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United States Department of Agriculture

Agricultural Research Service

Title: An Improved Method for Using a Microsatellite in the Rice Waxy Gene to Determine Amylose Class

Authors
item Bergman, Christine
item Delgado, Janis - TEXAS A&M UNIV
item McClung, Anna
item McClung, Anna
item Fjellstrom, Robert

Submitted to: Cereal Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 29, 2001
Publication Date: N/A

Interpretive Summary: A fraction of starch known as amylose is the primary determinant of rice texture. As a result, amylose content is used by rice breeders to predict the textural attributes of newly developed cultivars and market class is in-part based on it. The wet chemistry laboratory values currently used are influenced by where the samples were grown. This environmental effect sometimes results in amylose values that are on the border between two ric market classes. Such instances result in breeders having to grow a new rice line in multiple locations to ensure they know its market class. A DNA based tool known as the waxy microsatellite corresponds to the various market class amounts of amylose content. A relatively inexpensive, rapid method has been developed to analyze the waxy microsatellite in brown and milled rice and plant tissue. This method has been adopted by the USDA Rice Quality Evaluation Program for use in screening rice lines from the various spublic breeding programs.

Technical Abstract: Rice breeders must evaluate progeny across multiple years and locations in part due to environmental effects on amylose content, the primary constituent that influences rice end-use quality. A microsatellite correlated with the various classes of apparent amylose content in rice has been used to decrease the development time for the U.S. cultivars Cadet and Jacinto by several years. The objective of this project was to develop a relatively inexpensive method for assaying this microsatellite suited for screening large numbers of progeny and to evaluate this method by analyzing a diverse set of breeding lines and cultivars. Rapid multiple-kernel (brown and milled), single kernel and leaf tissue alkali DNA extraction procedures were developed. Enhanced resolution of allele classes and separation speed was achieved by electrophoresing PCR amplification products encompassing the waxy microsatellite in a polyacrylamide/SPREADEX gel matrix using a triple-wide mini electrophoresis unit. For germ plasm characterization, allele scoring accuracy and speed were improved by loading standards, consisting of three microsatellite classes in a single lane, several times across the gel. The microsatellite explained 88 percent of the variation in the apparent amylose content of 198 nonwaxy U.S. cultivars and breeding lines of diverse parentage, grown in four locations. The utility of this method was demonstrated by one technician analyzing a breeding population of 142 progeny in 1.5 days using relatively inexpensive laboratory equipment.

Last Modified: 7/24/2014
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