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Fully automated plant phenotyping

"This is botany 2.0, because it offers completely new opportunities"

In the Netherlands Plant Eco-phenotyping Center, plants are now viewed from all sides with cameras, sensors, robots, and automated systems in mesocosms, climate cells, greenhouses, and in the field.

When tomato plants are taken out of their greenhouses, they are put on conveyor belts and briefly disappear into a detection box in which camera systems record them from all sides. Then, each receives the pre-programmed amounts of water and nutrients. In another greenhouse compartment, cyclamen stand still at fixed distances but are regularly checked by a flying camera robot that records information about their plant architecture and flower development from all angles.

"Building these unique facilities was a long journey and sometimes took us as scientists outside our comfort zone. But it opens up a whole new world: we gain access to the development of root and canopy, from very small to very large. It enables us to answer very interesting agricultural and ecological questions', says Wageningen plant geneticist Mark Aarts, chairman of the NPEC management team and also the main applicant of the awarded more than eleven million euros grant. Wageningen University & Research and Utrecht University are jointly investing a similar amount in the center, the facilities of which are also available for experiments by researchers from other universities,

Time consuming
'This is botany 2.0, because it offers completely new possibilities', Aarts explains. 'We already have a good grasp of genetics. A complete genome of Arabidopsisyou can sequence for a few bucks these days. But it is very time consuming to determine exactly what these DNA differences mean for a plant's phenotype. We have all the techniques from genomics to metabolomics, but ultimately the most important are the changes that take place in the phenotype of a plant. That phenotype also changes over time and is the ultimate result of gene expression. What influence do environmental factors such as light, moisture, and temperature have on the development of plants, and what role do pathogens or the microbiome play in this? We are entering a new era with automated phenotyping. Now a researcher already has his hands full with getting a good dataset at one point in time after an experiment, but with the NPEC facilities, this can be done for many moments,' says Aarts.

Aarts has been conducting genetic research for years into the adaptation of plants to unfavorable environmental conditions in the model species of thale cress (Arabidopsis thaliana) and zinc burdock (Noccaea caerulescens). In particular, to look at the effects of the environment on photosynthesis, he has already developed the first automated high-throughput phenotyping platform: the Phenovator. At the time, it already had an unprecedented capacity and could screen 1,440 Arabidopsis plants several times a day for photosynthesis, growth, and spectral reflectance at eight wavelengths (Plant Methods, 2016).

'The new NPEC units enable us to monitor almost continuously the influence of various stress factors on plant development, both underground and above ground, from seedlings to potted plants and even crops in the field. In addition, thanks to reflection and fluorescence techniques, we can make observations down to the level of components and physiological responses of plants', says Aarts. In the greenhouse, tomatoes get in the unit through a conveyor belt system, as opposed to units in which plants are stationary, and the measuring systems move. 'We know that movement influences the development of plants, so this at least gives us the opportunity to address this,' Aarts explains.

'This is really the cream of the crop for plant scientists,' says Utrecht biologist Roeland Berendsen, a researcher in the plant-microbe interactions group and manager of the Institute for Environmental Biology. 'Almost all environmental conditions can be set in the smaller climate chambers. From frost to temperatures above 40 degrees and light intensities to full sunlight, up to ten times higher than usual in climate rooms. And that with nine colors of LED light. Ideal for research into the influence of shade on plants. It can accommodate all kinds of plants: especially Arabidopsis- and tomato plants, but preferably no maize', Berendsen smiles.

Equally impressive are the 36 mesocosms or ecotrons already in the NPEC building under construction. These are modules in which half a cubic meter of soil can be introduced and planted with the desired vegetation plants. When the valve closes, it is possible to fully control the soil temperature, lighting, and composition of the air inside. According to Berendsen, this is an ideal set-up to test, for example, under strict conditions, the interactions discovered in the large-scale and long-term BioCliVE experiment – ​​Biodiversity and Climate Variability Experiment – ​​with vegetation in the open air.


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