2006 Annual Report 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? Why does it matter? Weeds can be found in nearly all ecological systems in the United States. They cause economic losses to farmers and ranchers through reduction in crop yield and quality. Weeds also invade natural ecosystems, which can displace endangered species and devalue the land for recreational purposes. Managers of farms, ranches, recreational areas, forests, grasslands, nature preserves, railroad and highway rights-of-ways, and city and county weed districts also spend considerable resources to control weeds. The control measures for many weeds such as leafy spurge are expensive, inconsistent, or not compatible with local environmental conditions. Customer needs for acceptable control measures require the development of new and innovative biologically-based weed management strategies. We are using physiological, biochemical, molecular, genetic, and genomic approaches to develop new knowledge about fundamental processes related to the growth and development, reproduction, and genetics of weeds which is consistent with the component on Weed Biology and Ecology under National Program 304 - Crop Protection and Quarantine. The specific objectives of the project are: (1) to identify signaling pathways regulating seed and bud dormancy in leafy spurge, (2) to determine the function of individual genes involved in bud and seed growth and development, and (3) to investigate genetic diversity in Cirsium. 2.List by year the currently approved milestones (indicators of research progress) FY 2006 Objective 1.A: Develop a deep EST database for leafy spurge Conduct physiological experiments on seasonal and treated plants Objective 2: Prepare constructs (sense, antisense, double stranded) Objective 3.A: Develop SSR markers Collect and analyze Canada thistle samples Publication of results Objective 3.B: Develop nuclear and chloroplast markers Collect and analyze North American thistle samples FY 2007 Objective 1.A: Develop a deep EST database for leafy spurge Conduct physiological experiments on seasonal and treated plants Publication of results Objective 2: Study protein-protein interactions and conduct immunolocalizations Prepare constructs (sense, antisense, double stranded) Develop leafy spurge transformation system Objective 3.A: Collect and analyze Canada thistle samples Publication of results Objective 3.B: Develop nuclear and chloroplast markers Collect and analyze North American thistle samples Publication of results FY 2008 Objective 1.A: Design and test microarrays constructed from a unigene set Conduct physiological experiments on seasonal and treated plants Screen microarrays using characterized experimental materials Analyze microarray data Publication of results Objective 1.B: Clone genomic copies of differentially-expressed genes Sequence regulatory regions and identify likely cis-acting elements Prepare constructs and test function of cis-acting elements Objective 2: Study protein-protein interactions and conduct immunolocalizations Prepare constructs (sense, antisense, double stranded) Develop leafy spurge transformation system Publication of results FY 2009 Objective 1.A: Conduct physiological experiments on seasonal and treated plants Screen microarrays using characterized experimental materials Analyze microarray data Publication of results Objective 1.B: Clone genomic copies of differentially-expressed genes Sequence regulatory regions and identify likely cis-acting elements Prepare constructs and test function of cis-acting elements Clone trans-acting factors Publication of results Objective 2: Study protein-protein interactions and conduct immunolocalizations Prepare constructs (sense, antisense, double stranded) Transform plants and analyze resulting phenotype Publication of results FY 2010 Objective 1.A: Publication of results Objective 1.B: Publication of results Objective 2: Study protein-protein interactions and conduct immunolocalizations Prepare constructs (sense, antisense, double stranded) Transform plants and analyze resulting phenotype Publication of results 4a.List the single most significant research accomplishment during FY 2006. The single most significant accomplishment during FY2006 year aligns with Component VII - Weed Biology and Ecology of the National Program 304 on Crop Protection and Quarantine. It addresses problems on taxonomy and systematics. Canada thistle is a noxious weed in temperate regions of the United States (U.S.). Biological control strategies depend on understanding the genetic makeup of thistle population. Application of genetic marker technology led to the discovery that diversity of Canada thistle in the Northern Great Plains is much less than in Europe, which is consistent with its relatively recent introduction into the area. However, within populations, diversity is higher than one might expect for a vegetatively reproducing plant, indicating multiple introductions and/or maintenance of diversity through gene flow and sexual propagation. This information will be important to subsequent exploration for biological control agents in Eurasia. Short title: Population Genetics of Canada Thistle. 