Cornell Develops New DNA Testing Device
By John Zakour
In the past, plant breeders had to go through lengthy analysis to identify the plants that contained the specific traits they were looking for before they could use them to improve particular varieties. With the matrix mill (MM), developed at the New York State Agricultural Experiment Station in Geneva, what once took months now can be accomplished in a matter of days.
Norm Weeden, PhD, professor of horticultural science at Cornell who has extensively researched pea, apple, grape and bean genetics and breeding, was interested in developing the device because of the sheer numbers of plants he had to work with to find the traits he desired. "If we had to extract DNA from, for example, 2,000 plants using the usual procedure, it took about 10 weeks and cost about $8,000 for extraction only," said Dr. Weeden. The matrix mill reduces weeks to days, and the cost to about $50.
The true power of the matrix mill comes into play with marker assisted selection (MAS). A marker is a short fragment of DNA that identifies a particular region of the genome. If that region also contains a gene of interest (e.g., disease resistance or flavor), then the marker may be used to identify plants that contain the desired trait.
"The MM makes marker assisted selection a viable alternative, especially for smaller breeding operations or crops where the profit margin is small," Weeden added.
The MM reduces the time it takes to separate DNA from tissue. It works by breaking up 96 small tissue samples simultaneously in sodium hydroxide which releases the tissue's DNA into the NaOH and denatures the protein. After the extraction there is one easy step: neutralizing the NaOH and simultaneous diluting the DNA sample. The DNA is then ready for analysis. This saves about 10 hours per 100 samples, i.e., 10 hours of technician time vs. about five minutes of technician time for the extraction.
Sue Gardiner, PhD, program leader for New ZealandÆs horticultural research apple gene mapping program, first used the matrix mill for rapid preparation of DNA from apple leaves last year. "The MM has the advantage of enabling rapid preparation (10 times the normal rate) of DNA suitable for molecular marker screening," she said, also noting that the MM is convenient to use without a sophisticated laboratory. "The MM was easily transported to our research orchard, where a team of orchard technicians supervised by our lab technicians performed the extractions of DNA from small seedlings prior to planting the nursery."
Weeden first conceived the technology for creating the MM in the spring of '95. The prototype was built and tested over the following winter with co-inventors Joe Celeste and Dale Loomis. In the 1980s, Celeste and Loomis worked with John Sanford, plant breeder at Geneva, on the development of the gene gun—a Cornell invention that so revolutionized the science of genetic engineering, its prototype sits in the Smithsonian Institute.
Six matrix mills are currently in operation. One is in WeedenÆs lab ; five others are being field tested at sites that involve plant crops as well as animal tissue. Cornell University is looking for a partner to help commercially produce the device. Weeden and co-inventors have applied for a patent with the help of the Cornell Research Foundation.