1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter?
Rice is one of the world's most important grain crops and is the staple food for about half of the world. Over 3 million acres of rice are produced in the U.S., serving a domestic market that has doubled over the last 15 years and an important, but declining, export market. Eighty percent of the U.S. acreage is located in the south central region where rice producers are frequently challenged with economic losses due to diseases, weeds, insects, and physiological stress. Production costs for rice are particularly high due to expenses associated with controlling crop pests, the specialized equipment needed for rice production, and the crop's extensive water use. Although U.S. yields have been at record levels for the last several years, rice producers struggle to remain competitive because of declining world market prices, increasing production costs, and loss of export markets. There is a need to differentiate U.S. rice from being a generic commodity to a high value crop. Research that allows U.S. rice producers to reduce economic losses, increase productivity, and have a positive impact on the environment will help maintain a sound rice industry that provides consumers with a safe, inexpensive, high quality, and healthy food. Research that strengthens the U.S. rice industry helps to preserve national food security, supports the agricultural sector of a diversified economy, and is important for sustaining international trade.

Many agricultural areas are competing for natural resources with expanding urban and industrial areas, and there are growing concerns to maintain and enhance environmental quality. Developing resource-saving rice production methods, systems with greater farm-gate value (e.g., organic), or alternative crops will help sustain agriculture in these areas. In addition, global warming has been associated with the production of greenhouse gases, which are a result of some agricultural practices as well as industrialization and burning of fossil fuels. Development of improved cropping systems that conserve natural resources while mitigating the negative effects of greenhouse gases through increased sequestration of carbon dioxide and nitrous oxide will help to maintain a vibrant diversified economy and benefit the environment.

The objective of this research program is to develop improved rice germplasm that will benefit southern rice producers and the U.S. rice industry through research in breeding, genetics, biotechnology, pathology, and cereal chemistry. An understanding of the genetic control of traits and the development of more efficient selection methods for breeders will allow cultivars to be developed more quickly to meet the changing demands of the marketplace. The development of molecular markers that are physically linked to genes controlling economically important traits is an example of technology that is being used to benefit the U.S. rice industry. Understanding the genetic control of yield, milling quality, processing and sensory traits, tolerance to biotic and abiotic stresses, and health-beneficial components of the rice grain will help farmers, millers, and processors of the U.S. rice industry remain competitive in the global marketplace. The application of new knowledge in rice genetics will result in more efficient selection procedures that will help U.S. rice breeders in the development of improved cultivars. The study of alternative cropping systems will result in better use of natural resources (plants, soil, water), more efficient crop production, and a reduction in the negative effects of greenhouse gases through increased sequestration of carbon and nitrogen from the atmosphere. These factors coupled together will help sustain agriculture and will maintain a healthy rice industry that can continue to provide consumers with high quality food products that are inexpensive and suitable components of a healthy diet.

Specific goals of this research project are:.
1)develop genetic markers associated with economically important traits in U.S. rice germplasm;.
2)develop improved rice cultivars and germplasm along with more accurate methods for trait characterization; and.
3)identify and evaluate alternatives to conventional rice cropping systems that are economically viable and enhance the environment.

Goals of this research project pertain to the Genome Characterization and Genetic Improvement sub-component of National Program 301 - Plant, Microbial, and Insect Genetic Resources, Genomics and Genetic Improvement, and to the Cropping System and Tillage sub-component of the Carbon Cycle and Carbon Storage section of National Program 204 - Global Change. Specific national program objectives that are addressed through this research include: Objective 1.2.7 Identify genes responsible for plant product quality and resistance to disease, pests, and weather losses; Objective 1.2.8 Maintain, characterize, and use genetic resources to optimize, safeguard, and enhance genetic diversity and promote viable and vigorous plant production systems; Objective 3.2.4 Develop and release to potential users varieties and/or germplasm of agriculturally important plants that are new or provide significantly improved (either through traditional breeding or biotechnology) characteristics enhancing pest or disease resistance; and Objective 5.2.3 Develop approaches that mitigate the impact of poor air quality on crop production and provide scientific information and technology to maintain or enhance crop and animal production while controlling emissions that reduce air quality or destroy the ozone layer.

