Root Phenomics

Root Phenotyping

Root Development and Root Phenotyping

In contrast to the intensive breeding efforts for shoot development, root development is much less intensively used to enhance plant performance. Yet farmers have far more influence on changing the root environment in the soil – for example by their choice of tillage, watering and fertilising methods – than they will ever have on the aerial environmental conditions of their fields.  

As roots are generally growing in dark, non-transparent soil, the amount of information available about root architecture and root development is increasing far more slowly than the knowledge about shoot development. Especially high-throughput test series showing the dynamic development of root systems have remained difficult to design. Many requirements of root growth and data acquisition are conflictive (e.g. growing in the dark – imaging in light; covering large soil volumes –technical limitations of looking through soil ). 

LemnaTec scanalyzer3D technologies

Root development and root phenotyping using LemnaTec scanalyzer3D technologies

To make the best of a bad situation, LemnaTec has developed plant carriers that allow the root system to grow in the dark under relatively low temperatures, with shades that will open just for the image acquisition in the scanalyzer3D root imaging units. Roots hitting the walls of these transparent vessels are imaged in their dynamic behaviour over time, which allows drawing conclusions by modelling the time span of growth even before they hit the wall. In addition, NIR-measurements of soil humidity profiles can detect from which areas visible as well as non-visible roots extract their water. Thus, it is possible to assess in detail a functional parameter of the root system, and not merely the result of the historic root development, in contrast to methods where root systems are analysed through harvesting. Such experiments can be performed in real soil samples, but peat or artificial, even transparent media are also an option.

For small, petri dish- or multiwell-based root experiments like slant agar plates, the scanalyzerHTS offers high resolution imaging as well. The scanalyzerHTS can moreover be used to quantify root cyst-nematodes grown on root systems in petri dishes.

Root phenotyping and root development are assessed under high-throughput conditions with LemnaTec scanalyzer3D systems, by using transparent pots or columns. In this way, real soils can be utilised as root environment, thus solving the problem of non-transparency of soil.

Soil Water Content and Soil Humidity

Soil Water Content and Soil Humidity

Soil water content is the physical parameter used to characterise the availability of water for plants in the soil. Besides the fundamental gravimetric method of measuring the water content of a soil sample, a wide range of other approaches is available. The aim of these alternative methods is either to provide a fast measurement value (soil conductivity) or to provide values for continuous measurements over longer periods (gypsum block conductivity, tensiometers, thermal conductivity). All approaches need calibration for individual soils if absolute values are actually needed, and they can have a restricted linearity at high or very low moisture ranges. Most alternative methods describe the physical properties of a very restricted solid volume, which then becomes the representative for a larger bulk volume. By contrast, weighing defined soil portions with a general, known dry weight provides an average humidity value for the entire container and enables easy calculation of water balances.

Soil water content is either calculated as an absolute value (g water /g soil), or relative to the water holding capacity (% of water holding capacity). In all cases, it must be considered that soil water content provides well-characterised values, but the actual biologically available water content for the plants may be significantly different. An extreme example: Biologically available water in a loamy soil is continuously reduced over time, however when lowering the absolute soil humidity with peat soils, the water availability remains close to constant over a wide soil humidity range, before the value then drops very fast.

Control soil water content

Using LemnaTec scanalyzer conveyor systems and watering units to control soil water content and soil humidity

To provide similar basic growth conditions for plants, it is necessary to grow each plant or group of plants in a pot with a comparable amount of soil (based on dry weight). This is achieved by filling the pots with the same amounts of soil of a known, homogeneous soil humidity. Based on such data, the absolute amount of water in each pot can be measured and controlled by LemnaTec scanalyzer watering and weighing units. These systems can weigh the pots and plants one or several times per day. Shot weight changes during plant growth can be corrected by image-based biomass estimates, but in most cases the soil weight remains on a high level, in comparison with plant weight.

Soil humidity distribution in different soil layers of transparent root columns can be assessed by near infrared imaging of the root columns, showing exactly where the plants extract the water from the soil.

If data is to be collected in short intervals , an additional option is to install soil humidity sensors in the individual pots and save resulting data to the central LemnaBase.

For an optimal environmental simulation, soil water content and soil humidity are controlled for each plant individually to measure the response of the plants to specific environmental conditions.

