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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS
2009 Annual Report


1a.Objectives (from AD-416)
Objective 1: Phenotypically and genotypically characterize the rice National Small Grains Germplasm Collection (NSGC) and conserve genetic stocks, mutants, and mapping populations in the Genetic Stocks Oryza (GSOR) to promote greater use by the research community. Sub-objective 1.A. Characterize accessions in the NSGC rice collection for 27 descriptors and rejuvenate seed of low inventory genetic seedstocks. Sub-objective 1.B. Perform structure analysis following genotypic and phenotypic evaluation of the NSGC Core collection. Sub-objective 1.C. Expand the GSOR collection to 15,000 accessions and establish a web-based ordering and distribution system. Objective 2: Evaluate rice germplasm to identify genetic resources having enhanced nutritional properties and added-value for the food industry. Sub-objective 2.A. Identify genetic variability for antioxidant capacity and the content of main classes of polyphenols and carotenoids in rice germplasm. Sub-objective 2.B. Structurally identify and quantify major flavonoid and proanthocyanidin compounds in rice genotypes with different bran color. Sub-objective 2.C. Determine the effect of processing on rice bran phytochemicals. Sub-objective 2.D. Identify quantitative trait loci (QTL) associated with rice grain elemental content. Sub-objective 2.E. Measure genotype and environment interactions on starch structure and grain quality. Sub-objective 2.F. Determine the impact of non-conventional cultural management practices on rice grain quality. Objective 3: Map new resistance genes for blast disease and straighthead disease identified in germplasm accessions. Sub-objective 3.A. Mine novel blast resistance genes from indica rice germplasm for use in U.S. breeding programs. Sub-objective 3.B. Decipher genetic mechanism for resistance to straighthead, a physiological disease. Objective 4: Map genes associated with grain quality traits, including rice paste viscosity and grain chalk. Sub-objective 4.A. Genetically map starch paste viscosity variation as a predictor of rice processing quality. Sub-objective 4.B. Genetically map grain chalk formation which influences milling quality.


1b.Approach (from AD-416)
Additional germplasm and data will be added to the NSGC rice collection for distribution to the public via GRIN. The Core collection will be characterized for sheath blight disease resistance, grain mineral accumulation, straighthead tolerance, protein content, and cold tolerance, and genetic markers will be identified that are associated with these traits. The Genetics Stocks Oryza (GSOR) collection will be expanded to 15,000 accessions that are curated and distributed to the research community through a searchable on-line database. Selected accessions from the NSGC collection will be evaluated for health- beneficial compounds like polyphenols, flavonoids, and carotenoids, and the influence of the environment and processing methods on levels of these compounds will be evaluated. Germplasm will be evaluated under flooded and aerobic conditions to understand the genetic mechanisms controlling nutrient uptake. Mapping populations will be developed,and rice gene microarray chips will be used to identify chromosomal regions associated with nutrient uptake. The genotype x environment interaction on key enzymes in the starch pathway will be studied to determine how they impact starch structure and processing quality. In an effort to understand how rice quality will be impacted by crop rotation systems, 5 to 10 rice cultivars will be grown using conventional tillage/no-till, permanent flood/intermittent-flushing, different fertilization rates, and different crop rotations, and agronomic and cooking quality traits will be evaluated to provide insight as to how changing cropping systems will impact rice milling and cooking quality. Novel genes for blast and straighthead disease resistance will be identified using mapping populations. Markers and germplasm will be released to breeders for developing improved cultivars. Sequence variation around a SNP in exon 10 of the rice Waxy gene will be evaluated to determine what impact it has on RVA paste viscosity characteristics. Genetic markers will be developed that can be used in breeding for elevated pasting profiles, which is desired for rice used in canning, instantizing, and other food preparation processes. We will fine map several QTL previously identified to be associated with grain chalk. Progeny from the selected recombinant lines will be grown in two environments and chalk amounts quantified with a Winseedle Image analysis system. Segregation of tightly linked SSR and SNP markers will be analyzed to pinpoint recombination points and candidate genes in the finely mapped region. Genetic markers developed from this research will be used by breeders to develop new cultivars that have greater translucency, higher milling yield, and consistent cooking quality.


