcane during the development of Yellow Canopy Syndrome 
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Annelie Marquardt , Gerard Scalia , Priya Joyce , Jaya Basnayake and Frederik C. Botha
pp. 523-533

Yellow Canopy Syndrome is a still undiagnosed condition of sugarcane in Australia, causing significant yield losses. Plants are shown to have decreased photosynthetic activity and an increase in sugar levels in the leaves before yellowing, which is consistent with a disruption of phloem loading of sucrose causing a feedback regulation effect. Understanding the effects yellow canopy syndrome has in the plant is vital for future development of control methods and to reduce yield loss.


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Expression of a Nicotiana tabacum pathogen-induced gene is involved in the susceptibility to black shank 
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Roxana Portieles , Eduardo Canales , Osmani Chacon , Yussuan Silva , Ingrid Hernández , Yunior López , Mayra Rodríguez , Ryohei Terauchi , Hideo Matsumura , Carlos Borroto , Jonathan D. Walton , Ramon Santos and Orlando Borrás-Hidalgo
pp. 534-541

Plant diseases affect most plants in the nature and lead to yield losses in agriculture. We identified a plant gene that contributes to the plant susceptibility to pathogens. The inactivation of plant genes that contribute to disease susceptibility might trigger the resistance. This approach might provide novel strategies for disease resistance breeding.

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In situ detection of laccase activity and immunolocalisation of a compression-wood-specific laccase (CoLac1) in differentiating xylem of Chamaecyparis obtusa 
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Hideto Hiraide , Masato Yoshida , Saori Sato and Hiroyuki Yamamoto
pp. 542-552

Conifers forms a special secondary xylem, the so-called ‘compression wood’, to lift inclined stems and branches upward. Our in situ assays demonstrated a compression-wood-specific laccase of Chamaecyparis obtusa (Siebold & Zucc.) Endl. were localised to the highly lignified region of the compression wood cell wall (S2L), where laccase activity was also high. These findings suggested the compression-wood-specific laccase is responsible for the S2L lignification.


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Stomatal conductance scales with petiole xylem traits in Populus genotypes 
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Caroline A. Brocious and Uwe G. Hacke
pp. 553-562

Leaf hydraulics are increasingly being researched as a driver of overall plant performance and growth. Five Populus genotypes were studied to determine what aspects of leaf anatomy impact function. Calculated water flow through the petiole strongly correlated with gas-exchange measurements, suggesting that petiole structure influences leaf hydraulics.

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Phosphite-induced reactive oxygen species production and ethylene and ABA biosynthesis, mediate the control of Phytophthora capsici in pepper (Capsicum annuum) 
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Peiqing Liu , Benjin Li , Ming Lin , Guoliang Chen , Xueling Ding , Qiyong Weng and Qinghe Chen
pp. 563-574

The aim of this study was to elucidate the molecular mechanisms underlying phosphite (Phi)-induced resistance to Phytophthora capsici. We proposed that Phi-induced reactive oxygen species production, ethylene and abscisic acid (ABA) biosynthesis mediate the control of P. capsici, and ABA functions through CaMPK17-1-mediated MAPK signalling. We showed a novel aspect of Phi in the development of new protection strategies against Phytophthora.

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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.

    FP15339  Accepted 24 May 2016
    Different photosynthetic acclimation mechanisms are activated under waterlogging in two contrasting Lolium perenne genotypes
    Barbara Jurczyk, Ewa Pociecha, Janusz KoÅ›cielniak, Marcin Rapacz

    FP15242  Accepted 25 May 2016
    The effect of elevated CO2 and virus infection on the primary metabolism of wheat
    Simone Vassiliadis, Kim Plummer, Kevin Powell, Piotr TrÄ™bicki, Jo Luck, Simone Rochfort

    FP16062  Accepted 20 May 2016
    Water deficit stress tolerance in chickpea is mediated by the contribution of integrative defence systems in different tissues of the plant
    Davinder Kaur, Satvir Grewal, Jagmeet Kaur, Sarvjeet Singh, Inderjit Singh

    FP16036  Accepted 20 May 2016
    Phenotyping oilseed rape growth-related traits and their responses to water deficit: the disturbing pot size effect
    Anaelle Dambreville, Mélanie Griolet, Gaëlle Rolland, Myriam Dauzat, Alexis Bédiée, Crispulo Balsera, Bertrand Muller, Denis Vile, Christine Granier

    FP16098  Accepted 18 May 2016
    Genotypic variation in photosynthetic limitation responses to K deficiency of Brassica napus L. is associated with potassium utilization efficiency
    Zhifeng Lu, Jianwei Lu, Yonghui Pan, Xiaokun Li, Rihuan Cong, Tao Ren

    FP16060  Accepted 15 May 2016
    In vivo and in vitro approaches demonstrate proline is not directly involved in the protection against superoxide, nitric oxide, nitrogen dioxide and peroxynitrite
    Santiago Signorelli, Camila Imparatta, Marta Rodríguez-Ruiz, Omar Borsani, Francisco Corpas, Jorge Monza

    FP16095  Accepted 13 May 2016
    Ecophysiology of leaf trichomes
    Christopher Bickford

    FP15384  Accepted 05 May 2016
    Truncation of grain filling in wheat (Triticum aestivum) triggered by a brief heat stress during early grain filling - association with senescence responses and reductions in stem reserves
    Hamid Shirdelmoghanloo, Daniel Cozzolino, Iman Lohraseb, Nicholas Collins

    FP16018  Accepted 03 May 2016
    Reduced soybean photosynthetic nitrogen use efficiency associated with evolutionary genetic bottlenecks
    José Rotundo, Lucas Borrás

