Weeding the Gems

The UK Plant Phenotyping Network is a BBSRC sponsored network that has supported meetings and workshops since 2012. A representative from GARNet sits on the UKPPN committee so it was a pleasure to attend the UKPPN Root Phenotyping Meeting that recently took place in the Department of Plant Science at the University of Nottingham.

For someone whose previous research involved growing Arabidopsis plates on agar plates or in controlled growth chambers, this workshop was a real eye-opener as it highlighted the excellent science that is largely aimed at discovering how plant roots interact with their local environment.

This work does mostly not involve Arabdopsis although many of the studies investigate aspects of root growth whose fundamentals have been discovered from lab-studies of the worlds favourite weed. The meeting was hosted by Professor Malcolm Bennett and some of his current Arabidopsis work involves the hydrotropic response which is perfectly aligned to the in-terra studies of how cereal and Brassica roots interact with the available nutrients and water. This work has been facilitated by an amalgamation of research grants that ultimately resulted in the building of the Hounsfield Facility. This purpose built facility contains a generous greenhouse, a human-sized automated robot and three different imagers for CT scanning.

This has allowed a better understanding of how roots interact with soils. However applying more scientific rigour to this process has only been made possible by the analysis software that has been developed at CIPB alongside this imaging technology. During the UKPPN meeting Stefan Mairhofer (CPIB) outlined the development of the Root Phenotyping Pipeline that has allowed researchers to make statistical sense of the CT data that they obtain from the Hounsfield facility. Later in the same session Stefan Gerth (Frauhofer Institute for Integrated Circuits) presented their own technology that they are using for root phenotyping with CT imaging. Finally Erik Esveld (Wageningen) introduces the potential for using XRT imaging to analyse plants grown on drained Rockwool.

Earlier in the day the meeting started with a session on field phenotyping that included an introduction to ‘Shovelomics’ from Tobias Wojciechowski (Julich). He described how they are developing methods for the imaging of whole root systems that have been dug up from the soil. As expected, one difficulty with this work is inconsistency and indeed Tobias showed that the variation between root samples in a plot was greater than that seen between different geographic genotypes isolated from Germany, Norway or Austria. The software that has been developed in house at Julich is able to take 40K images overnight and this data is held in the <a href="http://dirt.iplantcollaborative cialis site officiel.org/welcome” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://dirt.iplantcollaborative.org/welcome’, ‘Digital Imaging of Root Traits’]);” target=”_blank”>Digital Imaging of Root Traits (DIRT) platform,  now being administered through CyVerse. Perhaps there is no greater contrast than the physical digging up plants versus the in silico analysis on CyVerse but perfectly shows the interdiscplinary work occuring in this research area!

The field phenotyping session ended with an enjoyable trip out into the Sutton Bonnington research sites to have demonstrations of Electrical Resistance Tomography by Andrew Binley (this technique allows the measurement of soil water levels) and also Tractor-Mounted Soil Coring from Larry York (which produces soil cores to be used for later root analysis). Pleasingly, the soil water levels predicted by the EMI could be observed in the soil cores.

It might have been unusual for a conference to take people out into the field but it really highlighted the level of challenge that it will take to effectively phenotype a varied field populations of plants!

The second day of the meeting focused on root imaging and modeling, with the audience blown away by the incredible images shown by Jonathan Lynch (Penn State University and University of Nottingham) generated using laser ablation tomography. In this technique root sections are destructively imaged and then digitally reconstituted using 3D software to give fantastic videos that investigate the length of root sections.

Professor Lynch discusses the importance of aerenchyma cells that are found in the cortex of many cereal plants. These essentially empty cells enable a lower overall metabolic cost, therefore clearly benefits the overall energy costs of the plant. Detailed phenotype analysis of aerenchyma has made possible by the RootScan software that has been developed in the PSU Roots lab and is freely available for use.

Later in the session Huw Jones from NIAB described a novel method for the estimation of root biomass. They put together two items that young researchers are told should never mix: soil and PCR. In this technique they perform qPCR on soil samples using primers that are specific for your plant of interest, which allows the approximation of the root biomass within the sample. This technique has also been used to estimate the interactions between plants and weeds across a range of soil depths and struck me as a relatively inexpensive way for this type of analysis, which can provide useful data about the composition of a soil sample.

The keynote talk of the modeling session was Johannes Postma (Julich) who provided an enthusiastic explanation of his attempts to link root phenotypes, soil content and plant biomass. One predicted finding that corresponded with real-life data was that plants with root aerenchyma showed increased biomass in soils with reduced phosphorous. It was excellent to hear this analysis as for much of the meeting the link between root phenotype and yield was not fully made. This is likely to do with the challenges of the imaging technology and the difficulties in fully correlating complex root phenotype with yield.

This meeting demonstrated that the field (pardon the pun) of root phenotyping has great strength especially within the UK, France and Germany. On day one of the meeting Gabriele Pastori (BBSRC) introduced the recently published European Strategy Forum on Research Infrastructures (ESFRI) Roadmap which has “identified the new Research Infrastructures (RI) of pan-European interest corresponding to the long term needs of the European research communities”. Through the work of the UKPPN and others, this document introduces a proposed area of interest in Plant Phenotyping, called EMPHASIS.

This roadmap is used as an introduction to technologies for which the EU would be interested in developing cross-border infrastructure, by facilitating the legal and financial tools necessary for these type of linkages. At this early stage the EMPHASIS project has no funding associated with it yet the involvement of the BBSRC demonstrates that there is willingness on a national level to discuss future possibilities for funding this area of research. Ultimately any grant funding will come from research bodies within each contributing nation so over the next few years it is encumbent on the UK Plant Phenotyping community to decide how this which occur. Later in the meeting the leader of the French Plant Phenotyping Network (FPPN), Francois Tardieu describes how they have brought together 15 collaborator organisations to tackle phenotyping challenges (see image below)

The UK would not look to replicate French or German efforts but rather focus on areas of expertise in which the UK is a world-leader and will provide greatest input toward a pan-European plant phenotyping network. A significant amount of work has already gone into the highlighting of this area for possible European involvement so watch this space to find out how the UKPPN and others can convince UK funders to support this wider initiative.

Overall this was an excellent final meeting of the UKPPN grant and since the first UKPPN gathering the research community has clearly come a long way. It is hoped that the EMPHASIS project and other initiatives will continue to support plant phenotyping across all scales from molecular analysis through to whole field phenotyping and environmental considerations.

Storify of tweets from the meeting put together by the Susie Lydon at CPIB.