Science - November 22, 2018

Genes+environment = plant. New research centre for phenotyping starts up

Albert Sikkema

A complex interaction between genes and environment determines the characteristics of a plant. That interaction is the focus of a big new research centre: Netherlands Plant Eco-phenotyping Centre. With the knowledge acquired there, scientists hope to breed robust lettuce. Or salt-resistant potatoes.

Text Albert Sikkema illustration Geert-Jan Bruins

Standing in the greenhouses at Unifarm on the Wageningen campus is a huge metal cupboard. ‘This is the Robin,’ says Rick van de Zedde proudly, indicating the Robin PSI Plant Screen System. The cupboard contains three sensors which can perform very precise measurements on plants. They measure the photosynthesis capacity, the number of leaves and the surface area and colour of the plant. ‘The Robin is mobile. We drive it to a compartment full of plants, put the plants in one by one and measure them.’

22 million

The Robin marks the start of the Netherlands Plant Eco-phenotyping Centre (NPEC). This spring this phenotyping centre received 11 million euros from research financier the Netherlands Organisation for Scientific Research (NWO). The participating universities, Wageningen and Utrecht, are putting 11 million euros into it between them. In the centre, researchers can study plants under different environmental conditions. This can be done in the Robin, and soon also in its big brother, the Robin 2, through which plants roll on a fully automated conveyer belt. There will also be advanced climate cells, a research greenhouse, and drones for measuring the effect of the environment on all kinds of crops.

Van de Zedde, a robotics researcher in the Plant Sciences Group, is developing Wageningen’s branch of the new centre (see inset) together with programme developer René Klein Lankhorst and Wageningen plant researchers. The centre will be finished in two years’ time and then all Dutch plant scientists can make use of its facilities for a fee.

P is for Phenotype

The phenotyping centre can be summed up in a formula: G+E+P. Here, G stands for the plant’s genotype and E for environment. Combined, these two determine P, the phenotype. ‘If you breed the same variety in different climatic zones, you often get different plants,’ explains Klein Lankhorst. ‘Now we can determine the genotype quickly and cheaply, but we don’t know enough about how environmental conditions influence plant development.’

For this reason, the centre plans to set up climate cells that simulate a variety of environmental conditions. Plants can be exposed to temperatures ranging from -5 to +42 degrees, while the light intensity and composition, the CO2 level, the humidity and the growing conditions can be programmed precisely in each climate cell. This enables the researchers to measure things like the impact of drought and salt on plant development.

Root growth

WUR already has a climate cell in which it is possible to ascertain the photosynthesis, growth and development of hundreds of plants at the same time. With this ‘Phenovator’, researchers of Genetics and Horticulture have already been able to identify several genes in the model plant Arabidopsis that drive plants’ adaptation to changing light conditions, says Klein Lankhorst. These groups can expand the research in the new facility, because it will have four new climate cells with the latest sensors, in which key decorative plants, vegetables and field crops can be scanned as well.

The NPEC is also going to design a rhizotron, working closely with Professor Christa Testerink of Plant Physiology. This piece of equipment will be used to measure the effect of environmental conditions on plant roots, so researchers can find out how salinized soils hamper root growth or how seed germination in the soil is affected by cold.

Kas en proefvelden

Besides the climate cells, the phenotyping centre will also have a new research greenhouse. This greenhouse of 32 by 28 metres will contain four compartments in which the lighting, the CO2 level and the temperature can be regulated independently of each other. New equipment will then record the effects of those variable conditions precisely. Van de Zedde: ‘To measure the effect of environmental interventions on plant growth, we used to have to pick the leaves and have them measured by researchers. In this greenhouse, the plants are moved to sensor equipment, and sensors go to the plant. This means we can determine the total leaf mass of a plant automatically and with great precision.’

Finally, NPEC is going to monitor the plants in the open air. ‘We want to analyse plants in different regions under different climate conditions,’ says Klein Lankhorst. ‘We therefore want to place a mobile sensor network in the trial fields that collects data about the soil, temperature, rainfall, light exposure, and the like. A vehicle with cameras and GPS  will provide data about the development of the plant and we can compare the data from the climate cells with the crops’ performance in the field.’

Big data

Since the cameras and sensor will generate large amounts of data, and the researchers prefer to process that data fully automatically into applicable information, NPEC is in fact a Big Data project as well. So Dick de Ridder’s Bioinformatics chair group has been consulted. ‘We’ve decided that every machine will have its own data storage and that we shall link all the data at a higher level,’ says Van de Zedde. To this end, NPEC will further develop a European data platform created by French institute INRA.

The advantage of this is the NPEC does not have to reinvent the wheel. Working closely with the French, the centre is now going to establish agreed definitions and parameters for phenotyping, so that researchers can record all the data unambiguously. ‘We must make sure we can compare experiments and reuse data.’

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The Wageningen branch of the phenotyping centre NPEC will consist of climate chambers, a new research greenhouse and trial fields, all equipped with mobile sensors that record the development of the plants. Illustration Haans Industrial Design

‘Collaboration thanks to NWO’

The Netherlands Plant Eco-phenotyping Centre (NPEC) is to be a national research facility which all Dutch plant scientists can use. It is funded from fund the Netherlands Organization for Scientific Research (NWO) reserves for large-scale scientific infrastructure. Half of the centre will be located in Wageningen and the other half in Utrecht.

‘This is a collaboration made possible by the NWO,’ says programme developer René Klein Lankhorst. ‘Both Wageningen and Utrecht had submitted proposals for a phenotyping centre to the NWO, which responded that a single proposal would stand a better chance. Then the two parties put their heads together.’

Utrecht and Wageningen are now developing complementary facilities. Utrecht concentrates on the interactions between plants and microbes, such as underground bacteria and fungi, while Wageningen concentrates on the interaction between plants and abiotic stress factors such as drought and salinization.

NPEC Wageningen will be run by Unifarm and co-financed by WUR’s Shared Research Facilities, which manages and rents out expensive research facilities. Wageningen researchers who want to make use of NPEC pay a fee, just like external users. ‘But not the full rate, because NWO, WUR and Utrecht University are contributing too,’ says Klein Lankhorst. He calls on Wageningen researchers to orientate themselves to possible phenotyping research. The new centre will open in two years’ time, but certain facilities are already available.

Robust lettuce and salt-tolerant potatoes

It will take another two years before phenotyping centre NPEC is fully operational, but it is close to having its first client. Professor of Plant Physiology Christa Testerink wants to use the new facility for her research project LettuceKnow, which aims at developing more robust and stress-proof lettuce varieties. ‘We want to sow and phenotype 500 varieties of lettuce seed. That means we shall measure how robust the various types of lettuce are and monitor how they cope with different kinds of stress such as salt or drought, how the roots develop and how the plant’s growth and architecture proceeds. You need a facility like NPEC to carry out these kinds of measurements on a large scale.’

Testerink also wants to breed potato varieties in brackish soil in the planned rhizotron at NPEC. ‘That will be unique research because then I can measure both the underground and the above-ground development of hundreds of potato plants at the same time, fully automatically. Some potatoes suffer a lot from salt stress, and others less. I want to trace that back to the potatoes’ DNA. To do that, you need a large number of plants – hence NPEC.’