2.List the milestones (indicators of progress) from your Project Plan.
Year 1 (2004) Identify DNA markers associated with the Pi-k "Leah" blast resistance gene useful for U.S. breeding efforts. Register new rice cultivars for specialty markets. Identify DNA markers associated with alkali spreading value and amylose content in diverse germplasm and crosses. Determine genetic variability for fatty acid profiles, lipid content, phenolics, and hydrolytic stability in diverse cultivars. Identify DNA markers associated with photoperiodism in a wide cross. Develop an improved screening method for measuring field fissuring using cultivars. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

Year 2 (2005) Register new rice cultivars for specialty markets. Register Lemont/Teqing rice mapping population and microsatellite data. Determine if there is a yield penalty associated with the presence of major blast resistance genes when disease is not present. Determine genetic variability for tocols and gamma oryzanols in diverse cultivars. Develop an improved method for determining surface lipid content in milled rice as a measure of degree of milling. Determine performance of rice cultivars under organic and conventional production systems. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

Year 3 (2006) Identify DNA markers associated with the Pi-i blast resistance. Verify the impact of TeQing introgressions in Lemont background on mesocotyl elongation. Identify early tillering QTL and their association with seedling vigor. Identify DNA markers associated with novel resistance gene for blast race IB49. Identify DNA markers associated with sheath blight resistance in a narrow U.S. cross. Verify the importance of previously mapped QTL for sheath blight resistance in new genetic population. Identify genomic variation associated with starch synthesis genes in diverse cultivars. Identify QTL associated with grain shape, milling yield, and grain chalk in a wide cross. Determine method for evaluation of bran thickness and its association with grain fissuring in several cultivars. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

Year 4 (2007) Identify DNA markers associated with partial resistance to blast. Verify the impact of TeQing introgressions in Lemont background on sheath blight resistance. Identify DNA markers associated with milling yield in a segregating long-grain crosses. Develop an improved method for quantifying amylose and amylopectin contents using HPLC. Develop an improved method for determining molecular size and structure in rice starch. Determine the impact on quality of rice produced under organic and conventional systems. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

Year 5 (2008) Develop molecular markers and fine maps for early tillering genes and mesocotyl elongation genes using crosses among selected introgression lines. Develop an improved method for field screening of germplasm for tolerance to reduced water usage. Develop a mapping population for tolerance to reduced water usage. Develop knowledge on the physiological factors controlling early tiller initiation and elongation. Compare the impact of organic and conventional production on soil microbes and organic matter. Compare the impact of rotational crops on weed control in rice. Compare U.S. cultivars for growth rates and yield under reduced water usage. Compare field performance of cultivars under conventional and reduced water usage. Compare methane emissions from rice grown under organic and conventional systems. Compare C/N sequestration of different rotational crops and rice. Compare methane emissions from rice grown under reduced water usage and conventional management. Compare methane emissions of conventional rice production and minimum tillage methods. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

4a.What was the single most significant accomplishment this past year?
Development of Genetic Markers for a Broad Spectrum Disease Resistance Gene in Rice: The ARS Rice Research Unit in Beaumont, TX, developed DNA markers that are associated with the Pi-z blast resistance in rice. Blast is a fungal disease of rice that can cause significant crop losses for rice farmers worldwide. It usually takes breeders several years of testing to confirm the presence of a blast resistance gene in potential new cultivars. The Pi-z gene conveys resistance to several races of blast that occur in the US. Use of DNA markers associated with this gene will improve the speed and efficiency of development of new rice cultivars having improved disease resistance and will help reduce the need for fungicide applications.

4b.List other significant accomplishments, if any.
Identification of Natural Genetic Variation for Phytochemicals in Rice: The ARS Rice Research Unit in Beaumont, TX, identified high levels of tocopherols, tocotrienols, and gamma-oryzanol phytochemicals in over 170 accessions of US and international rice. These phytonutrients are found in rice bran and potentially have positive effects on human health. Identification of high concentrations of these compounds increases the value of the rice crop and provides new opportunities for development of rice-based functional foods. These results demonstrate the feasibility of developing new rice cultivars having improved levels of phytochemicals.

Development of an Improved Method for Assessing Degree of Milling: During the rice milling process, bran components and lipids are removed from the grain in order avoid problems with rancidity and off-color during grain storage. Having an efficient method for determining the amount of bran and lipids that are removed from the grain will facilitate research on quantifying phytochemicals and oil in the rice bran that may enhance crop value. The ARS Rice Research Unit in Beaumont, TX, has developed a gas chromatographic procedure for quantifying surface lipids that is highly correlated with results from the standard Goldfisch method but is more reproducible and requires less time. This improved method can be used to evaluate large numbers of rice germplasm lines to identify those that possess high concentrations of oil or phytochemicals that would be useful in rice breeding programs.

