The previous article described the evolution in DNA isolation in plant material due to evolving techniques such as Next Generation Sequencing (NGS). The standard process for gDNA isolation using magnetic beads is also described. This article will go into more detail on the challenges on gDNA isolation from plant material.
Grinding and lysis of samples
As mentioned in the previous post, the process starts with grinding the samples. This step is done by adding grinding beads into the sample, closing the sample carrier (plate or tube) and placing the samples into a tissue grinder. The challenges in grinding samples are due to the detergent based lysis buffers and the remaining grinding beads in the sample.
If grinding is performed in presence of the lysis buffer, the detergent will form a foam layer on top of the sample. This will result in difficulties when automating the DNA isolation process. A detergent free lysis buffer would be a big advantage as this would allow the process to be more efficient and faster. However, most commonly the grinding and lysis step are separate steps in the process.
Variety of crops
Another very common challenge is the variety of crops. Some crops are more difficult to process than other crops. This normally results in an adapted process per crop type and sometimes even in adapted processes for different breeds of the same crop. When performing DNA isolation on a wide variety of crops, this results in many different protocols all with their own specific volumes of reagents per step. In a high throughput setting, this is hard to maintain and may result in a higher error rate due to human errors.
A standardized method with only a few variables would be ideal for a high throughput and high variety DNA isolation setting.
Price per sample
With an increased throughput, the cost per sample becomes an important factor for the isolation of DNA from plant material. When working with human material, the sample is precious and rare and very often it involves an invasive process to get the sample. However, with plant material, the sample availability is high and nearly unlimited. A fully grown crop will result in thousands of samples for DNA isolation if needed. This results in a lower risk of faulty isolations, as the possibility to repeat is nearly unlimited. However, due to increased demand on early information, the need for a high quality DNA isolation increases. Many DNA isolation processes are based upon an in-house developed and optimized method. These methods are cheap per sample, but are often difficult to automate.
A magnetic bead based process in the price range of home-brewed methods would solve the challenge of the price per sample, while being suitable for automation.
The next post
In the next post of this series of articles, we will discuss the solutions for gDNA isolation of a variety of crops with limited adaptations to the standard protocol. The process is also downscaled successfully to approach the price setting as demanded in the field of plant genomics.