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? Why 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. Over 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 unstable 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, agricultural systems with greater farm-gate value (e.g., organic), and alternative crops will help sustain agriculture in these areas. In addition, some agricultural practices have been associated with the production of greenhouse gases and global warming. 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 an agricultural economy while benefiting 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 efficient breeding methods will allow cultivars to be developed more quickly to meet the changing demands of the marketplace. 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 strong rice industry that can continue to provide consumers with high quality food products that are inexpensive and suitable for 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 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 by year the currently approved milestones (indicators of research progress)
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. 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. 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. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders.

Year 3 (2006) Register Lemont/TeQing rice mapping population and microsatellite data. (Delayed from FY2005) Determine if there is a yield penalty associated with the presence of major blast resistance genes when disease is not present. (Delayed from FY2005) Determine performance of rice cultivars under organic and conventional production systems. (Delayed from FY2005) 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. 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.List the single most significant research accomplishment during FY 2006.
Genetic markers for rice disease resistance. As a result of the RiceCAP grant funded by USDA CSREES National Research Initiative, ARS and Texas A&M University scientists at Beaumont, TX, identified DNA markers associated with resistance to sheath blight disease in rice. Sheath blight is a fungal disease of rice that causes significant losses in yield and quality; however, there are very few sources of genetic resistance that are adapted to production in the U.S. Five gene regions controlling sheath blight resistance were identified in a segregating cross of US germplasm, and two of these regions may contain true resistance genes, independent of plant height and maturity. Development of molecular markers associated with disease resistance genes will facilitate the development of new rice cultivars that are less susceptible to economic losses due to disease and will reduce the need for costly fungicide applications. This research supports NP 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.

4b.List other significant research accomplishment(s), if any.
Utilizing natural genetic diversity to improve rice. ARS scientists at Beaumont, TX, identified genomic variation associated with starch synthesis genes in a set of some 1700 world germplasm cultivars collected from over 100 countries. Amylose content and grain gelatinization temperature are the product of starch synthesis genes and are two of the most important rice end-use quality parameters that determine market class and consumer preference. Two major sequence mutations in the granule bound starch synthase enzyme corresponded with approximately 90% of the variation found in amylose content. Two mutations in the soluble starch synthase enzyme were associated with about 83% of the variation in rice grain gelatinization temperature. DNA markers that are associated with these natural mutations will be useful to select for these important rice end-use quality traits in rice cultivar development programs. This research supports NP Objective 1.2.7 Identify genes responsible for plant product quality and resistance to disease, pests, and weather losses.

5.Describe the major accomplishments to date and their predicted or actual impact.
The research goals and accomplishments of this project address National Program 301 research component Genomic Characterization and Genetic Improvement. During the life of this project, four new rice cultivars have been developed, germplasm accessions in the National Germplasm Collection have been characterized for genetic markers associated with disease resistance and grain quality traits, and improved methods have been developed for evaluating grain fissuring, lipid content, and phytochemicals in rice. Genomic regions have been identified that are associated with resistance to blast, panicle blight, and sheath blight diseases, mesocotyl elongation that improves seedling vigor, photoperiodism, starch synthesis genes, and grain milling quality. These accomplishments have resulted in new germplasm, cultivars, and improved methods for developing cultivars that will help sustain the US rice industry.

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?
Genetic markers have been transferred to geneticists and breeders to facilitate understanding the genetic control and inheritance of traits in rice. Germplasm has been developed and characterized for traits and genetic markers that will facilitate use of genetic resources for crop improvement by scientists. New methods for evaluation of grain quality traits have been developed and transferred to scientists to improve the nutritional and functional quality of rice. New rice cultivars have been developed and released to farmers that will help meet the needs of conventional and specialty markets for the rice industry.

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).
Bergman, C.J., Chen, M.-H., Goffman, F.D. 2006. Whole grain rice and health benefits. Texas Rice, Highlighting Research in 2006. p. XII-XIII.

Chen, M.-H., Fjellstrom, R.G., Pinson, S.R., McClung, A.M., Bergman, C.J. 2006. Rice functionality, starch structure and the genes. Texas Rice, Highlighting Research in 2006. p. XII.

Fjellstrom, R.G., Pinson, S.R., Kepiro, J.L., McClung, A.M., Sharman, A., Tabien, R.E., Shank, A.R. 2006. Sheath blight resistance in southern rice. Texas Rice, Highlighting Research in 2006. p. VIII.

Kepiro, J.L., Fjellstrom, R.G., McClung, A.M. 2006. Studying the inheritance of high milling yield in Cypress. Texas Rice, Highlighting Research in 2006. p. VII-IX.

Pinson, S.R., Fjellstrom, R.G., Shank, A.R., Oard, J., Groth, D., Jia, Y., Jia, M. 2006. Incorporating foreign sheath blight resistance genes into US rice germplasm. Texas Rice, Highlighting Research in 2006. p. VI-VII.

Review Publications
Pinson, S.R., Hulbert, S., Liu, K., Nelson, J.C. 2005. Correlation between QTLs conferring resistance to four different diseases with each other and with RGAs identifies key regions for future research [abstract]. 5th International Rice Genetics Symposium, Manila, Philippines. p. 95.