EMPHASIS on Plant Phenotyping

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Published on: February 28, 2017

Some readers might have heard of the EMPHASIS project but the likelihood is that the majority have not……yet it might be extremely significant for the future of plant science across Europe…. which, yes, even in these uncertain times, should include UK researchers!

The European Strategy Forum on Research Infrastructures (ESFRI) supports high quality research infrastructures across all disciplines and includes diverse projects such as ELIXIR, A distributed infrastructure for life-science information  and SKA, the Square Kilometer Array Telescope. The process of receiving support from ESFRI starts with inclusion in their annual Roadmap document that leads onto a series of discussions that aim to set the official agenda for the program. This might then result in the establishment of an official infrastructure project a further 5 years later. Importantly this is a different type of project when compared to Horizon2020 or FPs as the funding does not come from a centralised EU pot but is rather distributed from within the individual participating countries.


Last year was an exciting time for European Plant Phenotyping as through the work of Belgian, German, French and UK researchers, the EMPHASIS project (European Infrastructure for multi-scale Plant Phenomics and Simulation for food security in a changing climate) was included in the ESFRI Roadmap in 2016. Within the UK, it was largely members of the UKPPN (UK Plant Phenotyping Network) who worked with the BBSRC to ensure that UK scientists were represented in the EMPHASIS project that was included in the ESFRI Roadmap.

The genesis of EMPHASIS could be traced back to the FP7-funded EPPN (European Plant Phenotyping Network) which was the starting point of the overall aim to develop complimentary tools for lab, greenhouse and field phenotyping that integrates high-tech automated platforms with computer-aided measurements and data management.


EMPHASIS-PREP takes shape.

The EMPHASIS-PREP project has now been funded by Horizon2020 and over the coming years will document the strengths and weaknesses of European plant phenotyping before producing a final document that will highlight why the entire EMPHASIS project should be supported and how it might be regulated across up-to-30 participating countries. As the money for UK scientists will come directly from RCUK, it is hoped that issues surrounding Brexit will not be as significant an issue for this scheme as it might with other centrally administered EU funding. This will support a UK research infrastructure that integrates with European partners and conforms to certain EMPHASIS-defined access requirements to researchers from across the EU.

The EMPHASIS-PREP project is split into 6 work-packages and the BBSRC have taken the lead with WP5, which tackles the legal frameworks that are needed for the project to succeed with minimal interference.


The group participating in EMPHASIS-PREP is much smaller than the proposed final EMPHASIS project so those members involved at the present time (which will be expanded over the course of the discussions) have signed the ‘EMPHASIS Manifesto’ in which they agree to work for the good of the whole future consortium.

Ultimately the aim of EMPHASIS is to host all the necessary infrastructure for state-of-the-art phenotyping and can be split into five very broad topics:

> Controlled conditions: Phenotyping platforms in (semi-) controlled conditions for high resolution and high throughput phenotyping.

> Intensive field: Smart/ Intensive field experimental sites for high throughput phenotyping

> Lean field: Translational, coordinated network of field experiments with lean, efficient phenotyping close to practical breeding setups

> Modelling: Modelling platforms for testing existing or virtual combinations of alleles in a variety of climatic scenarios and management practices

> e-Infrastructure: establish interconnections between different nodes/ installations.


The final organisation of the project will take a classic European Hub-and-Node organisation. The EMPHASIS Hub will likely reside in Germany whilst each national Node will attempt to lead the organisation of the countries phenotyping infrastructure so that it is open, inclusive and conforms to the overall aims of the EMPHASIS program.

As this is a five-year process it will clearly be extremely complicated to organise and over the coming year EMPHASIS-PREP are holding regional meetings to introduce the aims of the project and to receive feedback from those participating countries. As the project planning gains pace then these meetings may become more frequent and could be organized on an individual national level.

These early EMPHASIS-PREP meetings have three main goals:

> Inform: about the EMPHASIS project

> Document: the status of plant phenotyping in each country

> Discuss: future national plans for plant phenotyping

In the early stages of EMPHASIS-PREP the UK will be represented by the University of Nottingham specifically led by Malcolm Bennett, Darren Wells and Tony Pridmore. They will work closely with the BBSRC to ensure that UK interests are represented at each meeting. The location of each meeting can be found on the EMPHASIS website.


What does it mean for me now?

At the moment not a great deal.

