RESOURCESRESOURCES

Phenomics

List of worldwide facilities undertaking global assessments of plant phenotypes.

AraPheno

https://arapheno.1001genomes.org/

AraPheno is a public database collection of Arabidopsis thaliana phenotypes.

This Database allows to search and filter for public phenotypes and to obtain additional meta-information.

 

Biotron, Canada

http://www.thebiotron.ca/

A purpose built facility housing specialized environmental chambers, laboratories and equipment dedicated to research in the fields of environmental sciences, biotechnologies and engineering. They encourage international access to the facility for both research and training. 

EMPHASIS

https://emphasis.plant-phenotyping.eu/

EMPHASIS is a pan-European distributed infrastructure listed on the ESFRI Roadmap for multi-scale plant phenotyping and simulation for food security in a changing climate. EMPHASIS aims at  supporting  the exploitation of crop genetic diversity required for the enhancement of plant productivity and progress in plant breeding. The infrastructure will enable diverse users to quantify a diversity of plant traits and the analysis of genotype performance in in current and future agro-climatic scenarios.

European Plant Phenotyping Network

https://eppn2020.plant-phenotyping.eu/

The EPPN2020 is a research infrastructure project funded by Horizon 2020 Programme of the EU that will provide European public and private scientific sectors with access to a wide range of state-of-the-art plant phenotyping facilities, techniques and methods, and help boost the exploitation of genetic and genomic resources available for crop improvement that represents a major scientific challenge for this coming decade.

EPPN hosts regular calls for proposals for users to interact with European plant phenotyping resources.

International Plant Phenomics Network

https://www.plant-phenotyping.org/

A space for news about international phenomics activities.

Lepse, Montpellier

http://www1.montpellier.inra.fr/ibip/lepse/english/

Research at the Laboratory of Plant Ecophysiological responses to Environmental Stresses focusses on the analysis and modelling of plant responses and adaptation to variable environmental stresses.

Mutant genotype and phenotype dataset

http://www.plantphysiol.org/content/early/2012/01/13/pp.111.192393.short?rss=1

Lloyd and Meinke have made a dataset of 2400 genes with loss-of-function phenotypes in Arabidopsis. The complete dataset is found in Supplementary Table 2 of the Plant Physiology paper.

National Plant Phenomics Centre

http://www.plant-phenomics.ac.uk/en/

The National Plant Phenomics Centre based at IBERS, Aberystwyth University, features a state of the art automated greenhouse - the only one of its kind in the UK and one of only a few in the world - to enable researchers to study plants in a dynamic non-destructive manner that has not hitherto been practical.

The centre will develop and make extensive use of computer aided imaging (machine vision) and advanced methods for data handling and interrogation.

BBSRC have provided funding to run the facility as a National Capability which supports access to the NPPC by UK researchers. This is further supplemented by external funding from the European Union under the FP7 Capacities Programme (http://www.plant-phenotyping-network.eu/), which provides support for technology development and transnational access.

To find out more, contact John Doonan

New European Ecotron of Montpellier

http://www.ecotron.cnrs.fr/

The European Ecotron is a research platform dedicated to the study of ecosystems and organisms in the context of environmental changes. It is open for all international scientists who are working in Ecology Research.

Phenophyte

https://omictools.com/phenophyte-tool

PhenoPhyte is a new cost-effective web-application for semi-automated quantification of two-dimensional traits from digital imagery using an easy imaging protocol. Although developed and optimized for use with Arabidopsis rosettes, it can be used with rosettes or detached leaves from other species. 

The application can quantify plant growth by taking a series of images over time and herbivory using before and after images.

Paper: Green et al., (2012) Plant Methods 8:45

Plant Image Analysis

http://www.plant-image-analysis.org/

A wide range of analysis tools for all aspects of plant phenotyping. 130+ programs and counting....

The Australian Plant Phenomics Facility

http://www.plantphenomics.org.au/

The High Resolution Plant Phenomics Centre is located in Canberra at CSIRO Plant Industry and the Australian National University. It focuses on deep phenotyping and reverse phenomics.

The Plant Accelerator® is a world-leading plant phenomics facility offering state-of-the-art plant growth environments and the latest technology in high throughput plant imaging for the repeated measurements of the physical attributes (phenotype) of plants automatically and non-destructively. 

Tools and Resources from CPIB

http://www.cpib.ac.uk/tools-resources/

The Centre for Plant Integrative Biology (CPIB) at the University of Nottingham brings together biologists, engineers, mathematicians and computer scientists to address plant science questions. They have developed a number of tools and resources, which are available at: www.cpib.ac.uk/tools-resources

Wageningen University Phenotyping

https://www.wur.nl/en/product/Phenotyping.htm

In the process of breeding to develop new varieties, large numbers of plants are evaluated in order to select the best specimens. Automatically measuring plant characteristics is fast and objective, and it saves time and money.

Wageningen UR Greenhouse Horticulture can make an important contribution to this process by utilising modern greenhouses and climate chambers, physiological knowledge, automated measurements, and the use of models to analyse data.