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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS
2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Phenotypically and genotypically characterize the rice National Small Grains Germplasm Collection (NSGC) and conserve genetic stocks, mutants, and mapping populations in the Genetic Stocks Oryza (GSOR) to promote greater use by the research community. Sub-objective 1.A. Characterize accessions in the NSGC rice collection for 27 descriptors and rejuvenate seed of low inventory genetic seedstocks. Sub-objective 1.B. Perform structure analysis following genotypic and phenotypic evaluation of the NSGC Core collection. Sub-objective 1.C. Expand the GSOR collection to 15,000 accessions and establish a web-based ordering and distribution system. Objective 2: Evaluate rice germplasm to identify genetic resources having enhanced nutritional properties and added-value for the food industry. Sub-objective 2.A. Identify genetic variability for antioxidant capacity and the content of main classes of polyphenols and carotenoids in rice germplasm. Sub-objective 2.B. Structurally identify and quantify major flavonoid and proanthocyanidin compounds in rice genotypes with different bran color. Sub-objective 2.C. Determine the effect of processing on rice bran phytochemicals. Sub-objective 2.D. Identify quantitative trait loci (QTL) associated with rice grain elemental content. Sub-objective 2.E. Measure genotype and environment interactions on starch structure and grain quality. Sub-objective 2.F. Determine the impact of non-conventional cultural management practices on rice grain quality. Objective 3: Map new resistance genes for blast disease and straighthead disease identified in germplasm accessions. Sub-objective 3.A. Mine novel blast resistance genes from indica rice germplasm for use in U.S. breeding programs. Sub-objective 3.B. Decipher genetic mechanism for resistance to straighthead, a physiological disease. Objective 4: Map genes associated with grain quality traits, including rice paste viscosity and grain chalk. Sub-objective 4.A. Genetically map starch paste viscosity variation as a predictor of rice processing quality. Sub-objective 4.B. Genetically map grain chalk formation which influences milling quality.


1b.Approach (from AD-416)
Additional germplasm and data will be added to the NSGC rice collection for distribution to the public via GRIN. The Core collection will be characterized for sheath blight disease resistance, grain mineral accumulation, straighthead tolerance, protein content, and cold tolerance, and genetic markers will be identified that are associated with these traits. The Genetics Stocks Oryza (GSOR) collection will be expanded to 15,000 accessions that are curated and distributed to the research community through a searchable on-line database. Selected accessions from the NSGC collection will be evaluated for health beneficial compounds like polyphenols, flavonoids, and carotenoids and the influence of the environment and processing methods on levels of these compounds will be evaluated. Germplasm will be evaluated under flooded and aerobic conditions to understand the genetic mechanisms controlling nutrient uptake. Mapping populations will be developed, and rice gene microarray chips will be used to identify chromosomal regions associated with nutrient uptake. The genotype x environment interaction on key enzymes in the starch pathway will be studied to determine how they impact starch structure and processing quality. In an effort to understand how rice quality will be impacted by crop rotation systems, 5 to 10 rice cultivars will be grown using conventional tillage/no-till, permanent flood/intermittent-flushing, different fertilization rates, and different crop rotations, and agronomic and cooking quality traits will be evaluated to provide insight as to how changing cropping systems will impact rice milling and cooking quality. Novel genes for blast and straighthead disease resistance will be identified using mapping populations. Markers and germplasm will be released to breeders for developing improved cultivars. Sequence variation around a SNP in exon 10 of the rice Waxy gene will be evaluated to determine what impact it has on RVA paste viscosity characteristics. Genetic markers will be developed that can be used in breeding for elevated pasting profiles, which is desired for rice used in canning, instantizing, and other food preparation processes. We will fine map several QTL previously identified to be associated with grain chalk. Progeny from the selected recombinant lines will be grown in two environments and chalk amounts quantified with a Winseedle Image analysis system. Segregation of tightly linked SSR and SNP markers will be analyzed to pinpoint recombination points and candidate genes in the finely mapped region. Genetic markers developed from this research will be used by breeders to develop new cultivars that have greater translucency, higher milling yield, and consistent cooking quality.


3.Progress Report
Progress was made on all planned aspects of the program during FY10. In addition to the milestones and accomplishments reported, progress was made in several other areas. The Genetics Stocks collection (GSOR) was expanded by 3% this year, and some 6700 accessions were distributed to researchers. Ninety percent of these were sent to US programs, with the remaining sent to researchers in eight countries. A mapping population, MY2, that was developed as part of the RiceCAP project has been released to the public and is available through GSOR. The rice Core collection, representing 10% of the NPGS world rice collection, was further characterized for resistance to sheath blight disease and genotyped with 155 microsatellite markers. Some 50 germplasm accessions were identified with excellent resistance to this globally important disease. The mini-core, which represents 1% of the NSGC collection, has been evaluated for silicon content in rice hulls, which is a valuable co-product that is used in the production of industrial polymers and for yield components. Association analyses are pending. The first steps in commercialization of the cultivar Rondo, which was released last year, have started with foundation seed being produced, industrial processing trials initiated, and field production under organic management being tested. The program experienced some slow-downs due to a pest problem in the greenhouse that required a redirection of labor for quarantine management of the greenhouses throughout the year. Due to a vacancy in the cereal quality lab, a reduced number of grain chemistry assays on the germplasm collection were achieved. In addition, progress on mapping grain chalk has been delayed for two years. The original mapping population was lost due to hurricane damage in the field. Subsequent efforts to rejuvenate the population were not successful. However, one of the mapping populations that is being used to identify novel blast resistance genes is also segregating for grain chalk. This will allow this component of the program to be resumed.


