Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) Develop scientific knowledge that will enhance the US rice industry and contribute to a sustainable agricultural system along the Gulf Coast using classical, quantitative, and molecular genetics along with grain chemistry, plant physiology, and systems agronomy. The development of rice cultivars will become more efficient and effective through the characterization and improvement of germplasm, new knowledge on the genetic control of economically important traits, and the development of improved phenotypic and molecular methods for identifying progeny containing desired combinations of genes. Using rice as a model system, increased knowledge of the organization of the rice genome will ultimately lead to a better understanding of the structure of more complex cereal genomes and will extend the impact of this research beyond the US rice industry and Gulf Coast region. Alternative crops and cultural management practices that enhance rice production efficiency and value will be developed that will help sustain agriculture in this region. Cropping systems that mitigate the negative effects of global warming and preserve natural resources will be identified. This research will strengthen the US rice industry, help preserve national food security, sustain international trade, and support the agricultural sector of a diversified economy. Approach (from AD-416) The development of genetic markers associated with economically important traits will provide breeders with new tools for cultivar development. This program will identify chromosomal regions that possess genes controlling grain and whole-part traits that breeders desire to improve using genetic populations adapted to US growing conditions. Improved methods will be developed to facilitate the integration of molecular maker technology into breeding programs. Ultimately, this research will lay the foundation for a greater understanding of genomic organization in other cereal grains. For rice production to remain sustainable in the US, new rice farming systems must be developed that reduce competition for water resources, increase profits to farmers through reduced input costs or increased market value, and positively impact the environment. New cultural management systems that include reduced water usage, organic management, and rotations with alternative crops will be compared with conventional rice production practices to assess the impact on natural resources and the environment. Plant genetic resources will be identified that have high biomass production and are well to temperature stress conditions and rainfall patterns of the US Gulf Coast. Combinations of plant genetic resources and cultural management practices will be identified that enhance the capture of atmospheric carbon and nitrogen in soil organic matter and in plants to help mitigate the negative environmental effects of greenhouse gases. Accomplishments Marker-assisted selection for long grain rice milling yield: Milling yield, the proportion of un-broken grains obtained after milling, can appreciably influence rice crop value. Unfortunately, high milling yield is a difficult trait to select for because it is complexly inherited and environmentally sensitive. Researchers at the Rice Research Unit in Beaumont, TX, evaluated several physical and chemical rice grain attributes in a gene mapping population to determine component traits that have the greatest effect on milling yield. Genetic markers associated with two significant milling yield component traits, grain chalkiness and greenness, were identified. In addition, we found that simply measuring the proportion of whole kernels after hulling rough rice is an efficient, cost-saving way to estimate milling yields. These markers and methods can be used by rice breeders to enhance selection and development of new cultivars with high milling rice yield. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits and Component 3: Genetic Improvement of Crops, Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties) Development of a robust genetic marker to identify popcorn-like fragrance in rice: Aromatic rice has a natural popcorn flavor and commands a premium in the marketplace. Researchers at the Rice Research Unit in Beaumont, TX, developed an easy to use genetic marker found in the recently cloned rice fragrance gene and tested it in over 2,000 aromatic and non-aromatic rice accessions and breeding lines. The marker was highly successful in identifying the presence of the fragrance gene, demonstrating that it can be used by breeders to develop improved aromatic rice varieties for this expanding high value market. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits) DNA sequence variation explains differences in starch structure that impact rice cooking quality: Rice cooking and processing quality is partially controlled by the amount of amylose in the starchy grain. Although amylose content is known to be controlled by sequence variation in the Waxy gene, the relationships between genetic variation and the contents and structures of starch sub- fractions was not understood. Scientists at the Rice Research Unit in Beaumont, TX, demonstrated that the contents of amylose and amylose sub- fractions correlated with two sequence variation sites in the Waxy gene. In addition, a third sequence alteration site in the Waxy gene was associated with rice cultivars having similar amylose contents but differing in a long-chain component of starch. These results suggest that changes in the long-chain component of starch, its structure and content, are correlated to the sequence variations observed in the Waxy gene which modify functional properties of rice. Results from this research will enable marker-assisted breeding of rice cultivars with enhanced grain quality characteristics for diverse consumer preferences and food processing applications. