App Note
Using the phytoGEM DNA extraction method with the Hydrocycler: a new high-throughput approach to plant molecular SNP screening
Since Mendel studied the basic principle of genetics in peas, the use of genetic-driven decision in plant breeding has been growing constantly. Nowadays, genetic markers are largely brought into play to avoid the need of phenotyping. The so-called marker-assisted selection (MAS) applies diagnostic markers to forecast the phenotype and optimize the selection of new crops. Since the comprehensive sequencing of plants, such as maize, has become readily available, single nucleotide polymorphisms (SNPs) have been widely used in MAS.
However, the extraction of DNA from plants is generally difficult and time-consuming, due to the presence of a tough cell wall and several contaminants, such as polysaccharides, polyphenols, tannins, and alkaloids. Overcoming this issue in DNA extraction will set the springboard for more efficient plant molecular breeding.
In this application note, we show a novel workflow combining different technologies to reduce time, plastic consumption, and costs of plant DNA extraction, as well as increase the analysis throughput. The workflow suggested here includes:
- MicroGEM’s phytoGEM chemistry for rapid temperature-driven extraction (TDE) of DNA from seeds, leaves, and roots of rapeseed plants (Brassica Napus);
- Hydrocycler (LGC) to run high-throughput TDE and Kompetitive Allele Specific PCR for the genotyping.
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Related Products
PDQeX phytoGEM
Suitable for studying plant genotypes and genetic variation, endophytic plant pathogens, genetic mapping, fingerprinting, microsatellite marker-assisted selection, and for evaluating the authenticity of exported plant varieties, botanical extracts and molecular detection of food adulterant.
Produces double-stranded DNA suitable for PCR and qPCR.
Each kit contains PDQeX prepGEM, Histosolv, enhancer, GREEN+ buffer, and extractor tubes.
For processing larger samples, we recommend the PDQeX phytoGEM HC kits. These kits have the traditional advantages that come with using the PDQeX Nucleic Acid Extractor but also include the new HC extraction cartridges.
These new HC extraction cartridges allow for more sample to be loaded into the cartridge before the purification matrix becomes overloaded. This results in a higher final yield of extracted DNA, meaning the PDQeX phytoGEM HC kits are better suited for sequencing workflows where a higher yield of DNA is encouraged.
PDQeX phytoGEM Punch Tool and Tip
Used with MicroGEM storage cards to cut out plant sample and transfer to a PDQeX cartridge.
PDQeX phytoGEM Punch Tool Replacement Tip
Used with MicroGEM storage cards to cut out plant sample and transfer to a PDQeX cartridge.
phytoGEM Cards
Used with the PDQeX phytoGEM Crusher Tool and Punch Tool when transferring plant samples for processing and storage.
Available in 500 or 1000 units.
phytoGEM Starter Kit
The phytoGEM Starter Kit is MicroGEM’s all-in-one solution for preparing and processing plant DNA samples.
Includes 1 crusher tool, 1 punch and tip, 50 phytocards, and 50 phytoGEM reactions.