New Primer Helps Identify More DNA Markers

DNA makers are important tools for identifying genes that control traits of interest to plant breeders, such as disease resistance or fruit quality. DNA markers are usually generated using “primers,” short segments of DNA that are used by geneticists to look for genes that control specific traits. In general, geneticists use random primers in their search for DNA markers, but that process is often long and arbitrary, and it can result in researchers spending a lot of time and money to identify just one DNA marker.

To streamline the process, Agricultural Research Service geneticist Amnon Levi and plant pathologist Pat Wechter have developed a new method for identifying DNA markers. They used genomic data to search for small pieces of DNA, called “oligonucleotides,” that are prevalent in watermelon genes and could be used as primers. Levi and Wechter believed that these new primers would generate a larger number of markers because they are more targeted than random primers.

Zhangjun Fei, an ARS-funded bioinformatics researcher at the Boyce Thompson Institute for Plant Research in Ithaca, New York, collaborated with Levi and Wechter and wrote a computer script to identify oligonucleotides that exist in high numbers in genes of watermelon. They named the new primers “high-frequency oligonucleotides targeting active genes,” or HFO-TAG for short.

Working from the U.S. Vegetable Laboratory in Charleston, South Carolina, the scientists and fellow ARS and university colleagues tested their theory on 12 closely related watermelon cultivars. The researchers found that the HFO-TAG primers identified more DNA fragments than random primers did. Finding more fragments means researchers have a greater chance of finding DNA markers for genes that control desirable traits. And they don’t have to invest as much time and money to identify the markers.

Levi and Wechter are currently using the HFO-TAG primers to look for watermelon genes that control disease or pest resistance and fruit quality. The primers will also be useful in genetic studies and genetic mapping of watermelon.

According to the scientists, this simple and straightforward method can be applied to genetic studies of other plants as well as animals. A full description of this study has been published in the Journal of the American Society for Horticultural Science.—By Stephanie Yao, formerly with ARS.

Amnon Levi and Pat Wechter are with the USDA-ARS U.S. Vegetable Laboratory, 2700 Savannah Hwy., Charleston, SC 29414; (843) 402-5326 [Levi], (843) 402-5318 [Wechter].

"New Primer Helps Identify More DNA Markers" was published in the July 2011 issue of Agricultural Research magazine.