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits and Component 3: Genetic Improvement of Crops, Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties) The fine structure of amylopectin associated with rice gelatinization temperature: Gelatinization temperature of rice grain is one of the important end-use quality determinants for use by the food processing industry and has been demonstrated to be strongly associated with one of the starch synthesis genes, Alk. However, the relationship between genetic variation in the Alk gene and the structure of amylopectin, one of two starch polymers, and the impact on rice gelatinization temperature has not been determined. Scientists at the Rice Research Unit in Beaumont, TX, evaluated the fine structure of amylopectin using 100 genetically diverse germplasm accessions grown in two locations. The fine structures of amylopectin were strongly correlated with sequence variations in the Alk gene and the onset of starch crystal melting, but less so with the thermal energy required for melting. This indicates that changes in amylopectin structure are a result of sequence variations in the Alk gene that are functional changes. This research enables efficient marker- assisted breeding of rice cultivars having enhanced grain quality characteristics suitable for special food industry applications. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits and Component 3: Genetic Improvement of Crops, Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties) Organically produced rice has little impact on cooking, processing or sensory qualities: Consumer demand for organically produced foods is dramatically increasing but little is known about the impact of organic cultural management on cooking, sensory, or nutritional properties of rice. Researchers at the Rice Research Unit in Beaumont, TX, and at the Southern Regional Research Center in New Orleans, LA, conducted a three-year field study to evaluate differences in texture, flavor, and cooking quality of five rice varieties grown under conventional and organic management methods. Results indicated that organically produced cultivars typically had lower protein content, which increased the slickness and decreased the roughness and hardness of the cooked rice, factors considered desirable in consumer markets. In addition, little impact was seen on cooking quality indicating that industry end users could easily use organically produced rice in their processed products. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 3: Genetic Improvement of Crops, Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties) Development of a genetic tool for fine-mapping of agronomic genes in rice: Several rice gene-mapping populations are available today that are useful for identifying chromosomal regions associated with economically important traits. However, these are not well suited for fine-mapping or functional analysis of specific genes. Scientists at the Rice Research Unit in Beaumont, TX, and at the Dale Bumpers National Rice Research Center in Stuttgart, AR, have developed a fine mapping population derived from two genetically diverse rice cultivars from China and the US and have characterized it with 115 genetic markers. This research was partially funded by the USDA-CSREES-NRI RiceCAP project and will impact geneticists interested in associating DNA sequence information with traits of interest to breeders. The mapping population has already been used to verify the location and genetic effect of several chromosomal regions associated with seedling vigor, resistance to sheath blight disease, and erect plant architecture. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits and Component 3: Genetic Improvement of Crops, Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties) Technology Transfer Number of Invention Disclosures submitted: 3 Number of Non-Peer Reviewed Presentations and Proceedings: 12 Number of Newspaper Articles,Presentations for NonScience Audiences: 23
Impacts
(N/A)
Publications
- Chen, M.H., Bergman, C.J. 2007. A method to determine the content, molecular weights, and weight- and molar-based distributions of degree of polymerization of amylose and fine-structure of amylopectin. Carbohydrate Polymers 69:562-578.
- Yan, W., Rutger, J.N., Bockelman, H.E., Fjellstrom, R.G., Chen, M.H., Tai, T., McClung, A.M. 2007. Development and evaluation of a core subset of the USDA rice (Oryza sativa L.) germplasm collection. Crop Science. 47(2):869- 878.
- Jia, Y., Coarrea-Victoria, F., McClung, A.M., Zhu, L., Liu, G., Wamishe, Y. , Xie, J., Marchetti, M.A., Pinson, S.R., Rutger, J.N., Correll, J.C. 2006. Rapid determination of rice cultivar responses to the sheath blight pathogen Rhizoctonia solani using a micro-chamber screening method. Plant Disease. 91:485-489.
- Champagne, E.T., Bett Garber, K.L., Mcclung, A.M., Grimm, C.C. 2007. Effects of organic fertility management on physicochemical properties and sensory quality of diverse rice cultivars. Cereal Chemistry. 84(4):320-327.
- Samonte, S.O., Wilson, L.T., Pinson, S.R., McClung, A.M., Lales, J.S. 2006. Nitrogen utilization efficiency: Relationships with grain yield, grain protein, and yield-related traits in rice. Agronomy Journal. 98:168-176.