4b.List other significant research accomplishment(s), if any. Another significant accomplishment during FY2006 year aligns with Component VII - Weed Biology and Ecology of the National Program 304 on Crop Protection and Quarantine. It addresses problems on reproductive biology and seed bank dynamics. Rice is a model experimental plant and weedy rice is a problem in some crop production systems. USDA-ARS and North Dakota State University researchers discovered that many regions of the weedy rice genome that harbor dormancy genes also contain genes for other negative weedy traits like seed shattering, awn, pericarp color, and hull color. In addition, the dormancy genes are networked by epistasis and it is likely that network helps maintain intact adaptive haplotypes (genome areas containing a variety of linked genes for weedy traits) during the evolution of weeds. This research indicates the importance of dormancy for survival of weedy and wild species and suggests that the linked dormancy genes might not be a good resource for imparting resistance to pre-harvest sprouting. Short title: Seed Dormancy and Adaptation in Weeds. 4c.List significant activities that support special target populations. Significant Accomplishments/Activities that Support Special Target Populations: None. 4d.Progress report. Progress Report: None. 5.Describe the major accomplishments to date and their predicted or actual impact. A goal of the Weed Biology and Ecology component of National Program 304 on Crop Protection and Quarantine is to define and clarify factors that regulate vegetative reproduction, seed dormancy, and the population genetics of weeds. Leafy spurge is a noxious perennial weed and an experimental system for fundamental research on bud and seed dormancy and vegetative reproduction. Management of this weed depends on knowledge about its biology and reproduction. Scientists in Plant Science Research (USDA-ARS, Fargo, ND), in collaboration with the University of Illinois, developed an expressed sequence tag (EST) database containing approximately 19,000 unique sequences. The database delivers novel information on expressed genes and sets the stage for examining global patterns of gene expression in dormant and growing underground adventitious buds and dormant and non-dormant seeds of leafy spurge. Canada thistle is a noxious weed in temperate regions of the United States. Biological control strategies depend on understanding its population genetic structure. To aid in understanding the genetics of this noxious perennial weed, microsatellite (SSR) markers were developed. The microsatellites and other markers were tested on a limited sample of North American populations. Some markers detected polymorphic alleles; these are vital to examine the genetic structure of Canada thistle worldwide in an effort to discover new biological control agents. 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? We provided scientific data and information in oral and poster presentations on the growth and development of leafy spurge buds, genomic analysis, and dormancy in weeds seeds at a variety of regional, national, and international scientific meetings. We provided information to weed control associations members through participation in and presentation of talks at local and regional meetings. Expressed sequence tags have been submitted and are accessible to other investigators through the National Center for Biological Information web site. A major constraint to the adoption of technology is insufficient basic knowledge concerning the biology of weeds. 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). Gilbert, D. 2006. Energy-rich portfolio of new genome sequencing targets for Department of Energy Joint Genome Institute (DOE JGI). News release refers to Drs. Anderson and Horvath contribution to the cassava genome sequencing efforts underway by the DOE. Foley, M.E. 2005. Seed dormancy in leafy spurge. Leafy Spurge News 27 (1):2. Foley, M.E. 2005. ARS researchers focus on genetics of Canada thistle populations. North Dakota Noxious Weed Quarterly 2 (3):3-7. Foley, M.E. and J.V. Anderson. 