3.Progress Report
Each year rice breeders from the southern US evaluate 200 potential new cultivars as part of the Uniform Rice Regional Nursery (URRN). ARS evaluated these materials for critical grain quality traits, response to inoculation with the rice blast pathogen, response to inoculation with the sheath blight pathogen, and genetic markers associated with grain quality traits and major blast resistance genes. Data from 2008 were presented at the southern US rice breeders meeting prior to planting in 2009. In 2009, ARS entered 18 new breeding lines as part of the URRN trial that is conducted in 5 states. Yield tests were completed that evaluated over 60 breeding lines that were derived from a cross between the cultivar Jefferson and the wild weedy relative O. rufipogon. Results from these tests, along with data from 2007, demonstrated that genes from the weedy species resulted in a 20% increase in grain yield. Two of the best lines from this project have been entered into the 2009 URRN trial. Plans were made and a study implemented in 2009 to evaluate the mini-core for biomass production and yield components that is being conducted in Arkansas and Texas. A collaboration was established with the Southern Regional Research Center (SRRC), New Orleans, LA, to evaluate aromatic cultivars from different sources to determine if a sensory panel can detect different flavors. Another collaborative study was initiated with SRRC to determine if rice cultivars with different bran colors differ in flavor. Some 120 commercially released rice cultivars were fingerprinted with 15 microsatellite markers that are spread across the 12 rice chromosomes. This information can be used by breeders, geneticists, and foundation seed programs as a means of quality control to verify a cultivar's identity and seed purity.


4.Accomplishments
1. Pigmented rice bran has phytochemicals with an antioxidant capacity that may have health benefits: Comprehensive information regarding phytochemical profiles in rice having different bran colors is lacking. ARS scientists in Beaumont, Texas, determined the concentrations of phytochemicals, including vitamin E compounds as well as phenolics, flavonoids, anthocyanins, and proanthocyanins, in the bran of white, light brown, brown, purple, and red color rice cultivars. Phytochemicals are antioxidants that may account for health-beneficial properties associated with eating whole grain brown rice. High antioxidant activity was found in some purple and red bran cultivars. In addition, rice bran was found to be an effective natural oxidation inhibitor when used as an ingredient in foods. Thus, rice bran has the potential to be used directly as a functional food and as an ingredient. The information will be useful to the rice breeders for enhancing rice health-beneficial components and to the food industry interested in utilizing rice bran or whole grain as functional food.

2. New method for selecting improved milling quality in rice: Rice milling quality is a complex trait difficult to select for in breeding programs. Scientists at the Rice Research Unit in Beaumont, Texas; Dale Bumpers National Rice Research Center in Stuttgart, Arkansas; and University of Arkansas, at Stuttgart, Arkansas, documented a new method for resistance to rice kernel fissuring using a laboratory technique that requires only a small amount of seed. Seed of genetic lines segregating for milling quality were exposed to controlled levels of humidity. Rice lines that were selected to be resistant or susceptible to fissuring were found to maintain their fissuring rating in subsequent generations. This new laboratory method will help geneticists to map fissure resistance genes and breeders to eliminate fissuring-susceptible offspring early in the breeding process so that they can focus on resistant progeny for further trait selection.

3. Addressing the dilemmas of measuring amylose content in rice grain: Amylose is a component of rice starch that determines cooking, processing, and eating quality. As part of the International Network for Quality Rice an ARS scientist at the Rice Research Unit in Beaumont, Texas, has joined 27 rice cereal quality laboratories from around the world to develop an improved and consistent method for measuring grain amylose content. Amylose is usually quantified measuring the iodine binding capacity. Survey results demonstrated that repeatability of this method was high within laboratories, but the reproducibility between laboratories was low. The major sources of the variability were identified to be associated with the methods used in calibration. This study highlights the need to standardize the way amylose is measured and presents research opportunities for doing so.

