Phenotyping at the Department of Plant and Environmental Sciences.

The Department of Plant and Environmental Sciences (PLEN), at the Faculty of Science, University of Copenhagen, is currently developing and testing a mobile Phenotyping platform based on multi spectral imaging. The platform has been named PhenoField.

The platform consists of a box that using an outside mounted moveable cover can enclose the crop from wind and light.

Mounted inside the box is a panel of diodes that emit a stroboscopic light in 9 different wavelengths from 450 to 850 nm. Top-most and centrally mounted in the box is the camera, which when the box is positioned over the crop, and the cover has been lowered to the soil surface, takes a series of images of the crop. The images are shot from a height of 1 meter above the plants. The box is illustrated in figure 1.

Since the system is fitted tightly around the crop and includes its own light source, it is possible to lessen the bias that can normally arise when reflectivity is measured with naturally occurring sunlight as the light source. These error sources can for example be changes in the incoming angle of the light and changing cloud cover during a set of measurements.

Figure 1: PhenoField consists of a double layered white box. The inner layer has the light source with 9 different wavelengths and the camera. The outer layer of the box can be lowered (from a preset height) onto the ground, encasing the crop. The box is transported in the field by a tractor and a crane mount.

A series of images consists of 9 separate images. 1 image from each of the wavelengths the light source can emit. This gives us a so-called multispectral image (figure 2).

The multispectral image contains information that enables us to perform advanced studies of the effects on the plants phenotype from changes in e.g. leaf composition, cell changes, stress due to water shortage, temperature fluctuations, weeds, diseases, pests and other relevant factors.

One of our motives for developing this platform is the challenges modern plant breeding faces, necessitating that the pace of plant breeding has to be sped up in the future.

The platform is expected to give information about changes in the plants before the symptoms are visually present to the unaided human eye. Thus the screening process can be more expedient and more independent of e.g. destructive biomass harvest.

Figure 2: The images shot with the PhenoField platform. Here images of a grassy patch with Dandelions (genus Taraxacum). Here shown are 5 of the total of 9 images in an image set of one crop/patch, thus 5 of the total 9 wavelengths imaged in the series.

PhenoField in the future

Looking further ahead our strategy is, that the platform is incorporated into different types of research projects, where it is desirable to test new genotypes - with their resulting phenotypes in the scale of field trials.

This ought to result in both objective and precise data about the specific crop being tested, but also in time contribute to generating a knowledge database. The purpose of this database is to create a combined overview of already tested genotypes, whereby it will be possible to also across national borders easily exchange knowledge of plant breeding of crops under varying climatic circumstances.

The prototype PhenoField is in its current form a prototype that will be is sought expanded to contain other sensors and cameras, enabling more detailed analysis.

The resulting increase in the nuance of the data is expected to give a more precise knowledge and thus a better foundation for decision-making.

At the same time it is also expected that such a system will speed up the screening of new phenotypes, thereby optimizing modern plant breeding as we know it.

In the short run we wish to introduce several platforms at the research facilities at PLEN, making it possible to work with phenotyping in the greenhouses, the climate chambers, semi-field setups and - as already implemented in the fields. Figure 3 shows a representation of the phenotyping infrastructure were aiming to build.

Figure 3: The infrastructure relating to several both mobile and stationary phenotyping units at PLEN. It involves both technical staff, miscellaneous needed competencies to handle the platform equipment, the data and the facilities where the units are used.

PhenoField is currently (spring/summer 2012) being tested at the Tåstrup research farms at PLEN. The platform is used for evaluating forms of Spring Barley and their characteristics to 3 specific plant fungal pathogens. 

[Text: Jesper Svensgaard / Translation: Jesper Cairo Westergaard]