Fast, Cost-Effective DNA Extraction: a Competitive Advantage in the Cannabis Industry
New Plant gDNA extraction Protocol to the Rescue!
July 29, 2021
One of the key strategies for staying ahead in any competitive industry is rapid rollout of new and differentiated products before your competitors do. For the cannabis industry, molecular plant breeding is hands down the fastest way to create new plant strains with desired traits. There’s just one problem, the genomic DNA you need to work with is locked away behind a cell wall that makes it very tough and expensive to access. A newly published DNA extraction protocol might be about to change all that.
Molecular breeding in all plants, including cannabis, is hampered by the problem of obtaining high-quality sequence-ready genomic DNA (gDNA) from plant tissue samples. Unlike animal cells, plants are protected by a tough, cellulose cell wall that has long been the bane of plant breeding scientists, as it protects the individual cells, preventing them from being ruptured to enable access to the DNA within. Without easy access to high-quality gDNA, technologies such as genotyping-by-sequencing (GBS) that underpin molecular breeding research become difficult, if not impossible.
In a recent paper in the journal of Plant Methods, Anderson et al., describe a rapid, low-cost protocol for reliably preparing high-quality sequence ready genomic DNA from even the most challenging plant species, all without the use of any organic solvents, magnetic beads, or other expensive components.
The researchers used the Pall AcroPrep™ Advance 96-Well 1ml Filter Plate as a key part of the protocol, using it to separate the DNA from the cell debris. The AcroPrep Filter Plate could be used repeatedly for multiple consecutive individual extractions but using a fresh well for each extraction. This cost-effective modification ensured consistent plant gDNA quality, as well as being highly scalable in an automation-friendly 96-well format.
Pall’s AcroPrep Plates incorporate a silica-based quartz glass fiber media to allow for
efficient binding of DNA and RNA while providing smooth flow and rapid processing of samples. The enhanced membrane on the plate ensures high yields of contaminant-free DNA for downstream applications such as PCR and sequencing. The well geometry results in reduced hold-up volume and higher recovery of DNA whilst still being automation friendly. AcroPrep Plates suitable for plant gDNA extraction are available in 96-well format (350 µL and 1 mL well volumes) and in 384-well format (100 µL well volume).
The researchers demonstrated that by using their modified 96-well plate-based grinding and DNA extraction protocol, microgram quantities could be extracted inexpensively from fresh, freeze-dried or silica gel–dried plant tissue from a range of plant species, including challenging species such as white clover. DNA quality is paramount for sequencing and restriction enzyme-based GBS platforms, which require high molecular weight gDNA largely free of contaminants, such as polysaccharides. These contaminants can inhibit sequencing quality as well as restriction enzyme activity and subsequent procedures, thereby providing a source of inconsistent or unreliable SNP data, which has significant implications for genotype analysis.
This novel plant gDNA extraction protocol is a very powerful tool for any plant breeding researcher, enabling a single operator to generate microgram quantities of high-quality sequence-ready gDNA. The researchers not only demonstrated that the extraction protocol influenced the quality of the resulting gDNA and, in turn, the sequencing quality but also calculated that this can be done from 192 samples in three hours, at a cost of approximately $0.62 per sample (as opposed to the standard $6 – 9 per sample for other methods). All without the need for a fume hood and without exposing researchers to hazardous organic solvents.
The ready availability of gDNA from plant specimens opens up all of the tools of modern molecular biology for cannabis breeding, accelerating the research and development of new strains with desired properties as a key driver of new product introduction.
1. Anderson, C.B., Franzmayr, B.K., Hong, S.W. et al. Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing. Plant Methods 14, 75 (2018). https://doi.org/10.1186/s13007-018-0336-1