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United States Department of Agriculture

Agricultural Research Service

Development of DNA Markers that Distinguish Commercial U.S. Rice Cultivars
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Biotechnology offers new tools that will help in rice cultivar identity preservation and verification. This is becoming a significant issue as the number of commercial cultivars that are being made available to the U.S. rice industry increases. Some of these cultivars may have special properties that are important to niche markets whereas others may possess proprietary technology. Moreover, many U.S. breeding programs utilize a relatively narrow germplasm base making it difficult to phenotypically distinguish some cultivars. Having a set of molecular markers which differentiate among U.S. cultivars will benefit rice researchers, producers, seedsmen, mills and end-users that desire seed purity and identity preservation.

Over 30 commercial rice varieties representing conventional long, medium, and short grains from across the U.S. as well as several specialty rices were obtained for analysis. Most were cultivars that had been released from public breeding programs located in Arkansas, California, Louisiana, Mississippi and Texas. DNA markers that mapped to each of the twelve chromosomes in the rice genome were evaluated for their ability to distinguish cultivars. Several of these markers are located near genes that are important to many U.S. rice breeding programs and include Sd1 on chromosome 1, Pi-b on chromosome 2, Waxy on chromosome 6, and Pi-k on chromosome 11. DNA was extracted from leaf tissue from each of the cultivars using standard methods. PCR analysis was performed using a capillary electrophoresis genetic analyzer.

Although we did not use enough markers to clearly fingerprint all cultivars, our results indicate that a relatively small set of molecular markers can be used to distinguish most common U.S. rice cultivars that are commercially grown. These markers can be used to verify the identity of seedlots, production fields, and rice samples and can be performed using leaf tissue or rough, brown, or milled forms of rice grain. A summary of the cultivars use and their distinguishing molecular markers is presented in the chart.

Development of DNA markers

Last Modified: 2/23/2005
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