Evaluation Of Next Generation Phenotyping: The Australian Plant Phenomics Facility
Geoffrey B Fincher1 , Mark A Tester2 , Robert Furbank3 , Murray Badger4
- 1 Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- 2 Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- 3 High Resolution Plant Phenomics Centre, CSIRO Plant Industry, Canberra, ACT 2601, Australia
- 4 High Resolution Plant Phenomics Centre, Australian National University, Canberra, ACT 2601, Australia
Plant phenomics involves the measurement of traits such as leaf length or root architecture and their measurement is important for determining resistance to diseases and environmental stresses such as drought and salinity. Assessment of these characters is usually slow and this has become a bottleneck in the exploitation of genomic and related data for crop improvement. The science of genomics has accelerated so rapidly in the past few years that advances in manipulation of the genome now far exceed the ability and capacity to measure the effects of these manipulations （phenomics）.
The Australian Plant Phenomics Facility （APPF） is a $50 million project that has two nodes. At the first node, located at CSIRO Plant Industry and ANU in Canberra, new non-destructive phenomics technologies such as high resolution infra-red imaging are being adapted for in-depth application to individual plants and for use in the field.
The second node consists of the Plant Accelerator, which has recently been constructed on the Waite Campus of the University of Adelaide. It provides automated, high throughput, non-destructive imaging of plant populations in controlled environments. The Plant Accelerator node includes four “smarthouses”, which contain conveyor systems to deliver potted plants automatically to four imaging stations for high resolution, multi-aspect imaging at a range of visible and infra-red wavelengths. The Plant Accelerator has been used to generate data on the tolerance of wheat and barley lines to abiotic stresses such as salinity and borate toxicity, and the data have been compared with those obtained previously using several manual phenotyping protocols.
High-Throughput Phenotyping In Barley – The IPK Plant Phenomics Facilities
Anja Hartmann , Tobias Czauderna , Roberto Hoffmann , Christian Klukas , Thomas Altmann , Falk Schreiber , NILs Stein
- Leibniz Institute of Crop Plant Research （IPK）, Corrensstr. 3, 06466 Gatersleben, Germany
Automated high-throughput or high precision phenotyping remains one of the major bottlenecks in plant research since more and more plant genomes are being sequenced. In order to facilitate ways of automated phenotyping in the analysis of natural genetic diversity in cereal crops as well as in crop response to abiotic stresses, we are in the process of establishing a Lemnatec Scanalyzer system, which can accommodate 312 barley plants. Initial steps were made and lessons learned in course of setting up standardized calibration experiments. An image analysis software was developed （HT-Pheno） based on open source tools to allow for flexible basic determination of plant area. Extensive calibration experiments were performed to learn about the influence of environmental effects of the surrounding glasshouse. An overview of the initial experiences will be provided and discussed.
Keytrack Root Phenotyping - At The Root Of Development
Gert-Jan Speckmann , Bas de Regt , Shital Dixit , Koen Huvenaars , Jose Guerra , Harold Verstegen , Marco G.M. van Schriek
- Keygene N.V., Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
Plant roots are economically very relevant since the distribution pattern of the root system in the soil determines the zone of water and nutrient availability to plants and differences in root and root development is related to crop yields and abilities to escape drought and soil-borne diseases.
The KeyTrack system allows for efficient execution of root research in a high throughput manner. The KeyTrack platform is a robust phenotyping platform in a greenhouse setup. The phenotyping is based on imaging technology and uses the potential of a track that moves all plants fully automated through the greenhouse compartment and scanning areas. The plants grow in individual containers and are photographed at pre-set points in time and from different angles.
The research presented encompasses the creation of an automated root phenotyping protocol and image analysis pipeline. The material used for this research is the tomato LA716 S. pennellii introgression line library created by prof. Dani Zamir. The research described merges the phenotypic data generated with genotypic knowledge, to feed lead discovery and root development in tomato.
