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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
2010 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) that is conducted in 5 southern states. ARS evaluated these materials for critical grain quality traits, response to inoculation with the rice blast and sheath blight pathogens, and genetic markers that are linked with grain quality traits and major blast resistance genes. Data from 2009 were presented at the southern US rice breeders meeting in the Spring. In 2010, ARS entered 12 breeding lines as part of the URRN trial. Another 60 entries that targeted for aromatics market and for reduced water use were evaluated in preliminary yield trials. Purified seed and comprehensive agronomic data for documenting the release of a potential new cultivar to be named Charleston Gold were also accomplished. The program experienced some slow-downs due to a pest problem in the greenhouse that required a redirection of labor for quarantine management of the greenhouses throughout the year.


4.Accomplishments
1. Effects of cooking on brown rice health-beneficial compounds. Brown, unmilled rice contains fat-soluble and non-fat-soluble antioxidants that have potential health benefits. Because rice is consumed after cooking it is important to determine the effect of heating on the levels of these antioxidants. ARS scientists at Beaumont, Texas, subjected rice varieties that have different colors of bran to steam- and pressure-cooking methods. The results demonstrated that the fat-soluble antioxidants, like Vitamin E, were heat stable, whereas in the non-fat soluble group there was a more variable response depending on the specific compound, bran color, and cooking method used. This information will be useful to breeders who endeavor to enhance health-beneficial components in new rice cultivars and to the food industry interested in using rice/rice bran to develop nutritionally enhanced foods.

2. Can rice be considered a healthy starch for consumers? The incidence of diabetes has dramatically increased in recent years in this country. Starchy foods, like rice, are not recommended for people managing diabetes. ARS scientists at New Orleans, Louisiana, and Beaumont, Texas, evaluated 16 commercial rice cultivars and found that they differed in starch digestibility. Some cultivars were found that had high levels of resistant and slowly digestible starch, indicating that when consumed, the sugars would be slowly released into the bloodstream, as compared to other rice cultivars. This is important to consumers interested in moderating sugar in their diet. This study demonstrated that rice cultivars differ in the amount of nutritionally important starch fractions and offers the opportunity for developing new cultivars with improved dietary benefits.

3. Enhancing the health-beneficial properties of whole-grain brown rice through breeding. Consumption of whole grains is associated with a reduced likelihood of developing some diet-related diseases. Whole-grain brown rice offers consumers superior nutritional value compared with white milled rice. A mutant, developed from the US rice cultivar 'Drew' was found to have an enlarged embryo, a component of the grain that is a natural source of vitamins and oil. ARS scientists at Beaumont, Texas, and Stuttgart, Arkansas, in collaboration with a scientist at the University of Nevada, Las Vegas, determined that the giant-embryo mutant has higher levels of several phytochemical compounds with proposed health benefits as compared with other rice cultivars. This demonstrates the value of using mutation breeding techniques to improve the nutritional quality of rice. Breeders can use this genetic resource to develop new rice cultivars that have enhanced nutritional and economic value.

4. Genetic markers are linked to nutritional components in the rice grain. Little is known about the genes that control the production of compounds in the rice grain that are associated with health-beneficial properties. ARS scientists at Beaumont, Texas, in collaboration with scientists at Colorado State University, used genetic markers to investigate the nutritional compounds found in ten diverse rice varieties and demonstrated that the levels of these compounds were linked to rice subspecies classification and genetic markers. These results indicate that certain subspecies and genetic markers may guide rice improvement strategies for human health.


Review Publications
Patindol, J.A., Guraya, H.S., Champagne, E.T., Chen, M., Mcclung, A.M. 2010. Relationship of cooked rice nutritionally-important starch fractions with other physicochemical properties. Starch/Starke. 62:246-256.

Patindol, J.A., Guraya, H.S., Champagne, E.T., Mcclung, A.M. 2010. Nutritionally-important starch fractions of rice cultivars grown in southern United States. Journal of Food Science. 75:H137-H144.

Yan, W., McClung, A.M. 2010. 'Rondo', a long-grain indica rice with resistances to multiple diseases. Journal of Plant Registrations. 4:131-136.

Last Modified: 10/20/2014
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