4. Genetic mapping of texture properties in high amylose US rice: High amylose rice varieties fill an important market class in the US rice industry, but their texture (grain firmness and paste viscosity) properties can vary considerably. Scientists at the USDA-ARS Rice Research Unit in Beaumont, Texas, and the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, have identified and mapped genetic markers indicating the presence of specific genes controlling rice texture characteristics. Results showed that the largest changes of rice texture differences are regulated by a single gene that makes a starch synthesis enzyme in developing rice grains. DNA markers for this gene can be used in marker-assisted breeding to develop improved rice varieties with the textural attributes needed for superior processing quality markets.

5. Extracts from purple rice bran can be used as a food ingredient to prevent spoilage: ARS scientist in Beaumont, Texas, in collaboration with scientists at the Harry K. Dupree National Aquaculture Research Center, in Stuttgart, Arkansas, evaluated the effectiveness of purple rice bran extracts as natural antioxidants for meat products. Lipid oxidation is a major cause of quality deterioration in meat products during storage, rendering them undesirable for human consumption. Purple rice bran has been found to have high antioxidant capacity due to high concentrations of anthocyanin, vitamin E, and gamma-oryzanols. Minced catfish belly flap meat, which has a high lipid content and short shelf life, was treated with purple rice bran extract, and its lipid oxidation, color, and textural properties were monitored during 12 days of storage at 4C. The results demonstrated that purple rice bran extract was effective in retarding lipid oxidation and preserving texture compared with the control and was as effective as using synthetic antioxidants and rosemary extract, a popular natural antioxidant extract used in food applications. This research demonstrates that rice cultivars having colored rice bran may have added nutritional and functional value.

6. Development of improved genetic markers for selecting for rice cooking quality: Although a microsatellite DNA marker is available to breeders for selecting for amylose content and rice cooking quality, it is not adequate for discerning some pasting properties. ARS scientists in Beaumont, Texas, have developed an efficient method to evaluate three genetic markers using SNPs (single nucleotide polymorphisms) that characterize rice cultivars for amylose content and starch pasting properties, factors that determine cooked rice texture. SNP markers are easier to interpret than microsatellite markers. The simplicity of these assays makes it easy to utilize these markers as part of a marker-assisted selection strategy in rice breeding programs selecting for these important grain quality traits.


6.Technology Transfer

Number of the New/Active MTAs (providing only)1
Number of New Germplasm Releases1

Review Publications
Tabien, R.E., Samonte, O.B., McClung, A.M. 2008. Forty eight years of rice improvement in Texas since the release of cultivar Bluebonnet in 1944. Crop Science. 48:2097-2106.

Agrama, H.A., Yan, W., Lee, F.N., Fjellstrom, R.G., Chen, M., Jia, M.H., McClung, A.M. 2009. Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Science. 49:1336-1346.

Chen, M., Bergman, C.J., Pinson, S.R., Fjellstrom, R.G. 2008. Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection. Journal of Cereal Science. 48:781-788.

Min, B., Chen, M., Green, B.W. 2009. Antioxidant activities of purple rice bran extract and its effect on the quality of low NaCl, phosphate-free patties made from channel catfish (Ictalurus punctatus) belly flap meat. Journal of Food Science. 74(3):C268-C277.

Bryant, R.J., Anders, M.M., McClung, A.M. 2009. Effect of cultural management practices on the grain quality of two rice cultivars. Cereal Chemistry. 86(4):405-409.

Fitzgerald, M.A., Bergman, C.J., Ressurreccion, A.P., Moller, J., Jimenez, R., Reinke, R.F., Martin, M., Blanco, P., Molina, F., Chen, M., Kuri, V., Romero, M.V., Habibi, F., Umemoto, T., Jongdee, S., Graterol, E., Reddy, K.R., Bassinello, P.Z., Sivakami, R., Rani, N.S., Das, S., Wang, Y., Indrassi, S.D., Ramli, A., Rauf, A., Dipti, S.S., Xie, L., Lang, N.T., Singh, P., Toro, D.C., Tavasoli, F. 2009. Addressing the dilemmas of measuring amylose in rice. Cereal Chemistry. 86(5):492-498.

Last Modified: 7/25/2014
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