APPLICATION OF RICE GENOMICS TO DEVELOP SUSTAINABLE CROPPING SYSTEMS FOR THE GULF COAST
Title: RICE IDENTITY TESTING USING DNA MARKER ANALYSIS OF PROCESSEDOR ARCHIVED RICE TISSUE AND RICE-INGREDIENT FOODS
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2005
Publication Date: February 15, 2006
Citation: Fjellstrom, R.G., McClung, A.M. 2006. Rice identity testing using DNA marker analysis of processed or archived rice tissue and rice-ingredient foods. Rice Technical Working Group Meeting Proceedings, February 29-March 1, 2006, Houston, Texas. 2006 CDROM.
The highly regarded reputation of USA rice in the world marketplace rice has been achieved by delivering rice and rice products that meet rigorous standards of uniformity and quality. In this regard, seed dealers, farmers, millers, and processors are concerned that the rice seed they are handling is correctly identified and true to type. Since the composition of food products is also of significant importance to consumers and the food industry, the detection of unexpected genes or unwanted transgenes in rice products can be critical as well. DNA markers analyzed with the polymerase chain reaction (PCR) provide an effective analytical means to assay the identity and uniformity of rice products and a useful way to detect the presence of undesired genes in rice products. Since no single DNA marker can correctly identify a cultivar, we have devised a panel of 12 simple sequence repeat (SSR) DNA markers that can successfully ‘fingerprint’ most, if not all, USA rice cultivars. Initially, these fingerprinting markers were successfully utilized using DNA extracted from grain or fresh leaf tissue, which are common sources of tissue from seed dealers and farmers, who can frequently inquire about cultivar identity and purity. As post-harvest rice industry members increasingly request the identification of possible cultivars making up rice products found in the global marketplace, we wanted to find out how well these markers perform with DNA extracted from an assortment of rice products. Six fingerprinting markers were tested on DNA from a wide variety of rice tissues and rice-containing foods, which included: milled, parboiled, instantized, crisped, and puffed rice; rice flour, bread, milk, ‘cakes’, noodles, and vinegar; rice as an ingredient in soup (testing both grains and broth), baby food, beer, chocolate candy bars, and ready-to-eat pudding; cooked rice in frozen food meals; rice seed stored for 10 to 50 years; as well as recent to 78 year old herbarium leaf samples, hulls, pollen, and archaeological remains. A majority of the products tested were comprised of rice from known cultivars in order to test marker accuracy. Also tested were known mixtures of whole grain or flour in order to test sensitivity of detecting mixtures of rice products using markers.
In most cases, standard DNA extraction techniques and PCR conditions produced results for all the SSR markers tested from the various DNA sources. In some cases where DNA was isolated from highly processed (e.g., parboiled rice) or aged samples (e.g., >200 year old excavated single-seed samples), whole genome amplification techniques were used prior to PCR in order to obtain marker results. DNA marker fingerprint results routinely matched those expected from the specific cultivar-sourced materials. DNA marker mixtures were repeatedly detected when as little as a 1:49 mixture ratio was present in the tested samples. Our results show that: DNA markers can be accurately obtained from a surprisingly wide variety of rice tissues and foods containing rice; whole genome amplification techniques can be used to successfully obtain marker information with DNA isolated from highly degraded samples; and marker techniques are capable of detecting trace amounts of DNA (e.g., transgenes) that may be unexpectedly introduced into rice grain or flour. This technology is useful for identity preservation from the production field to delivery to the consumer.