2008 Annual Report 1a.Objectives (from AD-416) To develop early-maturing, production-efficent indica rice germplasm and also develop rice germplasm with improved and novel grain qualities by inducing mutants, identifying natural variants, and through innovative genetic methods. To introgress new genes for pest resistance and stress tolerance into cultivated rice from wild Oryza species. Evaluate germplasm and establish a Rice Genetic Stocks Collection. 1b.Approach (from AD-416) Develop highly production-efficient indica rice germplasm with suitable grain quality for U.S. markets through hybridization of early maturing, production-efficient indicas from central China with late maturing indica germplasm from IRRI. Initial recombinants will be jointly selected for early maturity and 20-22% amylose content followed by yield and quality evaluations creating a foundation of adapted indica germplasm which then can be tested for quality assessments, including grain shape, milling percentage and cooking quality. Induced mutation will be used to select early maturing lines in the IRRI germplasm. Early maturity enhances water use, i.e. fewer days of irrigation are required. Other atrributes of indica germplasm are more disease- and insect-resistance in addition to straighthead resistance. Induced mutation will be used to look for additional low phytic acid mutants to complement the low phytic acid-1 mutant already in hand, in order to further reduce phytic acid. The creation of a U.S. rice oil market has led to interest in developing higher-oil and altered fatty acid composition mutants. Agronomic performance of the giant embryo mutants available from Japan and China, is suspect, so the existing genes will be studied in different genetic backgrounds, as well as through induced mutation in U.S. rice varieties. There will be additional focus on inducing agronomically suitable mutants for semidwarfism and early maturity in the "gold-standard" aromatic rices of the world, basmatis and jasmines. Also the unstudied amylopection component of starch will be characterized for amylopectin chain lengths in order to determine how this affects cooking quality. The small number (ca. 100) of available Oryza species assessions will be screened for pest resistance and stress tolerance characters for backcrossing into cultivated germplasm. A Rice Genetics Stocks collection will be established for for seed propagated rice mutants, including morphological, developmental, and metabolic characters. In addition it will provide speciality handling and evaluation for rice accessions that cannot be handled by the National Small Grains Collection at Aberdeen, ID. 3.Progress Report The starch structure, amylose and amylo-pectin, was determined for ten rice genotypes, which included five U.S. long-grain japonica cultivars, three indica cultivars, and two japonica/indica hybrids. The starch structure in these genotypes is being compared to the grain quality and starch synthesizing enzyme activity to identify relationships between the enzymes and starch structure. Relationships between the indica and japonica sub-groups also are being examined. (NP301, Component 1B) Improved computational methods are needed in order for association mapping to correctly unveil the associations between DNA markers and phenotypic traits. To this end, 400 O. sativa and 100 O. rufipogon accessions are being phenotyped for approximately 19 plant traits, 23 seed traits, and 3 grain quality traits over two growing seasons. Also, the accessions are being genotyped with Single Nucleotide Polymorphisms (SNP) chips developed using Illumina and Affymetrix technology. (NP301, Component 1B) In order to improve crop plants, it is important to understand the traits man selected during the domestication process. To this end, 100 accessions of the rice ancestral species, O. rufipogon, are being characterized for most of the same traits as the O. sativa accessions over two different growing seasons. Over the past year, most of the O. rufipogon accessions were grown for one season. After the trait data collection is complete, comparisons will be made between selected trait and the various O. sativa subgroups, which most likely arose at different times during the domestication process. (NP301, Component 1B) Completely genotyped 1,790 accessions in the USDA rice core collection with 75 molecular markers covering the entire rice genome about every 35 cM; arranged foundation seed production of the elite germplasm line 4484-693 named 'Rondo' for release; rejuvenated 2,288 accessions of rice germplasm for the NSGC; prepared panicle sample of the 2,288 accessions for grain and panicle image recording; and generated 20,768 data points of 18 descriptors