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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS
2010 Annual Report


1a.Objectives (from AD-416)
1) Integrate small grains genetic and genomic data within the GrainGenes database and link to relevant external databases;.
2)Develop software and interfaces to enhance utility for researchers.


1b.Approach (from AD-416)
1) Extend development and curation within the GrainGenes project to include a suite of integrated databases and web-based resources for wheat, barley, rye, triticale, and oats research and improvement. .
2)Carry out projects involving direct and collaborative support to those aspects of small grains genomics/genetics/molecular biology relevant to crop improvement..
3)Target user needs through meetings, personal interactions, and electronic communication with the small grains research community. .
4)Develop improved displays and tools needed for improvement of the GrainGenes database and its inter-connections to other bioinformatics projects. Previously 5325-21000-007-00D (7/03). Replacing 5325-21000-010-00D (04/08). BSL-1 (4/08).


3.Progress Report
Curator processing of small grains research information allowed genetic and physical maps to be integrated into GrainGenes. For barley, three major genetic maps were added to the database, one with 3000 markers, one with 4700, and one with 7000, primarily SNPs and SSRs. For wheat, maps and QTLs have been added for five mapping populations from the USDA-supported Wheat CAP project. Wheat SNPs from an NSF-supported SNP discovery project were added to the GrainGenes database. These 2500 SNPs are the largest set of highly polymorphic, easily scored molecular markers available for mapping traits in wheat. The Hordeum Toolbox database, http://hordeumtoolbox.org, developed at Iowa State University, was moved to the GrainGenes server at Albany, CA for long-term availability. This database allows barley breeders from the USDA NIFA Barley CAP project to analyze genotypic and phenotypic data from elite breeding lines by association analysis to identify molecular markers for agronomic, quality and disease resistance traits.

An ARS research scientist served as key bioinformatics person for the National Institute of Food and Agriculture (NIFA) Agricultural Food Research Initiative (AFRI) [in-part funded] Collaborative Oat Research Enterprise (CORE) project, yielding the first major advance in oat expressed sequence tags, over 500,000 ESTs and assisted in the design of single-nucleotide-polymorphism (SNP) probes for the differentiation of twenty oat germplasm lines. Probe design and screening serves as first steps in establishing a marker-assisted selection system to genotype oat breeding lines for association mapping studies to improve key traits in oat; mapping studies are now underway as a North American project and currently expanding to be a global effort.

An ARS research scientist used bioinformatics tools to leverage the information contained within the GrainGenes database and used recent genome sequence data to help construct comparative maps for a diverse collection of grass species, in one case completing a 21 chromosome hexaploid map for oat and in another helping to build comparative maps of forage grass species to those of closely related species and sequenced genomes of Brachypodium, rice, sorghum and maize. Findings provided by observing comparative maps allow the researcher to focus on key traits and attributes that can be applied to a wide range of studies including crop improvement, bioenergy, and range ecology; these and other findings may lead us to a better understanding of the diversity in form and function of the grass species.

The website for the US Wheat and Barley Scab Initiative, www.scabusa.org, was enhanced with additional features and a more attractive appearance. A system was set up to send “FHB alerts”, real-time disease updates and field reports, to users' cell phones. The credit card processing system was changed to a new vendor, Authorize.net, to meet the requirements for information security. New modules were added to the website for security and blocking spam. The software used to operate the website, Xoops, was upgraded to the latest version.


4.Accomplishments
1. Integrating genetic and physical maps with developing genomic sequences. Increasing numbers of small grains genomic and expressed sequence tag (EST) sequences will be maximally utilized only when integrated with available genetic and physical maps of these species. As genomic sequencing and physical mapping of Triticeae scale up, there is a need to integrate this information with grass model systems, Brachypodium and rice. ARS scientists in Albany, CA refined and solidified protocols for collecting map data and displaying it in a user-friendly online format that enables comparing maps with each other. Information from model grass species is being staged using computational tools so that comparative views between related grass species are available. The physical map of the wheat relative Aegilops tauschii was integrated with other wheat genetic maps in the GrainGenes resource by use of common markers. A summary table of the wheat maps, and maps of other related grass species is available, and now includes a short list of the most important maps which will aid users who are not familiar with the full range of maps available.


Review Publications
Michalak, M.K., Ghavami, F., Lazo, G.R., Gu, Y.Q., Kianian, S.F. 2009. Evolutionary relationship of nuclear genes encoding mitochondrial proteins across grasses. Maydica. 54: 471-483

Close, T.J., Bhat, P., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J., Wanamaker, S., Bozdag, S., Roose, M., Moscou, M., Chao, S., Varshney, R., Szucs, P., Sato, K., Hayes, P., Matthews, D.E., Kleinhofs, A., Muehlbauer, G., Deyoung, J., Marshall, D.F., Madishetty, K., Fenton, R.D., Condamine, P., Graner, A., Waugh, R. 2009. Development and Implementation of High-Throughput SNP Genotyping in Barley. Biomed Central (BMC) Genomics. 10:582.

Luo, M.C., Deal, K.R., Akhunov, E.D., Akhunova, A.R., Anderson, O.D., Anderson, J.A., Blake, N., Clegg, M.T., Coleman-Derr, D., Conley, E.E., Crossman, C.C., Dubcovsky, J., Gill, B.S., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Lundy, K.E., Ma, Y., Matthews, D.E., Mcguire, P.E., Morrell, P.L., Nicolet, C.M., Qualset, C.O., Renfro, J., Tabano, D., Talbert, L.E., Tian, A., Toleno, D.M., Warburton, M.L., You, F.M., Zhang, W.J., Dvorak, J. 2009. Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae. Proceedings of the National Academy of Sciences. 106:15780-15785.

Last Modified: 11/27/2014
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