This module provides high throughput growth and deep phenotyping of small seedlings including the model plants Arabidopsis and Brachypodium in trays using digital growth and morphological analysis, pulse modulated chlorophyll fluorescence and infra-red thermography for photosynthetic and plant transpiration measurements under controlled environmental conditions (light, CO2 and humidity). This module interfaces with destructive sampling and carbon isotope discrimination.

• Growth and morphology
• Photosynthetic performance (Chl Fluor) under defined conditions
• IR screening for leaf temperature
• Automated destructive sampling for metabolites, protein, DNA and RNA, delta13C
• Leaf area / growth analysis
• Lesions / pathogen attack
• Architecture / morphology
• Morphological clustering
• PODD phenotypic dBase

The Small Model Plant Module provides high throughput growth and deep phenotyping of Arabidopsis in trays and other small seedlings using digital growth and morphological analysis, pulse modulated chlorophyll fluorescence and infra-red thermography for photosynthetic measurements under controlled environmental conditions (light, CO2 and humidity). This module will interface with destructive robotic sampling and carbon isotope discrimination.

Model Plant HTP Screening Module: Fluorogroscan

High Throughput Arabidopsis Screening : Growth and morphology Photosynthetic performance (Chl Fluor) under defined conditions IR screening for leaf temperature Automated destructive sampling for metabolites, protein, DNA and RNA, 13C delta Fluorogroscan was developed by Phytosphere Juelich. It uses a PAM imaging fluorometer to measure chlorophyll fluorescence and the image can be background subtracted to give projected leaf area for growth analysis and morphological characterisation. The camera steps across trays of 20 plants using an X-Y-Z robot, illuminating with a flash of very high light then measuring chlorophyll fluorescence. False colour images area produced which represent calculations of chlorophyll fluorescence parameters on a pixel by pixel basis. Regions of interest can be identified for screening in high throughput . Outputs can be false colour images for spatial information or CSV files of calculated values of dark adapted Fv/Fm (gives the “health” of the photosystems), commonly used in abiotic stress screening and for mutant screens (photoinhibition and pigment mutants). Steady state Fm’ and electron transport rate in the light can also be calculated as a surrogate for photosynthesis.

Fluorogroscan Measures Growth and Fv/Fm
Example of metadata on a drought experiment for arabidopsis where water was with-held at the arrow, compared to well watered controls. Note growth rate is more sensitive than fluorescence in this case.

Top Camera Growth Imaging

In-Cabinet real time imaging

Non-destructive Growth Analysis and Morphological Clustering

Images taken with the Lemnatec system and analysed for colour classification to allow quantification of chlorosis and lesions. Currently in use to screen KO lines for fusarium and other pathogen resistance genes.
leaf area / growth analysis lesions / pathogen attack architecture / morphology morphological clustering

Morphological "Fingerprinting"

Growth rate: relative growth measured using total leaf area. Eccentricity: degree of deviation of a conic section from being circular. Compactness: positioning of the leaves relative to the centre. Roundness or "stockiness" Surface Coverage
MAT or Morphological Analysis Tool is a commercial version of image analysis software we also have developed in house. This allows mathematical quantification of morphologies based on standard ontological plant descriptors. These can be graphed using polargrams or entered into a database (outputs CSV files) and PNG image files. This has been tested to cluster phenotypes of ABA sensing mutants and works well. I will provide you with an example of analysis of heterosis in crosses of LER and C24 and inheritance of rosette architecture.

Outputs from Arabidopsis HTP

	Arabidopsis Phenomic Database Relational database linking genotypes of all SALK Homozygous KO’s, transgenics, RIL’s and ecotypes to a defined and quantified set of phenotypic parameters (polar diagrams). Targeted Phenotyping Abiotic and biotic stress screens targeted RNAi and OE lines, relating non-invasive imaging to plant composition
More information than “no visible phenotype”!

Trays of stomatal response mutants of Arabidopsis compared to the wild type Ler imaged in cabinet with our FLIR FIR camera system