for enriching GRIN database. (NP301, Component 1B) 4.Accomplishments 1. Giant embryo mutant with high oil content: All reported giant embryo mutants are in short-grain rice; whereas, most of the rice consumed in the US is long grain. Using induced mutation techniques, scientists at the Dale Bumpers National Rice Research Center identified a giant embryo mutant with 37% more oil in Drew, a U.S. long-grain rice variety. As a whole-grain brown rice, this mutant has the potential to increase the value of rice through improved phytonutrient content by increasing antioxidants, such as oryzanol, tocopherols, and tocotrienols. These antioxidants have been shown to offer protection against chronic diseases such as heart disease and cancer, and lower serum cholesterol. This accession also can be used to study the genetic control of these antioxidants in a long-grain rice. (NP301, Component 1B) 2. Establishment of a diverse collection of 400 rice accessions: The danger of seed being mixed or incorrect is an ever-present danger when seed is increased from one generation to the next, and especially in germplasm collections. Scientists at the Dale Bumpers National Rice Research Center in Stuttgart, AR, in collaboration with Cornell University, Ithaca, NY, took a collection of 400 rice accessions from a diverse background, grew one single "reference plant" to maturity, and deposited the seed in a repository. These reference plants were genotyped with 36 SSR markers to obtain a molecular fingerprint of each accession and classify each accession into one of five rice sub-populations (or sub-groups). Also, scanned images of the panicles and seed with and without the hull (lemma and palea) were archived. These molecular fingerprints and scanned images will enable researchers using this seed in future studies to verify that they are true to type. This methodology has application to management of germplasm collections worldwide. (NP301, Component 1B) 3. In-depth characterization of a diverse collection of 400 rice accessions: Accurate phenotypic data is required to apply the association mapping methodologies recently developed for mapping genes in human populations to plant germplasm collections. At the Dale Bumpers National Rice Research Center in Stuttgart, AR, a collection of 400 rice (O. sativa) accessions was characterized for 19 plant phenotypic traits in the field over two growing seasons and 23 seed traits for one growing season. This detailed phenotypic data will be invaluable in conducting an association mapping study with rice to identify where genes controlling the phenotypic traits are located in the rice genome. In addition, expanding the number of phenotypic traits evaluated for these 400 accessions is a valuable addition to the U.S. rice germplasm collection. (NP301, Component 1B) 4. Genetic assessment of USDA rice germplasm collection: Utilization of a germplasm collection and mining valuable gene(s) in a collection is solely dependent on genetic assessment of the collection. The USDA rice core collection including 1,790 accessions, which is representative of the USDA rice world collection containing about 20,000 accessions, was completely genotyped with 75 DNA markers covering the entire rice genome about every 35 cM by ARS scientists at the Dale Bumpers National Rice Research Center, Stuttgart, AR. Analysis of the genotypic data will reveal the genetic diversity and population structure of the core collection. Association analysis of the genotypic data with phenotypic data determined on 26 traits allows for identification of DNA marker(s) linked with gene(s) controlling the phenotypic traits. The association mapping analysis will be expanded to explore gene(s) responsible for other traits, e.g., cold and drought tolerances, and reduction of grain arsenic concentrations. These analyses will aid rice breeders to identify novel germplasm and design strategies to transfer gene(s) of interest into new cultivars that will help the US rice industry to remain competitive in the world market. (NP301, Component 1B) 5. Development of molecular markers for straighthead resistance: Straighthead is a physiological disorder that can result in complete yield loss. and its causal factors are not clear which makes its evaluation very difficult. Researchers at the Dale Bumpers National Rice Research Center, Stuttgart, AR, identified two genetic markers located on chromosome 5 (RM413) and 12 (RM277) that were associated with straighthead resistance. These markers can be used to more accurately and efficiently select resistant plants in a breeding program. Breeding straighthead-resistant new cultivars will reduce yield losses due to abiotic stress and will help sustain rice production