Understanding Rice Cooking Properties Using Starch Structure Analysis: Limitations in analytical methods for quantifying components of rice starch make it difficult to determine how variation in starch components impacts rice cooking and processing quality. The ARS Rice Research Unit in Beaumont, TX, has developed new methods using size-exclusion chromatography coupled with multiple angle laser light scattering and differential refractive index detection that can be used to correlate differences in starch composition with rice functional properties. This information will be used in functional genomics studies to determine how genetic variation in starch synthesis genes is related to differences in rice cooking and processing quality.

Development of Three Rice Cultivars for the Southern US: The ARS Rice Research Unit in Beaumont, TX, has developed a new long grain cultivar, Presidio, and two specialty cultivars, Sabine and Carolina Gold Select, for production in the southern US. Development of new rice cultivars that have improved agronomic performance and unique cooking and processing qualities helps farmers to remain competitive and sustains agriculture in the US. Presidio has high milling quality and superior ratoon crop potential which improves crop value for farmers. Sabine rice has improved yield potential is particularly suited for use in parboiled and canned rice products. Carolina Gold Select rice was developed for a specialty cuisine market on the east coast. These rice cultivars will help US farmers provide high quality products for various segments of the US rice industry.

4c.List any significant activities that support special target populations.
None

5.Describe the major accomplishments over the life of the project, including their predicted or actual impact.
Research accomplished in this project addresses ARS Strategic Plan Goal 1. Enhance economic opportunities for agricultural producers and specific objective 1.2 Contribute to the efficiency of agricultural production systems. The project's research objective: Develop improved rice cultivars and germplasm and methods for phenotypic characterization addresses performance measure 1.2.5: Provide producers with scientific information and technology that increase production efficiency, safeguard the environment, and reduce production risks and product losses. During the life of this project four new rice cultivars have been developed, germplasm accessions in the National Germplasm Collection have been characterized for various grain quality traits, and improved methods have been developed for evaluating grain fissuring, lipid content, and phtyochemicals in rice. This project's research objective: Develop genetic markers associated with economically important traits in U.S. rice germplasm addresses national performance measure 1.2.7: Identify genes responsible for plant product quality and resistance to disease, pests, and weather losses. During the life of this project, accomplishments have been made towards this objective by the development of DNA markers that are associated with two genes for resistance to blast disease as well as with chromosomal locations controlling photoperiodism, grain amylose content, grain alkali spreading value, and resistance to panicle blight disease. These research goals and accomplishments are part of National Program 301: Plant, Microbial, and Insect Genetic Resources, Genomics, and Genetic Improvement.

6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products?
Talks and poster presentations were made at the 2005 annual rice field days that were conducted at Beaumont and Eagle Lake, TX. Over 600 members of the U.S. rice industry (farmers, millers, processors) attended these meetings and heard updates on ARS research in variety development, identification of genetic markers for economically important traits, the association of gene sequence with cooking quality and disease resistance, and the use of DNA markers to augment U.S. rice breeding efforts. In addition, four rice cultivars have been developed and released for production by southern US rice farmers.

7.List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below).
McClung, A.M. 2005. New release of 'Sabine' rice for the processing industry. Rice Production Update. p. 1.

Pinson, S.R. 2005. Putting sheath blight resistance genes to work in the rice field. Texas Rice, Highlighting Research in 2005. pp. VIII-IX.

McClung, A.M., Fjellstrom, R.G. 2005. Digging for gold. Texas Rice, Highlighting Research in 2005. p. IX. Fjellstrom, R.G. 2005. Molecular markers in rice breeding. Texas Rice, Highlighting Research in 2005. p. IX.

McClung, A.M., Chen, M., Bockelman, H.E., Bryant, R.J., Yan, W., Fjellstrom, R.G. 2005. Genetic markers reveal novel genes which control rice cooking quality. Texas Rice, Highlighting Research in 2005. p. X-XI.

Chen, M., McClung, A.M., Fjellstrom, R.G. 2005. A new tool for selection of cooked rice texture. Texas Rice, Highlighting Research in 2005. p. XIV.

McClung, A.M. 2005. Presidio rice - a new long grain rice with improved ratoon crop potential and milling yield. Texas Rice, Highlighting Research in 2005. p. XI.

Review Publications
Kepiro, J.L., Fjellstrom, R.G., McClung, A.M. 2005. QTL mapping of milling yield in southern U.S. rice with amplified fragment length polymorphism (AFLP) and micro-satellite (SSR) markers. Plant and Animal Genome Conference Proceedings. p. 146.