Location: Genomics and Gene Discovery
2010 Annual Report
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.
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.