The Success of Molecular Markers Hinges on Precise Phenotyping

As with nearly all living systems, the health of an organism is dependent on a number of factors, and these factors often have a compounding effect. The same can be said of plant breeding. It’s an evolution and one process builds upon itself. Simply put, the end result can only be as good as what or where you started.

Once the seed is planted in the ground, one of the biggest threats to that developing plant is pathogens. Plant breeders strive to develop hybrids that are resistant to different plant diseases. When seed companies improve a hybrid or a cultivar with resistance to disease, they must be able to ensure the stated resistances exist because customers are paying a premium for that characteristic.

The traditional testing procedure requires plants be grown out from seed in greenhouses, be inoculated with the disease of concern and then be evaluated for their response to disease. This is time consuming, costly and takes up greenhouse space.

During the past two decades, the use of DNA technology to expedite the process has been proven.

A hole punch of leaf tissue is taken of plants two to three days old, DNA is extracted and a tightly linked DNA marker is used to verify resistance. The process is known as marker-assisted selection and allows breeders to determine which varieties they should select and which ones they should discard. In some cases, up to 10 diseases can be assessed on the same sample, which is not possible with classical inoculation of plants.

The crucial point is that the process to find the molecular marker associated with a certain resistance gene is a whole research and development process in and of itself. It takes a great deal of work and resources to find the right markers and therefore, much of the success depends on the initial evaluation of resistant and susceptible lines (also known as phenotyping) needed for the project. A good marker is one that is tightly linked to the gene of interest with a distance of 1 cM or less.

The tighter the marker is linked, the better because there is less chance for crossover between the marker and gene of interest (GOI). As the initial disease reaction of inbred lines enhances, the distance between the marker and GOI gets tighter, significantly improving the chance of finding closely linked markers.

In other words, finding useful markers completely depends upon starting with clean materials and with distinguished resistant groups versus susceptible groups. Ambiguous phenotypic data will result in loosely linked markers and inaccurate results.

To develop a reliable marker requires constant collaboration and communication between lab and field researchers. This ensures maximum efficiency in finding the right markers, and a reliable marker can be used with high confidence and dependable results.

Once the marker has been developed and evaluated, marker-assisted selection screening can be adopted, which will facilitate the release of new materials.

A small leaf tissue can be harvested from anywhere in the world and shipped to a lab overnight for analysis. The laboratory can then determine if the samples are resistant or susceptible and transfer the results electronically to breeders anywhere in the world.

This process allows a breeder to move from region to region and work through more hybrids and more plots while using fewer resources. In many cases, the identification of high quality resistance markers will cut the timeline for the product development pipeline in half.