Page Banner

United States Department of Agriculture

Agricultural Research Service

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

Location: Genomics and Gene Discovery

2012 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.


3.Progress Report:
The GrainGenes project continues to collect appropriate datasets from cooperating research projects to provide ongoing public access to the products of those projects' efforts. A current major cooperator is the NSF-sponsored wheat D-genome physical mapping and sequencing project, http://avena.pw.usda.gov/wheatD/. As another part of this cooperation besides data exchange, the project's website is running on one of GrainGenes's server machines. Other projects for which GrainGenes provides all of the server, system, software, network, and security support include The Triticeae Toolbox (T3) and the US Wheat and Barley Scab Initiative (USWBSI) projects, both USDA-sponsored. Major infrastructure enhancements improving service for all hosted projects as well as the GrainGenes Database itself included installation of a new hardware firewall and an iKVM (KVM over IP, a device allowing console-level access to multiple server machines remotely). The USWBSI site http://scabusa.org was completely re-programmed to convert from the Perl language to PHP, providing a friendlier interface, more features, and improved maintainability.

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.


4.Accomplishments
1. A Breeder's Database. With the advent of inexpensive genotyping technologies, plant breeders now have a critical need and opportunity to combine molecular data about their breeding germplasm with their accumulated phenotypic information. Doing so will allow them to leverage computational methods such as association mapping and genomic selection to accelerate development of improved cultivars. The Triticeae Toolbox is currently the only publicly accessible database software package with demonstrated capability to manage large quantities of both genotype and phenotype data for crop species. It is being used by the Triticeae CAP (Capacity Building Project) project, many of whose 56 participants from 21 states are ARS researchers, and it is potentially adaptable to other U.S. crops as well.


Review Publications
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.

Last Modified: 10/1/2014
Footer Content Back to Top of Page