At least since the Covid pandemic, PCR analysis has also been familiar to the biological non-expert. Only a few people knew, that this molecular biology tool had already been used in plant breeding several decades earlier.

Tissue sampling as a starting point

The procedure that must always precede a genetic analysis using PCR is the same regardless of the object to be cultivated (plant or human). A tissue sample must be taken and DNA extracted from the sample, is then used for analysis.

Automated sampling and strong plants after sampling

In conventional plant breeding, DNA extraction from leaf tissue or seeds is a routine procedure. However, taking a tissue sample from a leaf is a time-consuming manual step that can lead to bottlenecks and delays in the overall workflow. Even automated solutions using robots cannot solve this problem, as they are also based on the manipulation of individual plants. In addition, the availability of sufficient leaf material is highly dependent on the cultivation conditions. In some cases, it is necessary to wait a long time for sufficient leaf mass so that tissue sampling does not stress the plant too much.
Sample preparation for seeds is not complicated by nature. The seeds to be tested can be transferred to the laboratory plates using various systems available on the market. During DNA extraction, however, the grain is destroyed and is no longer available for cultivation of the plant. This means that only random purity tests can be carried out with this tissue.
SMARTtray® solves precisely these problems of conventional procedures by using the root as the starting tissue. Thanks to the functions of the SMARTtray® device, 96 roots and thus plants are sampled in one step and individual plant manipulation is completely eliminated. This can reduce the sampling time by up to 90%.
The plants are not permanently stressed by the cutting of the roots and show a survival rate of 99.9%. In fact, a positive side effect can be observed. The sampling method leads to the plant subsequently forming more lateral roots. This transplanting effect makes the SMARTtray® plants more resistant than conventional cultivation methods.

Less inhibitors for the analysis methods

The success of any breeding depends on the quality of the genotyping results. A sufficient amount of DNA is required for both marker-assisted selection (MAS) and genotyping by sequencing. In addition to quantity, however, quality is the most important factor. When extracting DNA from leaf material, secondary metabolites such as chlorophyll can inhibit the PCR in the further process. Extraction from seed is increasingly causing problems with starchy crops. When extracting oilseeds, the oil released during cell disruption can also interfere with lysis.
The root, on the other hand, is not a storage tissue and is therefore low in potential inhibitors. A closer look at root physiology reveals other factors that make the root an ideal tissue for use in the breeding process.
The cell density in the root is higher than in any other plant organ. In addition, the root tip in particular consists of meristematic cells that divide quickly. The cell nucleus is known to contain DNA. The large number of small, fresh cells also increases the amount of DNA that can potentially be extracted and is significantly higher than in the parenchyma tissue of the leaf.
In order to generate as much root mass as possible as early as possible, SMARTtray® utilizes the root’s ability to be controlled very well by specific light conditions, better than leaf mass, for example. The LEDs integrated in the SMARTtray® growing station enable dynamic adjustment of the light intensity and composition, so that the plant has ideal conditions at all times to germinate well, then form a lot of root mass and, after sampling, is already stimulated to initiate the generative phase.

The right extraction method for the required application

The change to extraction from root tissue does not confront the user with any new challenges. Existing processes in plant breeding operations can be transferred 1:1 to the new tissue and can even be simplified or improved in quality. In addition, SMARTtray® takes the approach of supporting customers in selecting the most suitable method for their applications. To this aim, SMARTtray® works together with global partners in order to be able to offer the right extraction method for the intended application.

Whether marker-assisted selection (MAS), chip analysis or genotyping: if you know your roots, you can grow!