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Progress 10/01/04 to 09/30/05
Outputs
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. 3a List the milestones that were scheduled to be addressed in FY 2005. For each milestone, indicate the status: fully met, substantially met, or not met. If not met, why. 1. Register new rice cultivars for specialty market. Milestone Fully Met 2. Register Lemont/TeQing rice mapping population and microsatellite data. Milestone Not Met Progress slowed by resource limitation (human,fiscal,equipment, etc. 3. Determine if there is a yield penalty associated with the presence of major blast resistance genes when disease is not present. Milestone Not Met Progress slowed by resource limitation (human,fiscal,equipment, etc. 4. Determine genetic variability for tocols and gamma oryzanols in diverse cultivars. Milestone Fully Met 5. Develop an improved method for determining surface lipid content in milled rice as a measure of degree of milling. Milestone Fully Met 6. Determine performance of rice cultivars under organic and conventional roduction systems.
Milestone Substantially Met 7. Provide agronomic, quality and disease resistance characterization of the Uniform Rice Regional Nursery for breeders. Milestone Fully Met 8. Developed an improved method for quantifying amylose and amylopectin contents using HPLC, ahead of schedule. Milestone Fully Met 9. Developed an improved method or determining molecular size and structure in rice starch, ahead of schedule Milestone Fully Met 3b List the milestones that you expect to address over the next 3 years (FY 2006, 2007, and 2008). What do you expect to accomplish, year by year, over the next 3 years under each milestone? 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. Projected accomplishments from achieving these milestones include: Molecular Markers: Genetic markers will be developed that are associated with starch synthesis genes, grain shape, milling yield, grain chalk, the Pi-i blast resistance gene, resistance to a predominant race of the blast pathogen, resistance to the sheath blight pathogen, plant tillering, and seedling vigor. Germplasm Development and Characterization: Elite breeding material from
all of the southern US public rice breeding programs will be evaluated for agronomic, quality, and disease resistance characteristics, and these data will be provided to breeders to aid in their cultivar development process. The impact of incorporating genes for seedling vigor from an exotic source will be evaluated in a US cultivar. Development of Improved Methods: A new method for evaluating bran thickness will be developed that can be used to determine the impact on grain fissuring in rice cultivars. 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. (This milestone was accomplished ahead of schedule in 2005) Develop an improved method for determining molecular size and structure in rice
starch. (This milestone was accomplished ahead of schedule in 2005) 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. Projected accomplishments from achieving these milestones include: Molecular Markers: DNA markers will be developed that are associated with partial (field) resistance to blast and with milling yield. Germplasm Development and Characterization: Elite breeding material from all of the southern US public rice breeding programs will be evaluated for agronomic, quality, and disease resistance characteristics, and these data will be provided to breeders to aid in their cultivar development process. The impact of incorporating genes for sheath blight resistance from an exotic source will be evaluated in a US cultivar. It will be determined if rice produced under organic or conventional systems affects rice cooking,
nutritional, or sensory quality. Development of Improved Methods: New methods will be developed for measuring grain fissuring which impacts rice milling yield. 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. Projected accomplishments from achieving these milestones include: Molecular Markers: DNA markers will be developed that are associated with early tillering and seedling vigor, factors that influence rice yield. Germplasm Development and Characterization: Mapping population will be developed for evaluating reduced water usage; germplasm will be characterized for growth under reduced water usage, under organic production methods, and under minimum tillage methods. Elite breeding material from all of the southern US public rice breeding programs will be evaluated for agronomic, quality, and disease resistance characteristics, and these
data will be provided to breeders to aid in their cultivar development process. Development of Improved Methods: New methods for evaluating rice germplasm for reduced water usage, methane emissions, and C/N sequestration will be developed. 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. 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.
Impacts
(N/A)
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.
- McClung, A.M., Chen, M., Bockelman, H.E., Bryant, R.J., Yan, W., Fjellstrom, R.G. 2004. Characterization of a core collection of rice germplasm and elite breeding lines in the US with genetic markers associated with cooking quality. Proceedings, 2nd International Rice Functional Genomics Conference, Tucson, Arizona. p. 127.
- McClung, A.M., Shank, A.R., Marchetti, M.A., Bormans, C., Jodari, F., Johnson, C.W., Park, W.D., Fjellstrom, R.G. 2004. Marker assisted breeding for improving disease resistance in U.S. rice cultivars. Texas Plant Protection Conference. p. 27.
