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European Infrastructure for Plant Phenotyping
VIB Agro-Incubator Kerrebroek 66b – 9850 Nevele – Belgium
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EMPHASIS aims to create centralized access to phenotyping data by building and integrating compatible, consistent information systems. EMPHASIS will provide methods and interfaces for interoperability of datasets to manage, share, reuse and visualize heterogeneous, high-throughput plant phenotyping data stemming from different sources often in an interdisciplinary context.
The main objective is that datasets are findable, accessible, interoperable and reusable (FAIR standard) in such a way that the datasets can be analyzed by several groups inside and outside EMPHASIS. This requires software interfaces providing different levels of access to different users to allow a data analysis in relation to environmental conditions.
In addition, data organization and storage needs to be done in a secure way over long term periods, the data can be interpreted in a biological context and used for meta-analyses of experiments. The basic ontology of objects defined in EMPHASIS is described in the ontology of objects involved in phenotyping.
Network of field experiments with lean, efficient phenotyping close to practical breeding
Phenotyping in field experiments using minimal plant phenotyping equipment are performed in agriculturally-relevant and breeding-like conditions, which allows investigation of the (genetic) variability of measured plant traits in a range of environmental scenarios as a response to differences in field management, soil composition, or environmental conditions. Monitoring of the environmental conditions (i.e. abiotic and biotic conditions) are essentially the same as those in intensive fields, with sensor networks for measurement (e.g. temperature, radiation, rainfall, air humidity and soil water potential), at a temporal definition of typically one hour and should allow to understand differences in plant or crop performance and could explain statistical outliers which are not due to genetic variation of the species. The amount of plants, plots or fields per year is dependent on the experiments and should be statistically relevant, with the relevant number of repetitions according to the data analysis protocol. Throughputs are typically hundreds to thousands of (micro)plots.
A key objective for EMPHASIS will be to increase the capability of networks of field trials, number and geographical/ climatic coverage, and the coordination of existing infrastructures and their integration to facilitate analyses of plant performance across climatic gradients, the development of appropriate phenotyping methods and statistics. The scientific communities involved here are; biologists, geneticists, statisticians, agronomists, breeders, modelers and specialists of information systems and technology development.
Smart/ Intensive field experimental sites for high throughput phenomics
Intensive fields are installations set up to allow the detailed study in the field (natural light condition) of hundreds of plant micro-plots through frequent measures of several plant traits. Intensive fields are highly equipped in order to monitor both the plants phenotype and the environment during the plant growth cycle. The quasi-continuous data acquisition paired with the storage of time courses enables the study of the plant growth dynamics, which can be analyzed with respect to the dynamics of environmental variables. Intensive fields can therefore host experiments aimed at deciphering complex plant traits through the study of genotypic variation and genotype-by-environment interaction.
The combination of high frequency measurements and the high number of monitored variables (both phenotypic and environmental) makes intensive fields a framework for high throughput plant phenotyping under natural conditions. Additionally, some intensive field installations, referred to as semi-controlled intensive field sites, are equipped to alter specific key environmental conditions in order to simulate future climatic scenarios, for example through rainout shelters which can be used to generate drought or a FACE (Free-Air CO2 Enrichment) system to simulate elevated CO2 condition. There is usually a trade-off between the level of control and the throughput, intensive field installations typically involve some hundreds of micro-plots whereas high throughput field installations typically involve thousands of micro-plots.
Phenotyping platforms in (semi-)controlled conditions for high-resolution and high-throughput phenomics
Phenotyping installations under controlled conditions allow the investigation of the variability of measured plant traits as a response to well-defined and monitored environmental conditions (i.e. abiotic and biotic conditions) with a capacity of several hundreds to thousands of plants.
Facilities may also be linked to high precision platforms for deep phenotyping with lower throughput (tens to hundreds of plants) and measurements over shorter timescales (weeks) and time steps (minutes to hours).