Large Scale Phenotyping In Plant Breeding: An Example In Pepper
Fred van Eeuwijk1,2 , Gerie van der Heijden1, , Yu Song3 , Gerrit Polder1 , Anja Dieleman4 , Chris Glasbey3
- 1 Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC Wageningen, The Netherlands
- 2 Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
- 3 BioSS, King's Buildings, Edinburgh EH9 3JZ, Scotland
- 4 Wageningen UR Greenhouse Horticulture, P.O. Box 644, 6700 AP Wageningen, The Netherlands
The major objective of plant breeding is to develop superior genotypes using genetic, genomic and phenotypic information. More and faster automatic approaches become available to assess huge amounts of genetic and genomic information. In contrast, the collection of phenotypic information is still largely done by manual and visual assessments. An interesting option for large scale phenotyping is by （high throughput） image analysis systems. Within the EU-project SPICY （Smart tools for the Prediction and Improvement of Crop Yield; www.spicyweb.eu）, we have developed an imaging platform to record and measure pepper plants while they are growing in the greenhouse. For the analysis of the recorded images two approaches are adopted. The first approach is to measure and count plant parts like leaves, fruits and internodes. For this approach a combination of a range camera and stereovision is used to obtain a 3D reconstruction of the canopy for good segmentation. The other approach is aimed at the extraction of statistical features from the images without trying to segment individual plant parts from a background. The criteria for success in this case are high heritability, i.e., reproducible differences between genotypes, and strong genetic correlation with yield or its components.
The JüLich Plant Phenotyping Center （JPPC） Platform At Forschungszentrum JüLich Gmbh
Kerstin A Nagel , Fiorani Fabio , Ulrich Schurr
- Institute of Chemistry and Dynamics of the Geosphere ICG-3 （Phytosphere）, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
In recent years, plant phenotyping—from molecules to whole organisms—and the accompanying technological advancements have emerged as crucial assets to basic and applied research in plant biology and agriculture for academia as well as industry. The ability and capacity to phenotype plants using standardized protocols is currently the most important bottleneck to gain knowledge in functional genome research. JPPC （Jülich Plant Phenotyping Center） is at the forefront of cutting-edge research in this field, and in promoting the development of reliable experimental standards and practices. In this presentation we will highlight available applications at the JPPC platform focusing on new developments. Case studies will illustrate how the use of phenotyping infrastructure and sensors technology can be efficiently tied to relevant biological questions. In particular, we will show examples of applications that aim at reproducibly measure parameters of root growth and root system architecture in a range of conditions, from artificial growth media to soil in multiple environments （laboratory, greenhouses, and field）. Integration of methods at different scales into “phenotyping chains” gives insight into the mechanisms that cause resource use efficiency in root structure and function, and will improve our understanding of which root phenotypic traits can be transferred from controlled environments to field. These approaches aim at defining to what extent these traits can be transferred from crop to crop in pre-breeding and in agricultural production environments.
Development Of High Throughput Plant Phenotyping Facilities At Aberystwyth
Catherine J Howarth , Alan P Gay , John Draper , Wayne Powell
- IBERS Aberystwyth University Gogerddan Aberystwyth SY23 3EB U.K.
There is a need to develop high throughput plant phenomics to bridge the phenotype-genotype gap that will lead to the improvements in crop performance necessary to feed the growing world population. The facility under development at Aberystwyth will be based around automated non-destructive image analysis using a Scanalyzer 3-D HTS system developed by LemnaTec running in a new glasshouse complex. Detailed consultations with potential users have provided the specifications for the system. A central advantage of the approach is that it is inherently non-destructive, allowing repeated measurements to be made on individual plants in a pre-programmed sequence through time with minimal operator intervention. The system is designed to cope with small plants such as forage grasses, forage legumes, Brachypodium and Arabidopsis, and with larger plants such as oats, wheat, barley, maize and Miscanthus. The plant phenomics facility will be closely linked to both chemical phenotyping and genotyping facilities in Aberystwyth along with field trials. Use of the facility will accelerate the selection of appropriate germplasm for breeding varieties which will perform robustly under the conditions predicted for the UK and beyond in the future. Furthermore, it will provide a focus for trans-disciplinary research to facilitate the discovery of the genetic and environmental bases for variation in complex traits that underpin the major global challenges for food and energy security, water utilization and adaptation to a changing climate.