- Pinson, S.R., Li, Z., Tabien, R.E., Tai, T.H., Redus, M., Fjellstrom, R.G. 2004. Efficient analysis of markers, genes,and QTLs using a permanent rice gene-mapping population. Plant and Animal Genome Conference XIII. p. 141
- Fjellstrom, R.G., McClung, A.M., Shank, A.R. 2005. Microsatellite markers closely linked to the Pi-z blast resistance gene in rice. Plant and Animal Genome Conference. p. 144.
- Pinson, S.R., Li, Z., Tabien, R.E., Tai, T., Redus, M.A., Fjellstrom, R.G. 2005. The Lemont/Teqing RIL rice population provides unique opportunity for correlating molecular data with phenomics. Proceedings, 2nd International Symposium, Rice Functional Genomics, Tucson, Arizona. p. 150.
- Chen, M., Bergman, C.J. 2005. The influence of kernel maturity, milling degree and milling quality on rice bran phytochemical concentrations. Cereal Chemistry 82(1):4-8.
- Aluko, G., Martinez, C., Tohme, J., Castano, C., Bergman, C.J., Oard, J.H. 2004. QTL mapping of grain quality traits from the interspecific cross Oryza sativa X O. glaberrima. Journal of Theoretical and Applied Genetics. 109:630-639.
- Champagne, E.T., Bett Garber, K.L., Grimm, C.C., Thompson, J., Mcclung, A. M., Mutters, R. 2005. Effects of drain and harvest dates on rice sensory and physicochemical properties. Cereal Chemistry. 82:369-374.
- Champagne, E.T., Bett Garber, K.L., Grimm, C.C., Thompson, J., Mutters, R., Mcclung, A.M. 2005. Impact of varying drain and harvest dates on rice sensory and physicochemical properties. 287-291.
- Chen, M., Bergman, C.J. 2005. A rapid procedure for analyzing rice bran tocopherol, tocotrienol and g-oryzanol contents. Journal of Food Composition and Analysis. 18:139-151.
- Kepiro, J.L., McClung, A.M., Fjellstrom, R.G. 2004. Molecular genetic analysis of milling yield in rice using amplified fragment length polymorphism (aflp) and microsatellite (SSR) markers for QTL mapping. United States Japan Natural Resources Protein Panel. pp. 278-282.
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Progress 10/01/03 to 09/30/04
Outputs
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. Provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders. Year 2 (2005) Identify DNA markers associated with alkali spreading value and amylose content in diverse germplasm and crosses. 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 fatty acid profiles, lipid content, phenolics, and hydrolytic stability in diverse cultivars. 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) 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 photoperiodism in a wide
cross. Identify DNA markers associated with the Pi-i blast resistance. 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. Develop an improved screening method for measuring field fissuring using cultivars. 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. 3. Milestones:
A. List the milestones that were scheduled to be addressed in FY 2004. How many milestones did you fully or substantially meetin FY 2004 an dindicate which ones were not fully or substantially met, briefly explain why not, and your plants to do so. Year 1 (2004) Identify DNA markers associated with the Pi-Leah blast resistance gene useful for U.S. breeding efforts: Identification of new genes for blast resistance that broaden the spectrum of resistance in U.S. rice germplasm is of interest for rice breeders and pathologists. A novel blast resistance gene was identified in the USA cultivar Leah which displays a spectrum of resistance to blast races that is similar to the Pi-kh disease resistance gene. Molecular markers were developed to test in a segregating population if the Pi-Leah gene was located in the same region as Pi-kh. It was determined that the Leah factor conferring resistance to race IG-1 mapped to the same region on rice chromosome 11 as the IB-54 and IG-1 resistance
factors conferred by the Pi-kh gene. It was concluded that the cultivar Leah has a unique and previously- nidentified allele at the Pi-k locus. Annually provide agronomic, quality, and disease resistance characterization of the Uniform Rice Regional Nursery for breeders: Two hundred advanced breeding lines from four southern U.S. public rice breeding programs were evaluated for numerous agronomic, milling and cooking quality, and disease resistance traits. These data were provided to the rice breeding teams to help in their selection and development of new cultivars for the U.S. In addition to what was planned for Year 1, we have also made progress on additional milestones. Year 2 (2005) Identify DNA markers associated with alkali spreading value and amylose content in diverse germplasm: A combination of microsatellite and SNP molecular markers have been developed that explain amylose content and starch pasting properties in a large set of diverse world germplasm. In addition,
