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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #139839


item Hoffman, David
item Hang, An

Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2002
Publication Date: 3/1/2003
Citation: Hoffman, D.L., Hang, A. 2003. Conversion of a rapd marker to an sts marker for barley variety identification. Plant Molecular Biology Reporter. V 21 P 81-91

Interpretive Summary: Some of the more common six-rowed malting barley varieties grown in the northern Midwest have unique malting and brewing properties, but the seeds cannot be easily distinguished by visual inspection. It would be helpful to the malting and brewing industry to have a quick and accurate way to verify such varieties prior to malting and brewing. We previously reported a DNA method to distinguish closely related six-rowed malting varieties, but our technique required strict standardization among test laboratories in order to be successful. In this report, we describe in detail how we converted our original procedure into a more robust one that could readily used in other laboratories for the identification of mid-western six-rowed malting varieties and mixtures thereof. This information will also be of use to other scientists that need a way to convert similar procedures for different reasons.

Technical Abstract: Barley (Hordeum vulgare L.) variety identification is important to the malting and brewing industries. Because many of the new malting cultivars (or varieties) are very closely related, new and more effective identification techniques are needed. We report on a series on techniques that were used to convert a RAPD marker to a more stable STS marker that can differentiate barley Stander from Robust, an important distinction for the American malting and brewing industries. The techniques included: DNA extraction, RAPD amplification, random cloning of all amplified fragments, selection of clones by insert size, DNA sequencing of select inserts, design a barley-based primer pair, and detection of a single nucleotide polymorphism using restriction endonuclease Alu I. The barley-based primer pair was used to further sequence the RAPD fragment. Five single nucleotide polymorphisms between Robust and Stander, one of which could be detected by electrophoresis of DNA fragments differentially restricted by Alu I. The conversion technique was different than ones previously reported in that it did not require manual extraction of DNA fragments from a gel. This could be applied to other situations where RAPD marker conversion would be desirable.