1a.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.

1b.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.

4.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)

6.Technology Transfer

Number of invention disclosures submitted	3
Number of non-peer reviewed presentations and proceedings	12
Number of newspaper articles and other presentations for non-science audiences	23

Review 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.