4.Accomplishments
1. Improvement in the nutritional quality of rice grain. Arsenic is a common, natural element in agricultural soils, and low concentrations do occur in all food crops, including rice. High concentrations, though, are not desirable because of its potential detrimental impact on plant growth and yield and its potential toxicity to humans. ARS scientists in Stuttgart, Arkansas, along with researchers at Texas A&M University and University of Arkansas evaluated 25 cultivars selected from the USDA rice germplasm collection for arsenic content. They identified rice cultivars that have 50% lower arsenic content as compared to other cultivars and developed field management practices that can reduce accumulation of arsenic in rice grain. Breeders and researchers can use the identified cultivars with low arsenic concentrations as parents to develop new cultivars having improved nutritional value. Farmers can use the new cultural management practices to assure high nutritional quality of the rice grain.

2. Genetic diversity in the USDA Rice World Collection. The USDA maintains a collection of about 20,000 rice cultivars from 116 countries. Knowledge of the genetic structure, diversity, and inter-relationship of the cultivars in the collection is important for its effective use for breeding and genetic studies. ARS and university scientists in Stuttgart, Arkansas, developed a core subset that is representative of the whole collection and analyzed it with DNA markers. They determined the proportion of the collection that was associated with different rice sub-populations and the genetic diversity among cultivars from different geographic regions of the world. Researchers can use these results to find rice accessions that provide new sources of genes for inheritance studies and breeding new rice cultivars and hybrids. Cultivars having higher yield and improved resistance to diseases and environmental stress will help sustain rice production in the USA and abroad.

3. Release of a genetic mapping population for rice milling quality. Milling yield in rice is a major factor in determining crop value for farmers. Because this trait is controlled by several genes and is sensitive to changes in the field environment, it has been difficult for breeders to select for and make improvements in new varieties. ARS researchers at Stuttgart, Arkansas, and university scientists in Louisiana, Kansas, and Arkansas developed a large set of offspring derived from a cross between two rice cultivars that vary widely for milling yield and other agronomic traits. This population has already been used to track down DNA markers linked to milling quality. Breeders will be able to use these genetic markers to develop new rice cultivars that have higher milling quality and better economic value for farmers.

4. Utilizing the natural genetic diversity found in the USDA World Rice Collection. The USDA National Plant Germplasm System includes a collection of some 20,000 rice cultivars from around the world. These genetic resources are provided to researchers worldwide and must be periodically rejuvenated to produce fresh seed, as well as characterized for economically important traits. ARS scientists in Stuttgart, Arkansas, and Beaumont, Texas, rejuvenated over 1,600 accessions of rice, provided seedhead samples for image documentation, and supplied over 11,000 data points on plant and grain characteristics to the Germplasm Resources Information Network (GRIN) public database. The rejuvenated seeds and enriched database play an essential role for researchers that use this collection to better understand the genetic control of traits in rice.


Review Publications
Yan, W., Li, Y., Agrama, H.A., Luo, D., Gao, F., Ren, G. 2009. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molecular Breeding. 24(3):277-292.

Xie, J., Agrama, H.A., Kong, D., Zhuang, J., Hu, B., Wan, Y., Yan, W. 2009. Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon). Genetic Resources and Crop Evolution. 57:597-609.

Johnson, D.T., Lewis, B.A., Bryant, R.J., Liyanage, R., Lay, J.O., Pszczolkowski, M.A. 2009. Attractants for the Green June Beetle (Coleoptera: Scarabaeidae). Journal of Economic Entomology. 102(6):2224-2232.

Yan, W., McClung, A.M. 2010. 'Rondo', a long-grain indica rice with resistances to multiple diseases. Journal of Plant Registrations. 4:131-136.

Oard, J.H., Moldenhauer, K.K., Fjellstrom, R.G., Nelson, J., Linscombe, S.D., Silva, J., May, G.D. 2010. Registration of the MY2 Cypress/LaGrue rice recombinant inbred line mapping population. Journal of Plant Registrations. 4(3):1-5.

Agrama, H.A., Yan, W. 2010. Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder. Plant Breeding. 129:304-312.

Agrama, H.A., Yan, W. 2009. Association mapping of straighthead disorder induced by arsenic in rice. Plant Breeding. 128:551-558.

Zhao, K., Wright, M.K., Kimball, J.A., Eizenga, G.C., McClung, A.M., Kovach, M.J., Tyagi, W., Ali, M., Tung, C., Reynolds, A., Bustamante, C.D., McCouch, S.R. 2010. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One. 5(5):e10780. doi:10.1371/journal.pone.0010780.

Last Modified: 11/21/2014
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