markers were developed near the Alk gene encoding soluble starch synthase IIa that controls alkali spreading value in rice. Alkali spreading value was distinguished into two classes, low gel type and intermediate gel type, using the markers. Cultivars having a high gel type were found to the have intermediate form of the Alk gene along with low amylose contents. These markers can be used to more accurately and efficiently indicate cooking quality of rice germplasm than standard analytical methods and will enable breeders to use a broader array of genetic materials in varietal development programs. Determine genetic variability for fatty acid profiles, lipid content, phenolics, and hydrolytic stability in diverse cultivars: An evaluation of over 200 diverse rice cultivars demonstrated that there is significant genetic variation for lipid content, fatty acid composition, hydrolytic rancidity, oil concentrations, esterase activity and phenolic content in rice germplasm. This indicates
that genetic resources are available to develop rice cultivars that produce rice bran oil that is of high quality and quantity, which would add value to this important crop. In addition, rice cultivars with pigmented bran were found to have high phenolic content and high anti-radical activity. These traits are associated with providing protection against cancer and cardiovascular disease. Thus, these results may help expand the use of rice for its health-beneficial aspects. Year 4 (2007) Identify DNA markers associated with photoperiodism in a wide cross: Development of DNA markers associated with photoperiodism would facilitate the use of a wider range of germplasm in U.S. breeding efforts since many international rice germplasm sources are photoperiod sensitive and do not flower under U.S. growing conditions. We surveyed public DNA sequence database information around the hd-1 gene on rice chromosome 6, which controls photoperiod sensitivity, to identify polymorphisms and develop
PCR primers to test their linkage with photoperiodism. Genetic linkage analysis was analyzed among the progeny of a cross photoperiod- sensitive and photoperiod-insensitive cultivars from Asia. PCR primers flanking microsatelllite sequences were identified that could be used in selecting for photoperiod insensitivity in crosses between U.S. and international germplasm. Develop an improved screening method for measuring field fissuring using cultivars: Data compiled over three years indicates two modifications that will improve the reliability and efficiency of evaluating fissure resistance. Late-planted field plots, which are subjected to more extreme fluctuations in environmental conditions than those planted at optimum planting dates, are more reliable at distinguishing between fissure resistant and susceptible varieties of rice. In addition, grain breakage can be determined following dehulling, which forgoes the milling process, saves time and labor, and dramatically reduces the
seed sample size required for the test. B. List the milestones that you expect to address over the next 3 years (FY 2005, 2006, & 2007). What do you expect to accomplish, year by year, over the next 3 years under each milestone? Year 2 (2005) Molecular Markers: We have previously developed genetic markers that are associated with the gene that controls amylose content in diverse rice germplasm. This region will be more finely mapped using a genetic cross that is segregating for amylose content so that the chromosomal location of the markers relative to the gene can be determined. Germplasm Development: A rice mapping population and new conventional and specialty rice cultivars will be registered for public use. Germplasm Characterization: Elite breeding material from all of the southern U.S. public rice breeding programs will be evaluated for agronomic, quality, and disease resistance characteristics, and these data will be provided to breeders to aid in their cultivar development
process. Rice cultivars will be evaluated under organic and conventional cultural management methods to identify the best performing cultivars for this high-value market. Cultivars possessing different major blast resistance genes will be evaluated to determine if there is a yield penalty associated with resistance when disease is not present. Diverse rice cultivars will be evaluated for differences in tocols and gamma oryzanols, which are rice bran components having health beneficial aspects. Development of Improved Methods: An improved method for determining surface lipid content in milled rice will be developed that can be used as a more accurate measure of degree of milling. Year 3 (2006) Molecular Markers Genetic markers will be developed that are associated with starch synthesis genes, grain shape, milling yield, grain chalk, resistance to a predominant race of the blast pathogen, resistance to the sheath blight pathogen, plant tillering, and seedling vigor. Markers for these
important traits will facilitate development of new rice cultivars. Germplasm Characterization: Elite breeding material from all of the southern U.S. public rice breeding programs will be evaluated for agronomic, quality, and disease resistance characteristics, and these data will be provided to breeders to aid in their cultivar development process. The impact of incorporating genes for seedling vigor from an exotic source will be evaluated in a U.S. cultivar. Development of Improved Methods: A new method for evaluating bran thickness will be developed that can be used to determine the association of bran thickness with grain fissuring in rice. Year 4 (2007) Molecular Markers: DNA markers will be developed that are associated with the Pi-i blast resistance gene, with partial (field) resistance to blast, and with milling yield. Germplasm Characterization: Elite breeding material from all of the southern U.S. public rice breeding programs will be evaluated for agronomic, quality, and