Water Imaging

Near infrared (NIR) imaging can be used, for example, to obtain detailed information about the watering status of plant leaves and their reaction to limited water availability or external drought (e.g. during growth or storage periods). The following image shows how wheat – as a representative of cereals in general – dries down over time, changing the NIR absorption of the leaves in the NIR water band between 1450 and 1600 nm.

Water imaging in wheat: A bunch of wheat dries down in a warm environment. NIR imaging shows a huge increase in reflectance as water in the leaves is greatly reduced. Blue/green signal colours represent high water content, while yellow/red colours signify low water content (high reflection).

The wheat example shows the fast reaction to drought as just one application example of NIR imaging, namely to quantify water dynamics in plants.

Similar tests may certainly be performed with different plants in pots, assessing their reaction patterns to water stress under drought conditions.

Water Use Efficiency

Water use efficiency is a quantitative measurement of how much biomass or yield is produced over a growing season, normalised with the amount of water used up in the process. Besides absolute yield, water use efficiency is an important agronomic factor, especially in agricultural irrigation systems and in climate areas where a limited amount of water from the rainy season has to last for the whole growth period as no further rainfall can be expected.

Measurement of water use efficiency

Measurement of water use efficiency using LemnaTec watering stations

The most common method to measure the water use efficiency of individual plants or microplots is to weigh each pot or container on a regular basis and maintain full control over any water addition. In the classical approach, biomass or yield is measured once at the end of the test series, in a destructive way, by harvesting the pot or plot. The LemnaTec scanalyzer3D conveyor systems with their combination of weighing, completely controlled, individual watering and image-based plant phenotyping allow the quantification of a complementary dataset for water use and biomass development, which can be performed non-destructively several times a week. This provides a much deeper insight into the dynamics of water use efficiency over the entire growth period, which is also crucial in developing a better understanding of drought tolerance or drought resistance.

Monitoring of water use by weighing and refilling to a defined degree of soil humidity is the key element to establish reproducible data for assessing water use efficiency, especially when combining such data with non-destructive, image-based plant biomass data obtained with LemnaTec scanalyzer3D systems.

Waterlogging experiments

Integration of waterlogging experiments in LemnaTec plant phenotyping technologies

In periods of waterlogging, parts of or the entire root system of plants in soil becomes oversaturated with water. As a consequence, many soils tend to get anoxic, which is harmful for any root system. There is a large variation in tolerance levels concerning such waterlogging conditions over a shorter or longer time period. Corn and soy beans are particularly sensitive to waterlogging. Due to the climate and soil conditions in which soy beans are normally grown, waterlogging resulting in significant yield loss is a major problem in soy bean cultivation, for example in the US.

To simulate waterlogging, plants grown under normal conditions in only partially saturated soils can be flooded at a certain point in time, simply by raising the target weight value of the pot in the LemnaTec scanalyzer watering and weighing module to a higher value at which waterlogging will occur. Different degrees of waterlogging can be simulated, for example by filling pots to different water levels under the soil top level. In this case, no specific top lid is necessary, as water cannot spill over. The level of waterlogging can be easily maintained by adhering to the chosen target weight. Repeated weighing and watering can also provide information about how the plant is reacting towards this specific stress.

To remove the water again, a specific tube and suction unit is put into the soil of the pot during planting; in some specific pots, this is already pre-installed. Water that has accumulated at the bottom of the pot can also be sucked away automatically on LemnaTec scanalyzer conveyor systems. If more water should be slowly trickling down at a later time, it can be removed in a second suction process after the plants have had another turn on the conveyor. LemnaTec scanalyzer suction stations are generally installed as an add-on, in combination with LemnaTec scanalyzer watering stations, but also as individual units.

Thus, water can be reduced until full saturation of the soil, and plant activity will dry out the soil even further. In addition to the management of waterlogging in the pot, measurements of the soil redox status, soil temperature and soil humidity by individual pot probes are optional. To monitor the reaction of the plants, normal shoot imaging in the VIS/NIR/IR-ranges and fluorescence imaging in LemnaTec scanalyzer3D imaging units can be complemented by direct root observation in transparent columns (LemnaTec scanalyzer3D root imaging), as long as the soil medium allows a direct view through the transparent pot walls. 

While waterlogging conditions are very difficult to manage appropriately in field experiments, LemnaTec automated watering systems grant full control over the degree of waterlogging, while at the same time monitoring the reaction of shoots and roots to these stress conditions.