DROPS: An EU-Funded Project To Improve Crop Performance Under Drought Conditions
Francois Tardieu1 , Alain Charcosset2 , Xavier Draye3 , Graeme Hammer4 , Bjorn Usadel5 , Roberto Tuberosa6
- 1 INRA, UMR 759 LEPSE, 2 place Viala, 34060 Montpellier, France
- 2 INRA, Station de Génétique Végétale, Ferme du Moulon, 91190 Gif-sur-Yvette, France
- 3 Crop Physiology and Plant Breeding, Université catholique de Louvain, Croix du Sud 2/11, 1348 Louvain-la-Neuve, Belgium
- 4 Agricultural Production Systems Research Unit, The University of Queensland, Brisbane, Qld 4072, Australia
- 5 Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- 6 DISTA, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
DROPS （DROught-tolerant yielding PlantS） is an EU-funded project （2010-2015） that will develop novel methods and strategies to improve crop performance under drought conditions. An interdisciplinary approach based on phenotyping under controlled and field conditions will generate data that will be used for ecophysiological modeling to predict crop performance under fluctuating water regimes. QTL discovery for traits of importance under drought conditions will produce additional data for modeling crop performance based on QTL effects. The project will target root architecture, transpiration efficiency, vegetative growth maintenance and seed abortion in maize and durum wheat. DROPS will:
- Develop new screens under controlled and field conditions that will consider indicators which are （i） highly heritable and measurable in a high-throughput fashion in phenotyping platforms, （ii） based on metabolite concentration, sensitivity parameters of models or hormonal balance, （iii） genetically related to target traits and able to predict genotype performance in the field via simulation and/or statistical models;
- Explore the natural variation of the target traits by （i） linking the target traits to physiological pathways, genes or genomic regions, （ii） assessing the effects of a large allelic diversity for the four target traits via association genetics;
- Support crop improvement strategies by developing methods for estimating the comparative advantages of relevant alleles and traits in fields with contrasting drought scenarios. This will be achieved via field experiments and by developing new crop models able to estimate the effects of alleles on crop growth, yield and water-use efficiency.
A Platform For High Throughput Phenotyping Of Plant/Plant And Plant/Microorganisms Interactions.
Christophe SALON , Christian JEUDY , Celine BERNARD , Richard THOMPSON , Vivienne GIANINAZZI-PEARSON , Xavier REBOUD , Philippe LEMANCEAU , Jacques CANEILL
- UMR Agroecology, National Institute of Agronomical Research （INRA）, 17 rue Sully, BP86510, 21065 Dijon Cedex
To overcome crop yields stagnation due to increased occurrence of biotic and abiotic stresses, innovative methods have to be developed to produce high-quality food for the increasing world population while preserving/enhancing the quality of the environment. The High Throughput Plant Phenotyping Platform （PPHD）, located in Dijon, France （http://www.dijon.inra.fr/）, provides searchers with an infrastructure able to apply well-characterized biotic and abiotic constraints to several hundreds of genotypes （and so thousands of plants） and to accuray measure a series of functional traits. It allows establishing/testing causal relationships between genetic markers and phenotypes related to plant performance under a range of environmental conditions, including those forecasted by models of climate change.
PPHD is constituted of a building （hosting activities related to plant material preparation, plant growth and post growth analysis） with S2 modular greenhouses and climatic chambers. These are equipped with conveyors belts to homogenize plant growth conditions and automatically bring plant units to the phenotyping cabinets. Phenotyping is based on image analysis （visible light, near infrared and fluorescence） which allows characterizing non destructively and automatically i） a large variety of plant species and specifically designed high throughput rhizotrons ii） seeds or microorganisms, plantlets. Because of its specificity consisting in the high throughput study of plant/plant and plant（pathogene-symbiotic）micro organisms interactions at the shoot level and more specifically the root level, PPHD constitutes a major infrastructure for identifying determinants of plant adaptation to new cropping systems displaying enhanced agro ecological services.
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