disease resistance characteristics, and these data will be provided to breeders to aid in their cultivar development process. The impact of incorporating genes for sheath blight resistance from an exotic source will be evaluated in a U.S. cultivar. It will be determined if rice produced under organic or conventional systems affects rice cooking, nutritional or sensory quality. Development of Improved Methods: New methods for evaluating grain cooking and milling quality will be developed by creating new techniques for measuring grain fissuring, quantifying amylose and amylopectin contents, and determining molecular size and structure of components in rice starch. 4. What were the most significant accomplishments this past year? A. Single most significant accomplishment during FY 2004 (one per research project) The ARS Rice Research Unit in Beaumont, TX, developed DNA markers that are associated with alkali spreading value and amylose content, which are the most important factors
controlling rice cooking quality. Development of DNA markers that are associated with economically important traits will help breeders to develop improved rice cultivars more efficiently and effectively. Specific DNA sequence changes were identified that are associated with amylose content, gelatinizaton temperature as measured by alkali spreading value, and starch paste viscosity. Because the germplasm that was evaluated came from a diverse international background, the DNA sequence differences that were identified will be useful for working with most germplasm grown or introduced into the U.S. market. B. Other Significant Accomplishment(s), if any. A novel blast resistance gene was identified by ARS Rice Research Unit in Beaumont, TX, in the rice cultivar Leah. Identification of new genes that broaden the spectrum of disease resistance in U.S. rice germplasm is of interest for rice breeders and pathologists. Molecular markers were developed and were used to determine that the
Pi-Leah gene was located in the same region as the Pi-kh gene on chromosome 11. Having molecular markers that are associated with various genes for disease resistance will help breeders to pyramid these genes in new rice cultivars, which will increase the level of natural resistance and reduce the need for fungicides. Significant genetic variation for lipid content, fatty acid composition, hydrolytic rancidity, oil concentration, esterase activity, and phenolic content was determined by ARS Rice Research Unit in Beaumont, TX, in over 200 rice germplasm accessions. This indicates that exotic genetic resources are available to help breeders develop rice cultivars that have high rice bran oil quality and quantity. In addition, rice cultivars with pigmented bran were found to have high phenolic content and high anti- radical activity. These traits are associated with providing protection against human cancer and cardiovascular disease. These results may help expand the utilization of rice
into new health-beneficial foods. The ARS Rice Research Unit in Beaumont, TX, has developed DNA markers which are associated with photoperiodism insensitivity. Many international rice germplasm sources are photoperiod sensitive and do not flower under U.S. growing conditions rendering them difficult to use in breeding efforts. Molecular markers were developed near the hd-1 gene on rice chromosome 6, which controls photoperiod sensitivity. Markers were found to be useful in differentiating photoperiod-sensitive from photoperiod-insensitive progeny in a narrow cross as well as among cultivars from Asia and the U.S. These markers will facilitate breeding with photoperiod-sensitive cultivars by allowing breeders to quickly eliminate progeny that will not flower under U.S. conditions. As a result of collaboration between ARS Rice Research Unit in Beaumont, TX, and Louisiana State Experiment Station at Crowley, LA, six putative QTLs associated with bacterial panicle blight resistance
(caused by Burkholderia glumae) were identified in a rice mapping population. Identifying chromosomal regions that confer resistance to economically important diseases in rice will help breeders to develop improved varieties that require less fungicides for protection. Three of the QTL identified are located in regions where genes for resistance to sheath blight (caused by Rhizoctonia solani) and bacterial leaf blight (caused by Xanthomonas oryzae) have been mapped. Identifying DNA markers associated with resistance to these diseases will help breeders to develop new cultivars with resistance to multiple pathogens. A new specialty rice cultivar, Neches, has been developed by ARS Rice Research Unit in Beaumont, TX, for production in the southern United States. Neches is a waxy rice that possesses the same cooking quality traits as imported waxy rice and will offer a new opportunity for domestic farmers to compete with imports in this specialty market. Waxy rice (i.e., sweet or
