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.

3.Progress Report
The project contributes primarily to the goals of National Program 301 Plant Genetic Resources, Genomics, and Genetic Improvement. By developing knowledge on inheritance and rice grain chemical attributes, enhanced trait evaluation techniques, and improved rice germplasm (including cultivar releases), this project supports subcomponents 2C, 3A, 3B, and 3C of NP301.

Four improved rice cultivars for commercial production in the Southern US were developed over the life of this project. One release was a standard long-grain rice variety; three were specialty rices. Three germplasm lines were released that make eight new sheath blight resistance genes and their linked markers newly available to US rice breeders. Development of new rice germplasm and cultivars that have improved agronomic performance and unique cooking and processing qualities helps farmers to remain competitive and sustains agriculture in the US. (NP301, Component 3)

Knowledge on the genetic control of several economically important traits progressed significantly through the discovery and molecular tagging of genetic loci. Loci identified by scientists in Beaumont, TX, were associated with resistance to three different rice diseases, two key rice cooking/processing qualities, rice aroma, rice milling quality, photoperiod sensitivity, and tiller production. Genes for blast resistance, grain aroma, and rice cooking quality were mapped so precisely that all public US rice breeders now use marker-assisted selection for these traits. Because of synteny between species, the QTL results impact crop research beyond rice. (NP301 3A) The ARS rice variety development program was among the first public US breeding programs of any crop to merge molecular and traditional breeding strategies, a precedent now followed by all public US rice breeding programs. (NP301 3A, 3C)

Ability to discover and fine-map rice genes was enhanced through the development of a new rice gene-mapping population composed of TeQing-into-Lemont introgression lines (TILs). This population is uniquely suited for both fine-mapping and evaluation of the breeding value of foreign genes to US variety improvement programs. It has supported de novo mapping, verification, and/or fine-mapping of QTL for disease resistance, grain nutrition, and plant architecture. (NP301 2C)

Trait evaluation techniques for measuring lipase activity, grain storage protein, degree of milling, and rice grain fissure resistance (associated with milling quality) were developed or enhanced. As well as being critical to gene mapping studies, these improved evaluation techniques often prove immediately useful as breeder selection tools. (NP301 3A)

Diverse rice germplasm has been evaluated using novel genomic and phenotypic techniques to enhance its utilization by rice breeders and researchers. (NP301 3B) Genetic variation was newly identified among diverse rice cultivars for several phytochemicals known to affect human health (i.e., antioxidants), storage protein content, and rice bran oil content and quality. These studies enhance our understanding of the genetic and chemical attributes underlying rice grain functionality. (NP301 3A)

4.Accomplishments
1. Discovery of QTLs for Rice Milling Yield and Milling Component Traits: ARS scientists in Beaumont, TX, identified DNA markers associated with high 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 laborious trait to evaluate, and is complexly inherited and environmentally sensitive. A QTL mapping project involving a cross between a US cultivar and a foreign cultivar was collaboratively conducted with funding from the USDA-CSREES-NRI RiceCAP grant. Genes for high milling quality were found linked to markers on rice chromosomes 5 and 9. It is consistently difficult to obtain high milling yield rice varieties after making crosses between US adapted varieties and international varieties, which restricts the use of foreign rice germplasm in US breeding programs. It is anticipated that use of the markers linked to the milling quality QTLs identified herein will allow breeders to make more use of foreign rice germplasm. (NP301, Component 2)

2. Molecular Markers Tagging Genes for Resistance to Rice Sheath Blight Disease: As a result of the RiceCAP grant funded by USDA CSREES National Research Initiative, ARS and Texas A&M University scientists at Beaumont, TX, more precisely mapped a previously identified QTL associated with resistance to sheath blight disease in rice. This QTL was originally found to reside in a fairly large 37 cM chromosomal region. After genetic and molecular dissection of this QTL region, the SBR locus was more precisely mapped to the bottom 12 cM of chromosome 9. Interestingly, during the QTL dissection study, a locus for spreading culm (Spr) was newly discovered and mapped to the upper portion of the original QTL region. This means that the undesired Spr gene and the desired SBR gene are different loci. 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 US. 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. (NP301, Component 3)

3. Understanding the Effect of Protein on Pasting Properties of Rice: The cooking functionality of rice is strongly associated with the alleles of Waxy and Alk genes, and yet variation exists in functional traits within genotypes that have the same alleles for these genes. Storage protein has been shown to affect pasting properties, suggesting its potential role contributing to the variation. The effect of protein was assessed for 34 elite rice lines categorized into 6 groups based on the combinations of Waxy and Alk alleles. Within groups, protein contributed little to the differences among genotypes. Protein, however, affected pasting properties to different levels among groups. The knowledge will be useful to rice research scientists when further examining potential protein/starch interaction. (NP301, Component 3B)

4. Development of an Improved Fluorescence Microplate Method for Lipase Activity and Determination of the Correlation of Lipase Activity with Storage Stability of Rice Bran in a Diverse Germplasm: The short shelf life of brown rice limits its acceptance by the consumers, while the rapid development of rancidity in rice bran right after milling reduces its use for further processing and application. The activity of lipase contributes to a large part of this lipid deterioration. Having a rapid and sensitive method to determine the lipase activity will facilitate the screening of germplasm for low-lipase genotypes. An improved fluorescence microplate assay for lipase activity determination has been developed. This method was used to screen a diverse germplasm for assessing the genotypic diversity in lipase activity and its activity in correlation with the hydrolytic rancidity. The information will be useful in breeding programs focusing on improving storage stability of rice and rice bran. (NP301, Component 3B)

6.Technology Transfer

Number of New Germplasm Releases	1
Number of Non-Peer Reviewed Presentations and Proceedings	19

Review Publications
Chen, M., Bergman, C.J., Pinson, S.R., Fjellstrom, R.G. 2008. Waxy gene haplotypes: Associations with amylose content and the effect by the environment in an international rice germplasm collection. Journal of Cereal Science. 47:536-545.