in the U.S. (NP301, Component 2C) 6. Establishment of mapping populations to identify novel gene(s) for blast resistance: The biotype IE-1 of the rice blast fungal pathogen Magnaporthe oryzae has overcome the resistance conveyed by the blast resistance gene Pi-ta that has been incorporated into U.S. rice varieties for the past 20 years. ARS scientists at the Dale Bumpers National Rice Research Center, Stuttgart, AR, developed two mapping populations of 700 progeny to identify chromosomal regions harboring the novel resistant gene(s) using DNA markers. Progeny will be selected from these populations to develop recombinant inbred lines for fine-mapping of the novel blast gene(s). Once identified, these gene(s) will be combined with other blast resistance genes in new rice cultivars which will reduce losses due to disease and decrease reliance on fungicides. (NP301, Component 2C) 7. Identification of rice accessions having low grain arsenic: Arsenic in the food chain is harmful and should be reduced as much as possible, especially in rice, a staple food for half of the world's population. ARS scientists at the Dale Bumpers National Rice Research Center, Stuttgart, AR, have identified rice cultivars containing 50% less of arsenic than other accessions in the USDA rice world collection. These low arsenic germplasm accessions will play an important role in developing new cultivars that avoid arsenic accumulation under flooded conditions. The end result will be a healthier food that feeds much of the world's population. (NP301, Component 3C) 8. Improved yields found in tetraploid rice: Although diploid hybrid rice has a yield increase of 20% over the best traditional cultivars, scientists keep exploring avenues to obtain even greater plant vigor and yield to provide adequate food for the world's population. A collaborative project between the Dale Bumpers National Rice Research Center, Stuttgart, AR, and the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, P.R. China, developed autotetraploid hybrids that demonstrated enhanced grain fertility resulting in a yield increase of 20% over traditional hybrids. Results from this research provide an opportunity to further increase rice yield for global food security using this polyploidy strategy. (NP301, Component 3A) 9. Identification of QTLs for pre-harvest sprouting resistance: Pre-harvest sprouting of seed dramatically reduces seed quality during seed production. A collaborative project between the Dale Bumpers National Rice Research Center, Stuttgart, AR, and Sichuan Academy of Agricultural Sciences, Chengdu, P.R China, identified a major QTL (quantitative trait locus) qPSR8 between RM447 and RM3754 on chromosome 8 that explained 43% of pre-harvest sprouting variation. Application of such QTLs in marker-assisted breeding could result in improved cultivars with pre-harvest sprouting resistance. (NP301, Component 2C) 10. Establishment and growth of the Genetic Stocks-Oryza (GSOR) Collection: Rice genetic stocks collections are being developed as part of several federally funded research projects to understand the genetic control of traits. Although seed distribution centers were established for maize, barley, wheat, and tomato, none were available for rice to facilitate the use of the novel genetic resources by other researchers. A rice genetic stocks center was established at the Dale Bumpers National Rice Research Center, Stuttgart, AR, in 2003 under the name Genetic Stocks-Oryza (GSOR). The collection has grown from 19 individual mutants to over 23,000 different lines including three mapping populations and five mutant collections. Since its inception, 4,543 genetic stocks have been distributed to U.S. and international researchers to enhance our understanding of structural and functional genomics. (NP301, Component 3C) 6.Technology Transfer Number of the New MTAs (providing only) 2 Number of Non-Peer Reviewed Presentations and Proceedings 29 Review Publications Tu, Shengbin, Luan, L., Liu, Y., Long, W., Kong, F., He, T., Xu, Q., Yan, W., Yu, M. 2007. Production and heterosis analysis of rice (Oryza sativa L.) autotetraploid hybrids. Crop Science. 47:2356-2363. Luan, L., Tu, S.B., Long, W.B., Wang, W., Liu, Y.H., Kong, F.L., He, T., Yan, W., Yu, M.Q. 2007. Cytogenetic studies on two F1 hybrids of autotetraploid rice varieties showing extremely high level of heterosis. Plant Systematics and Evolution. 267:205-213. Gao, F.Y., Ren, G.J., Lu, X.J., Sun, S.X., Li, H.J., Gao, Y.M., Luo, H., Yan, W., Zhang, Y.Z. 2008. QTL analysis for resistance to pre-harvest sprouting in rice (Oryza sativa). Plant Breeding. 127:268-273. Agrama, H.A., Eizenga, G.C. 2007. Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica. 160(3):339-355.