glutinous) has been used in Asia as a dessert rice; however, in the United States, there is increasing demand by the ingredients industry for waxy rice flour and starch. Using rice in products other than whole-grain table rice will help diversify and expand the rice market for U.S. producers. For the first time, a subset of 1600 cultivars from the 17,000 rice accessions in the National Germplasm System were characterized for DNA markers that are associated with rice cooking quality by ARS Rice Research Unit in Beaumont, TX. DNA markers offer a more accurate assessment of the presence of genes for some traits than traditional analytical tests. This molecular marker information will be made available to the public via the ARS Germplasm Resource Information Network (GRIN) and will help researchers to identify germplasm that has novel cooking quality traits that can be used to develop improved U.S. rice cultivars. C. 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. Specific national program objectives that have been addressed through the accomplishments of the project include the following. In accordance with NPS Objective 1.2.7, "Identify genes responsible for plant product quality and resistance to disease, pests, and weather losses" the ARS Rice Research Unit in Beaumont, TX, has identified genetic markers in rice that are associated with: amylose content, gelatinization temperature, starch pasting properties, photoperiod insensitivity, the Pi-Leah blast resistance gene, and panicle blight resistance. These markers identify chromosomal regions that control economically important traits in rice which will help expedite breeding of new cultivars for the US. In accordance with NPS Objective 1.2.8, "Maintain, characterize, and use genetic resources to enhance genetic diversity and promote viable and vigorous plant production systems,"
the ARS Rice Research Unit in Beaumont, TX, has characterized up to 204 rice germplasm resources for fatty acid composition, lipid content, hydrolytic rancidity, oil concentration, and phenolic content. It was determined that these genetic resources will foster the development of rice cultivars with improved health beneficial aspects and added value. In addition, over 1600 rice accessions have been characterized for the first time with DNA markers associated with cooking quality traits. This information will be made publicly available through the Germplasm Resource Information Network (GRIN). In accordance with NPS Objective 3.2.4., "Develop and release to potential users varieties and/or germplasm of agriculturally important plants" the ARS Rice Research Unit in Beaumont, TX, has announced the release of a new specialty rice cultivar, Neches, that will provide farmers with a variety that can be grown domestically and compete with imported waxy rice. In addition, registration of the
conventional long- grain cultivar Saber, that was developed by the Rice Research Unit, has been published. 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 2004 annual rice field days that were conducted at Beaumont and Eagle Lake, TX. Over 800 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, how gene sequence controls rice cooking quality, development of improved methods for measuring grain fissuring, and use of DNA markers to augment U.S. rice breeding efforts. 7. List your most important publications in the popular press and
presentations to organizations and articles written about your work. Pinson, SRM. 2004. Developing Rice Varieties with Improved Fissure Resistance: Step1. Identifying Effective Breeder Selection Techniques. Texas Rice, July 2004 edition, Special section, pp. VII-VIII; http://beaumont.tamu.edu/eLibrary/newsletter/ 2004_Highlights_in_Research. pdf. McClung, Anna Myers. 2004. A Celebration of 50 Years of Progress in Rice Research by the USDA-ARS. Texas A&M University 57Th Rice Field Day. July 8, 2004. McClung, Anna Myers. 2003. Celebrating Agricultural Science in Your Shopping Cart. The Beaumont Enterprise. Nov. 27, 2003. Gipson, Naomi, and Anna McClung. 2004. Rice: A Culinary Delight. The Beaumont Enterprise. June 10, 2004.
Impacts
(N/A)
Publications
- Jia, Y., Wang, Z., Fjellstrom, R.G., Moldenhauer, K.A., Azam, M., Correll, J., Lee, F.N., Xia, Y., Rutger, J.N. 2004. Rice pi-ta gene is closely linked with resistance to the major pathotypes of the rice blast fungus in the U.S. Phytopathology. 94:296-301.
- MCCOUGH, S.R., TEYTELMAN, L., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., SCHNEIDER, D.J., CARTINHOUR, S.W., WARE, D., STEIN, L. DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA). GENOME RESEARCH. 2002.
- McClung, A.M. 2004. The rice plant: growth, development and genetic improvement. In: Champagne, E.T., editor. Rice: Chemistry and Technology. 3rd Edition. American Association of Cereal Chemists, Inc., St. Paul, MN. p. 25-48.
