Abstract
Detailed and standardized protocols for plant cultivation in environmentally controlled conditions are an essential prerequisite to conduct reproducible experiments with precisely defined treatments. Setting up appropriate and well defined experimental procedures is thus crucial for the generation of solid evidence and indispensable for successful plant research. Non-invasive and high throughput (HT) phenotyping technologies offer the opportunity to monitor and quantify performance dynamics of several hundreds of plants at a time. Compared to small scale plant cultivations, HT systems have much higher demands, from a conceptual and a logistic point of view, on experimental design, as well as the actual plant cultivation conditions, and the image analysis and statistical methods for data evaluation. Furthermore, cultivation conditions need to be designed that elicit plant performance characteristics corresponding to those under natural conditions. This manuscript describes critical steps in the optimization of procedures for HT plant phenotyping systems. Starting with the model plant Arabidopsis, HT-compatible methods were tested, and optimized with regard to growth substrate, soil coverage, watering regime, experimental design (considering environmental inhomogeneities) in automated plant cultivation and imaging systems. As revealed by metabolite profiling, plant movement did not affect the plants' physiological status. Based on these results, procedures for maize HT cultivation and monitoring were established. Variation of maize vegetative growth in the HT phenotyping system did match well with that observed in the field. The presented results outline important issues to be considered in the design of HT phenotyping experiments for model and crop plants. It thereby provides guidelines for the setup of HT experimental procedures, which are required for the generation of reliable and reproducible data of phenotypic variation for a broad range of applications.
Highlights
The genotype-phenotype-concept introduced by Johannson (1909) defined a phenotype as the overall constitution of an organism including all possible characteristics that can be assessed by a multitude of analytical methods ranging from morphological, physiological, anatomical traits to chemical composition
Plant phenotyping as an emerging area of science addresses the interaction of genotypes with their environment that manifests in multiple plant morphological parameters and in their accumulated biomass and yield
It is possible to record the objects from the top and several side views. This supports the assessment of architectural traits, colorization-related traits, and measures related to the water content (NIR) or levels of fluorophores including chlorophyll (FLUOR)
Summary
The genotype-phenotype-concept introduced by Johannson (1909) defined a phenotype as the overall constitution of an organism including all possible characteristics that can be assessed by a multitude of analytical methods ranging from morphological, physiological, anatomical traits to chemical composition. While major advances in genotyping and sequencing technology led to readily available detailed genomic data of huge, genetically diverse plant populations such as breeding material, diversity collections, or mapping populations, the acquisition of precise and comprehensive phenotypic information needed to understand the genetic contribution to phenotypic variation has been much more demanding. Screening of such large plant populations requires methods with increased precision and accuracy in phenotypic trait acquisition paired with decreased labor input as achieved by automation, remote control and data (image) analysis pipelines amenable to HT. Nowadays the term “phenomics” refers mainly to imaging based HT procedures that employ a wide range of electromagnetic radiation wavelength bands monitored by camera sensors detecting www.frontiersin.org
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