2005. Leafy spurge - a modern day model weed. RRVARC Research News From the Valley October p. 4. Chao, W.S., Anderson, J.V., and Horvath, D.P. 2005. Carbohydrates affect dormancy and growth in underground buds of leafy spurge. Leafy Spurge News Vol. XXVII (1):9. Anderson, J.V. 2005. Leafy spurge - unwelcome pest to a modern day model plant. Leafy Spurge News Vol. XXVII (1):8. Review Publications Fuerst, E.P., Anderson, J.V., Morris, C.F. 2006. Delineating the role of polyphenol oxidase in the darkening of alkaline wheat noodles. J. Agric. Food Chem. 54:2378-2384. Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). [Abstract]. Weed Science Society of America Abstracts 46:30. Horvath, D.P., Anderson, J.V., Chao, W.S. 2006. Microarray analysis identifies genes involved in crown bud dormancy in leafy spurge (Euphorbia esula L.). [Abstract]. Weed Science Society of America Abstracts 46:92. Horvath, D.P., Anderson, J.V. 2006. Leafy spurge: Development and use of a model plant for genomic analysis of bud dormancy. [Abstract]. Plant & Animal Genome XIV Conference. p. 96. Fuerst, E.P., Anderson, J.V., Morris, C.F. 2006. Polyphenol oxidase in wheat grain: whole kernel and bran assays for total and soluble activity. Cereal Chem. 83(1):10-16. Slotta, T.A., Horvath, D.P., Foley, M.E. 2006. Relationships of weedy and native thistles (Cirsium) in the Northern Great Plains. [Abstract]. Weed Science Society of America Abstracts 46:33. Gu, X., Kianian, S., Foley, M.E. 2006. Towards positional cloning of genes for dormancy and its related adaptive traits from weedy rice. [Abstract] Plant & Animal Genome XIV Conference. P. 96. Slotta, T.A., Rothhouse, J., Horvath, D.P., Foley, M.E. 2006. Estimating genetic diversity of Canada thistle within North Dakota. [Abstract]. Weed Science Society of America Abstracts 46:30. Anderson, J.V., Foley, M.E., Kennedy, A.C., Fuerst, P.E. 2006. Characterization of wild oat (Avena fatua) polyphenol oxidase and its potential role in seed longevity. [Abstract]. Weed Science Society of America Abstracts 46:31. Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.-Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). Plant Molecular Biology. 61:329-344. Foley, M.E. 2006. Selection and service - experience and advice on competitive grants. [Abstract]. Weed Science Society of America Abstracts 46:49. Jia, Y., Gu, Y.Q., Horvath, D.P., Anderson, J.V., Chao, W.S. 2005. Identification of differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula L.). [Abstract]. Annual Meeting of the American Society of Plant Biologists. Final Program and Abstract Supplement, Poster 670, Page 225. Chao, W.S., Anderson, J.V., Horvath, D.P., Foley, M.E. 2005. Fundamental research in the fight against leafy spurge ¿ bud dormancy and growth. [Abstract]. Invasive Species Workshop. Page No. 35. Gu, X.-Y., Kianian, S. F., Foley, M.E. 2006. Dormancy genes from weedy rice respond divergently to seed development environments. Genetics. 172(2):1199-1211. Gu, X., Kianian, S., Foley, M.E. 2005. Genetics of seed dormancy in weedy rice [abstract]. 5th International Rice Genetics Symposium. p. 124. Horvath, D.P., Soto-Suárez, M., Chao, W.S., Jia, Y., Anderson, J.V. 2005. Transcriptome analysis of paradormancy release in root buds of leafy spurge (Euphorbia esula). Weed Science. 53(6):795-801. Gu, X., Kianian, S., Foley, M.E. 2006. Isolation of three dormancy QTLs as Mendelian factors in rice. Heredity. 96(1):93-99. Gu, X.-Y., Kianian, S.F., Foley, M.E. 2005. Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice. Genetics. 171:695-704. Horvath, D.P., Anderson, J.V., Chao, W.S. Microarray analysis identifies genes involved in crown bud dormancy in leafy spurge (Euphorbia esula L.). [Abstract]. Weed Science Society of America Abstracts 46:92. Boda Slotta, T.A., Foley, M.E., Horvath, D.P. 2005. Development of polymorphic markers for Cirsium arvense, Canada thistle, and their amplification in closely related taxa. Molecular Ecology Notes. (5)917-919. DOI:10.1111/j.1471-8286.2005.01112.x. Foley, M.E. 2005. What is afterripening?. [Abstract]. American Society of Horticultural Science. 40(4):956. Anderson, J.V., Gesch, R.W., Jia, Y., Chao, W.S., Horvath, D.P. 2005. Seasonal shifts in dormancy status, carbohydrate metabolism, and related gene expression in crown buds of leafy spurge. Plant, Cell and Environment. 28(12):1567-1578. Chao, W.S., Horvath, D.P., Anderson, J.V., Foley, M.E. 2005. Potential model weeds to study genomics, ecology, and physiology in the 21st century. Weed Science. 53(6):929-937.