Please keep an eye out for developments and then contribute any thoughts and ideas that you have when the appropriate forums are opened up. GARNet has been a contributing member of the UKPPN and as we are mandated to support community infrastructures so we will endeavor to keep the UK community informed as the project rolls forward.

Hopefully in 2018 there will be a UK-based meeting in which members of our outstanding UK plant phenotyping community will be able to submit their opinions as to the direction of travel of this field (pardon the pun) of research that has enormous significance for the development of new crop varieties to mitigate the effects of climate change and ensure global food and nutritional security.

Arabidopsis Research Roundup: February 27th

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Published on: February 28, 2017

This weeks research roundup includes just three papers and includes a study from the University of Essex that looks at the growth response of Arabidopsis plants to ‘real-life’ fluctuations in light levels. Secondly is a very different type of study from the University of York that uses Arabidopsis as a model for the development of plants that are able to accumulate catalytically active and commercially viable levels of palladium. Finally is a Chinese-led study that includes Alan Marchant (University of Southampton) as a co-author and looks at the role of the ERF74-RbohD-ROS signaling module on the response to abiotics stress.

Vialet-Chabrand SR, Matthews JS, Simkin A, Raines CA, Lawson T (2017) Importance of fluctuations in light on plant photosynthetic acclimation Plant Physiol.

http://dx.doi.org/10.1104/pp.16.01767

Open Access

Tracy Lawson and GARNet committee member Christine Raines from the University of Essex Photosynthesis Group lead this study that aims to understand how plants respond to variation in light levels that occur over an ‘average’ day. This contrasts with the conditions used in a ‘standard’ growth chamber and they show that plant growth is significantly altered when the light levels fluctuate, even though the total amount of light that the plant receives is the same. The ultimate conclusion of the study is that the growth of plants under ‘square wave growth conditions’ does not accurately reflect what might be observed in the field. This is significant given the importance of moving research from model organisms, usually grown under controlled conditions into crop species grown in the field.

Tracy Lawson kindly takes less than ten minutes to discuss the paper with GARNet on our YouTube channel.


Harumain ZA, Parker HL, Muñoz García A, Austin MJ, McElroy CR, Hunt AJ, Clark JH, Meech JA, Anderson CW, Ciacci L, Graedel TE, Bruce NC, Rylott EL (2017) Towards financially viable phytoextraction and production of plant-based palladium catalysts. Environ Sci Technol. http://dx.doi.org/ 10.1021/acs.est.6b04821

Open Access

Elizabeth Rylott and Neil Bruce at the University of York lead this study that includes collaborators from the USA, Canada, Malaysia and New Zealand. They look into the options for phytoextraction of palladium, which forms nanoparticles in Arabidopsis roots. The metal taken from these roots had normal catalytic activity and could be obtained at up to 18g/kg dried tissue weight. These experiments were moved into mustard, miscanthus and sixteen willow species and although palladium can be taken up into the plant tissues, it could not be extracted at a level that would make it commercially viable. However the authors are confident that this is am important step toward attempts to develop field-suitable plants that can reduce the environmental impacts of palladium mining.


Yao Y,, He RJ, Xie QL,, Zhao XH,, Deng XM,, He JB,, Song L, He J, Marchant A, Chen XY,, Wu AM (2016) ETHYLENE RESPONSE FACTOR 74 (ERF74) plays an essential role in controlling a respiratory burst oxidase homolog D (RbohD)-dependent mechanism in response to different stresses in Arabidopsis. New Phytol. 213(4):1667-1681. http://dx.doi.org/10.1111/nph.14278

Alan Marchant (University of Southampton) is a co-author on this Chinese-led study that focuses on the role of the ERF74 transcription factor from the ETHYLENE RESPONSE FACTOR VII (ERF-VII) family in the response to abiotic stresses. The authors test the responses of plants with changed levels of ERF74, showing that they have altered responses to a range of stresses such as drought, light, heat and aluminum. erf74 mutants lack a typical reactive oxidative stress (ROS) burst due to low expression of the RESPIRATORY BURST OXIDASE HOMOLOG D (RbohD) protein. ERF74 directly interacts with the RbohD promotor and the paper shows that the whole ERF74-RbohD-ROS signaling module is activated in order for the plant to correctly response to a range of stresses, which each require maintenance of hydrogen peroxide homeostasis.

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