    FP15337  Accepted 28 April 2016
    Dew absorption by the leaf trichomes of Combretum leprosum in the Brazilian semi-arid region
    Ana Lucia Pina, Roberta Zandavalli, Rafael Oliveira, Fernando Martins, Arlete Soares

    FP16064  Accepted 27 April 2016
    Depicting how Eucalyptus globulus survives drought: involvement of redox and DNA methylation events
    Barbara Correia, Luis Valledor, Robert Hancock, Claudia Jesus, Joana Amaral, Monica Meijon, Glória Pinto

    FP15235  Accepted 18 April 2016
    Effects of plant growth stage and leaf aging on the response of transpiration and photosynthesis to water deficit in sunflower
    Fety ANDRIANASOLO, Pierre CASADEBAIG, Nicolas LANGLADE, Philippe Debaeke, Pierre Maury

    FP16037  Accepted 20 April 2016
    Root morphological traits that determine phosphorus-acquisition efficiency and critical external phosphorus requirement in pasture species
    Rebecca Haling, Zongjian Yang, Natalie Shadwell, Richard Culvenor, Adam Stefanski, Megan Ryan, Graeme Sandral, Daniel Kidd, Hans Lambers, Richard Simpson

    FP16025  Accepted 09 April 2016
    Salinity tolerances of three succulent halophytes (Tecticornia spp.) differentially distributed along a salinity gradient
    Louis Moir-Barnetson, Erik Veneklaas, Tim Colmer

    FP15348  Accepted 29 February 2016
    Rapid stomatal response to fluctuating light: an under-explored mechanism to improve drought tolerance in rice
    Mingnan Qu, Saber Hamdani, Wenzhen Li, Shimei Wang, Zhuo Chen, Qingfeng Song, Ming Li, Honglong Zhao, Tiangen Chang, Chengcai Chu, Xin-Guang Zhu


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 11 January 2016
Root-to-shoot signalling: integration of diverse molecules, pathways and functions

Sergey Shabala, Rosemary G. White, Michael A. Djordjevic, Yong-Ling Ruan and Ulrike Mathesius

2. Published 10 July 2015
Cryptic crassulacean acid metabolism (CAM) in Jatropha curcas

Klaus Winter and Joseph A. M. Holtum

3. Published 15 September 2015
Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions

Trevor Garnett, Darren Plett, Sigrid Heuer and Mamoru Okamoto

4. Published 15 September 2015
The significance of image compression in plant phenotyping applications

Massimo Minervini, Hanno Scharr and Sotirios A. Tsaftaris

5. Published 11 January 2016
Shoot–root carbon allocation, sugar signalling and their coupling with nitrogen uptake and assimilation

Lu Wang and Yong-Ling Ruan

6. Published 10 July 2015
Dynamic response of plant chlorophyll fluorescence to light, water and nutrient availability

M. Pilar Cendrero-Mateo, A. Elizabete Carmo-Silva, Albert Porcar-Castell, Erik P. Hamerlynck, Shirley A. Papuga and M. Susan Moran

7. Published 15 September 2015
Genetic diversity for root plasticity and nitrogen uptake in wheat seedlings

Vanessa J. Melino, Gabriele Fiene, Akiko Enju, Jinhai Cai, Peter Buchner and Sigrid Heuer

8. Published 12 May 2015
Towards a conceptual ABA ideotype in plant breeding for water limited environments

Abraham Blum

9. Published 8 March 2016
Chlorophyll fluorescence parameters allow the rapid detection and differentiation of plant responses in three different wheat pathosystems

Olubukola O. Ajigboye, Louise Bousquet, Erik H. Murchie and Rumiana V. Ray

10. Published 12 May 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

11. Published 10 June 2015
Assessment of drought tolerance and its potential yield penalty in potato

Heike Sprenger, Katharina Rudack, Christian Schudoma, Arne Neumann, Sylvia Seddig, Rolf Peters, Ellen Zuther, Joachim Kopka, Dirk K. Hincha, Dirk Walther and Karin Köhl

12. Published 10 December 2015
Signalling via glutamate and GLRs in Arabidopsis thaliana

Matthias Weiland, Stefano Mancuso and Frantisek Baluska

13. Published 13 April 2016
Temperature response of CO2 exchange in three tropical tree species

Martijn Slot, Milton N. Garcia and Klaus Winter

14. Published 12 May 2015
Novel chlorophylls and new directions in photosynthesis research

Yaqiong Li and Min Chen

15. Published 13 August 2015
What drives fruit growth?

Robert C. O. Okello, Ep Heuvelink, Pieter H. B. de Visser, Paul C. Struik and Leo F. M. Marcelis

16. Published 15 September 2015
Cellular pathways of source leaf phloem loading and phloem unloading in developing stems of Sorghum bicolor in relation to stem sucrose storage

Ricky J. Milne, Christina E. Offler, John W. Patrick and Christopher P. L. Grof

17. Published 10 December 2015
Root biomass in the upper layer of the soil profile is related to the stomatal response of wheat as the soil dries

Renu Saradadevi, Helen Bramley, Jairo A. Palta, Everard Edwards and Kadambot H. M. Siddique

18. Published 13 August 2015
The hydraulic architecture of Eucalyptus trees growing across a gradient of depth-to-groundwater

Sepideh Zolfaghar, Randol Villalobos-Vega, Melanie Zeppel and Derek Eamus

19. Published 11 January 2016
Root responses of triticale and soybean to soil compaction in the field are reproducible under controlled conditions

Tino Colombi and Achim Walter

20. Published 10 December 2015
Physiological trade-offs of stomatal closure under high evaporative gradients in field grown soybean

Viviana Medina and Matthew E. Gilbert

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