Location: Genomics and Gene Discovery
2012 Annual Report
The Hordeum Toolbox (THT, http://hordeumtoolbox.org) software and database were finalized and archived on the GrainGenes server in Albany, California. Aside from a few bug fixes, the software was frozen as it was at the termination of the Barley CAP project itself, as a permanent record of the accomplishments of that project. The entire database was transferred to The Triticeae Toolbox (T3, http://triticeaetoolbox.org), the database of the successor project the Triticeae CAP.
The Triticeae Toolbox (T3) databases for wheat and barley were created and brought online using the GrainGenes server in Albany, California, at address http://triticeaetoolbox.org. Software enhancements have been added for the curator to load data, and for users to analyze it and to download it. The Triticeae CAP curator has begun loading both phenotype and genotype (molecular marker allele) data for both species. The wheat database, which was initially empty, now has both kinds of data for over 4000 wheat lines, including 25 million genotyping data points. The barley database has grown similarly, in addition to inheriting all the data from the predecessor Barley CAP project. A new, more powerful server machine purchased by the Triticeae CAP as part of the collaboration was installed in the same server room as the GrainGenes server, and all T3 services were moved to it.
Using sequence data from twenty oat germplasm lines, a collection of single nucleotide polymorphism (SNP) markers has been prepared. Based on two successful rounds of probe design, chip creation, and screening on the Illumina GoldenGate assay system, another set of probes was created for the Illumina Infinium assay system. The latest chip design is a culmination of marker data derived from DArT, Roche 454, and Illumina sequence data. Enhancements were made to the SNP selection protocol. These SNPs have been used as the markers for six mapping populations, and a consensus map comprising 21 linkage groups representing the 21 chromosomes of hexaploid oat has been generated.
Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.
Ponciano, G.P., Mcmahan, C.M., Wengshuang, X., Lazo, G.R., Coffelt, T.A., Collins-Silva, J., Nural-Taban, A., Golley, M., Shintani, D.K., Whalen, M.C. (2012). Transcriptome and gene expression analysis in cold-acclimated guayule (Parthenium argentatum)rubber-producing tissue. Phytochemistry. 79:57-66.
Larson, S.R., Kishii, M., Tsujimoto, H., Qi, L., Chen, P., Lazo, G.R., Jensen, K.B., Wang, R. 2011. Leymus EST linkage maps identify 4NsL-5NsL reciprocal translocation, wheat-Leymus chromosome introgressions, and functionally important gene loci. Theor Appl Genet. 124:189-206.