Project deliverable Open Access
Morisse, Merlijn; Wells, Darren; Alary, Pierre-Etienne; Pieruschka, Roland; Dhondt, Stijn
The objective of EMPHASIS-PREP is to develop a long term, distributed, pan-European infrastructure for state-of-the-art plant phenotyping experimental platforms which aims to improve crop performance needed to cope with climate changes and to keep pace with population growth. To tackle these global challenges, novel approaches to identify improved plant phenotypes and explain the genetic basis of agriculturally important traits are required. The new and existing plant phenotyping platforms uses non-destructive, image-analysis based determination of the phenotype of plants and allow for a characterization of plant traits.
The criteria list provides a detailed overview of plant phenotyping infrastructure within the scope of EMPHASIS, all which can be divided into five major pillars of plant phenotyping infrastructure:
1. Plant phenotyping in (semi-)controlled conditions.
2. Intensive field experiments in highly equipped field sites or semi-controlled field sites.
3. Field sites with minimal equipment, which could be combined in a network of fields with
different environmental conditions.
4. Modelling platforms to support plant phenotyping data analysis.
5. Information systems for plant phenotyping data management supporting open science.
The criteria list was developed in discussion with the plant phenotyping community and by mapping the existing and upcoming infrastructures in pan-Europe. Four regional workshops have been organized to that end in different regions of Europe. Plant scientist of these regions were asked to present their plant phenotyping infrastructures and activities. Starting with this information these pillars of EMPHASIS could be confirmed. Furthermore, work package 2 (WP2), together with WP3 and WP4, has developed a survey to the community to extract more details of these infrastructures and to be able to translate this into a community driven criteria list for EMPHASIS.
The current criteria list presents a result up-to-date status of the ongoing participation and discussion with the plant phenotyping community in the development of EMPHASIS. It is thus still open for modifications in the course of ongoing stakeholder engagement.
By mapping the pan-Europe state-of-the-art infrastructures, the criteria list of EMPHASIS could be defined and subdivided in five pillars. Below these five pillars and their criteria are described as main results of the criteria list:
Pillar 1: Plant phenotyping in (semi-)controlled conditions can be defined as automated glasshouse and growth chamber infrastructures for plant phenotyping to characterize the architecture, growth and physiology of individual plants and monitor environmental conditions. Throughputs are typically 100s-1000s plants, thereby allowing the analysis of genetic variability and calculation of allelic effects in a large range of climatic scenarios.
Pillar 2: Intensive field experiments are field sites fully equipped for detailed environmental characterization at plot level, and vectors (typically ground or airborne) able to perform measurements of phenotypic variables such as leaf area, plant number, plant architecture or physiological status via, for example, hyperspectral or fluorimetric cameras. Plants are subjected to natural conditions of soil and climate, but some intensive field installations could have for example, modified rainfall or atmospheric conditions, via special equipment such as Free Air CO2 Enrichment (FACE), mobile rain-out shelters or heat shields. With throughputs of typically 100s – 1000s microplots, this allows assessing plant performance in climatic scenarios that mimics possible climate conditions of the future and novel management schemes.
Pillar 3: Field trials with precise environmental monitoring equipment, and equipment for precise measurement of yield components and grain moisture in thousands of micro plots. This is potentially combined with field-based imaging or remote sensing (airborne) systems. Individual fields are usually combined into a network of field trials over multiple geographical regions with different environmental conditions, thereby allowing estimation of yield of hundreds of genotypes across diverse climate scenarios.
Pillar 4: Modelling platforms are virtual platforms of different nature that have the intention to support plant phenotyping. It has been proven very difficult to form criteria for modelling phenotyping platforms, therefore, a number of different models that could be used to support plant phenotyping are described in this criteria list.
Pillar 5: plant phenotyping information systems, which aim to provide methods and interfaces to manage, share, reuse and visualize heterogeneous plant phenotyping data stemming from different sources, often functioning in an interdisciplinary context.