- McClung, A.M., Fjellstrom, R.G., Bergman, C.J., Bormans, C.A., Park, W.D., Marchetti, M.A. 2004. Registration of Saber rice. Crop Science. 44:693-694.
- Goffman, F.D., Pinson, S.R., Bergman, C.J. 2003. Genetic diversity for lipid content and fatty acid profile in rice bran. Journal of Agricultural and Food Chemistry. 80(5):485-490.
- Bergman, C.J., Goffman, F.D. 2004. A gas chromatographic procedure for determining rice degree of milling. In: Rice Technical Working Group Meeting Proceedings. February 29-March 4, 2004, New Orleans, LA. 2004 CD- ROM.
- Jia, Y., Rutger, J.N., Wang, Z., Singh, P., Martin, R., Pinson, S.R. 2004. Development and characterization of rice mutant populations for functional genomics of host-parasite interactions. American Phytopathological Society Annual Meeting. Phytopathology. 94(6):47.
- Fjellstrom, R.G., Shank, A.R., McClung, A.M. 2003. Mapping and genetic characterization of a novel blast resistance gene arising from the rice cultivar Leah. Plant and Animal Genome Conference Proceedings. P. 170.
- Chen, M., Bergman, C.J., Fjellstrom, R.G. 2003. Genetic variation at the waxy locus associated with starch pasting properties in international rice germplasm. Plant and Animal Genome Conference Proceedings. P. 168.
- McClung, A.M., Chen, M., Bergman, C.J., Fjellstrom, R.G. 2003. Mapping of rice thermal properties and its relationship to the alk and waxy genes. Plant and Animal Genome Conference Proceedings. P. 168.
- McClung, A.M., Pinson, S.R., Shank, A.R., Chen, M., Bergman, C.J., Fjellstrom, R.G. 2003. Progressing from putative QTLs to marker assisted selection in breeding [abstract]. Agronomy Abstracts. 2003 CDROM.
- SOHN, M., BARTON II, F.E., MCCLUNG, A.M., CHAMPAGNE, E.T. NEAR INFRARED SPECTROSCOPY FOR DETERMINATION OF PROTEIN AND AMYLOSE IN RICE FLOUR THROUGH USE OF DERIVATIVES. CEREAL CHEMISTRY. VOL. 81. ISS. 3. P. 341-344. 2004.
- Chen, M., Bergman, C.J., Fjellstrom, R.G. 2004. Waxy locus genetic variation associated with amylose content in international rice germplasm. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Chen, M., Bergman, C.J., Fjellstrom, R.G. 2004. Genetic variation at the waxy locus associated with starch pasting properties in international rice germplasm. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Pinson, S.R., Osborn, G.S. 2004. Improved methods for identifying fissure resistant rice. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Pinson, S.R., Shahjahan, A.M., Rush, M.C. 2004. QTLs for panicle blight resistance and their association with resistance to other diseases. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Fjellstrom, R.G., Chen, M., Bergman, C.J., McClung, A.M. 2004. Single nucleotide polymorphism markers at the rice alk locus controlling alkali spreading value. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Traore, K., Fjellstrom, R.G., McClung, A.M. 2004. Genetic diversity among West African rice varities for grain quality traits using chemical and DNA marker analyses. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Kepiro, J.L., McClung, A.M., Fjellstrom, R.G. 2004. Progress in developing dna markers for milling yield. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Fjellstrom, R.G., McClung, A.M., Gibbons, J., Deren, C. 2004. Development of genetic markers for semi-dwarf plant height and photoperiod insensitivity for marker aided selection in u.s. rice. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Shank, A.R., McClung, A.M., Fjellstrom, R.G. 2004. Development of improved methods for sheath blight evaluation. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- McClung, A.M., Shank, A.R., Bormans, C., Park, W.D., Fjellstrom, R.G. 2004. Are agronomic traits impacted by the presence of Pi- genes when blast disease is absent? In: Rice Technical Working Group Meeting Proceedings, February 29-Mach 4, 2004, New Orleans, LA. 2004 CDROM
- McClung, A.M., Shank, A.R., Kanter, D., Jodari, F., Beighley, D., Chen, M., Fjellstrom, R.G. 2004. The application of new markers for predicting blast resistance and cooking quality in rice. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.
- Goffman, F.D., Bergman, C.J. 2004. Relationship between hydrolytic rancidity, oil concentration and esterase activity in rice bran. Journal of the Science of Food and Agriculture. 80(6):689-392.
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