Advances in Genetic Purity Testing

- Farhad Ghavami

It’s not rocket science, even though it may sometimes seem that way when you read about advances in genetic purity testing or listen to a presentation on it. Here, I’ll share the nuts and bolts of the newest testing methods being used.

Historically, we’ve relied on plant grow-outs in the field for genetic purity testing. This method was dependent on the visual identification of plant characteristics — a process that was time consuming, affected by environmental conditions and only worked for characteristics that could be seen by the eye. Nonvisual characteristics, such as high oil content or tolerance to drought, could not be detectable from others by using field grow-outs.

Then we transitioned to protein-based molecular markers, and used methods such as isoelectric focusing or isozyme electrophoresis. However, if you’re using a protein-based test for genetic purity testing and you also want to check for the presence of a trait, a separate test must be conducted. With a DNA-based method, you can test for both the presence of the trait and genetic purity all in one. There are also a limited number of protein-based markers in the genome, which lowers their power of detection, especially for seed mixes and outcrossing.

Today many of the largest seed companies have shifted to DNA-based molecular markers for genetic purity testing. Methods that are DNA based are fast, accurate and allow us to use seed or any type of plant tissue.

There are a number of DNA-based testing methods, including SNP (single nucleotide polymorphism) markers and SSR (simple sequence repeat) markers. These markers got more common for genetic purity testing among other DNA-based molecular markers as their popularity increased in plant breeding.

SNPs are becoming more popular as millions of them are available in the genome of different crops. The more information and data we have on the genome, the higher quality purity panels we can create to test a variety against. SNP markers are also easy to automate, which allows the use of high throughput systems, thus making it more cost efficient.

By using the same SNP markers in the seed production stage that the plant breeder used in the development process, we’re able to keep the same genetic quality and not lose the integrity of the seed downstream.

With the breadth of SNP information available for different crops, a good SNP panel can be designed to be very accurate and detect genetic quality issues within a seed lot. Now, each company can differentiate themselves from the competition in terms of the quality and purity of the seed they produce.