Progress 05/14/08 to 05/13/13
Outputs
Progress Report 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. 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). This is the final report for this project which terminated on 05/13/2013 and was replaced by Project No. 5325-21000-021-00D, "Small Grains Database and Bioinformatics Resources", which started on 05/14/2013. Important discoveries were achieved during the course of this project, including the following: GrainGenes is a database for small grains that houses DNA marker, linkage mapping, phenotypic, and QTL data for the Triticeae and Avena. The GrainGenes project has maintained associations with current research endeavors directed at small grains improvement. GrainGenes has provided hosting of the servers, systems, software, network, and security support needed for the database support of research efforts in these crops. The breadth of support extends out to genetic mapping and sequencing efforts for wheat progenitor studies. Collaborations with programming developers has led to improved tool development. Enhancements have been made to streamline data export/import functions and provide specialized curatorial tools, and display of genotyping data. Other efforts have extended support to maintain the Triticeae Toolbox and the US Wheat and Barley Scab Initiative Projects, both USDA-sponsored. The GrainGenes staff has participated in enhancements to the Triticeae Toolbox which serves most small grains, connecting genotyping and trait data on core collections. This project has provided an accessible platform for biologists with average computer experience to pursue marker assisted selection and association mapping projects with large public datasets. It is the first publicly accessible database software package with demonstrated capability to manage large quantities of both genotype and phenotype data for crop species. Extensive datasets have been added to the barley section of the Toolbox and are now available for utilization by the public. Initially empty, the wheat section of the Toolbox now has data on over 4000 wheat lines, including 25 million genotyping data points. Oat research has been supported through collaborations that provided bioinformatics support for the first collection of oat expressed sequence tags that enabled comparative mapping of oat with other grasses. Further collaborative work resulted in the creation of linkage maps for this hexaploid species that resolved oat�s 21 chromosomes. This work included development of single nucleotide polymorphism marker resources that now allow the analysis of phenotypic data for marker assisted selection approaches to proceed. The project has also supported forage breeders by helping to develop comparative maps in basin wild rye, an important western forage species. The US Wheat and Barley Scab Initiative has been supported through the development of a dedicated web resource (www.scabusa.org) that provides tools such as the �FHB Alerts� service which is a messaging system to provide real-time updates to Fusarium head blight updates and field reports. Continual improvements to this site by project staff have provided web-forms, credit processing, database registration, and for organization of annual meetings. Accomplishments 01 Integrating new sequence analysis with physical map development. Extensive sequencing on-site has moved moved research ever closer toward a sequenced and organized wheat genome. Improved mapping methods have helped to build a general physical map for the Aegilops tauschii D genome combining technologies comparing BACs, germplasm, and reference sequences. A collection of tools is now available to detail genome annotation and predict genome content. Radiation Hybrid (RH) maps add fine structure resolution; however, still require mapping the markers. A potential improvement was tested using high-throughput genotype-by- sequencing methods using RH mutant lines and leveraging array markers to gauge presence/absence (in place of SNPs). The method refines assigning scored data to assist mapping and may have utility for other complex genome species. All these tools contribute toward creating a working model to decipher the wheat genome. 02 Triticeae Phenotyping and Genotyping. Extensive modifications to the Triticeae (T3) database have added more utility in being able to compare breeding lines with trait data. The interface now makes good use of statistical programs which allow select data selection and analysis. The Triticeae Coordinated Agricultural Project (TCAP) projects also yielded an increase in datasets for wheat and barley including many National Small Grains Collection datasets; over 25 million genotyping data points have been collected each for wheat and barley representing 390 thousand phenotypes scores. Many of these studies may have utility in germplasm improvement. 03 Improving Upon Database Approach. A shift in database efforts was developed to make more use of Generic Model Organism Database (GMOD) bioinformatics tools based on a content management system. The shift provides a modular form of the developing a database allowing a faster development time for new modules designed for data analysis. Many features already exist and an effort to move forward will also include testing this as a platform for the GrainGenes database. GrainGenes is currently working to best integrate new small grains reference genomes for data analysis. This serves as an adjustment toward new information technology capabilities. 04 Organizing Genome Data for Oat. A centralized resource was created for the Collaborative Oat Research Enterprise (CORE) effort, highlighting molecular markers which outline the first representation of twenty-one chromosomes for hexaploid oat. A shift in database efforts was developed to make more use of Generic Model Organism Database (GMOD) bioinformatics tools based on a content management system. The shift provides a modular form of the developing database allowing a faster development time for new modules designed for data analysis. Many features already exist and an effort to move forward will also include testing this as a platform for the GrainGenes database. GrainGenes is currently working to best integrate new small grains reference genomes for data analysis.
Impacts
(N/A)
Publications
- Hastie, A., Dong, L., Luo, M., Huo, N., Gu, Y.Q., Xiao, M. 2013. Rapid genome mapping in nano channel array for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One. 8:e55864.
- Brenchley, R., Spannagl, M., Pfeifer, M., Baker, G., D'Amore, R., Gu, Y.Q., Luo, M., Huo, N., Anderson, O.D., Dvorak, J., Hall, A., Mayer, K., Edward, K.J., Hall, N. 2012. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing. Nature. 491:705-710.
- Kumar, A., Simons, K., Iqbal, M.J., Jimenez, M., Bassi, F.M., Ghavami, F., Al, A., Wang, Y., Luo, M., Gu, Y.Q., Denton, A., Xu, S.S., Dvorak, J., Kianian, P., Kianian, S.F. 2012. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii. Biomed Central (BMC) Genomics. 13:597.
- Wang, Y., You, F., Lazo, G.R., Luo, M., Thilmony, R.L., Gordon, S.P., Gu, Y.Q., Kianian, S. 2012. PIECE: A database for plant gene structure comparison and evolution. Nucleic Acids Research. D1159-D1166.
- Oliver, R.E., Tinker, N.A., Lazo, G.R., Chao, S., Jellen, E.N., Carson, M. L., Rines, H.W., Obert, D., Lutz, J.D., Shackelford, I., Korol, A.B., Wight, C., Gardner, K.M., Hattori, J., Beattie, A., Bjornstad, A., Bonman, J.M., Jannink, J., Mitchell Fetch, J.W., Harrison, S., Howarth, C.J., Ibrahim, A., Kolb, F.L., McMullen, M.S., Murphy, J.P., Ohm, H., Rossnagel, B.G., Yan, W., Miclaus, K.J., Hiller, J., Maughan, P.J., Redman-Hulse, R.R. , Anderson, J.M., Islamovic, E., Jackson, E.W. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One. 8:e58068.
- Bragg, J., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., Vogel, J.P. 2012. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection. PLoS One. 7(9):e41916. doi:10.1371/journal.pone.0041916.
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. 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. Accomplishments 01 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 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 states are ARS researchers, and it is potentially adaptable to other U.S crops as well.
Impacts
(N/A)
Publications
- 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.
- 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.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. With wheat genome sequencing increasing on the research front, curator processing of small grains research information allowed genetic and physical maps to be integrated into GrainGenes. From the wheat capacity project (CAP), molecular markers yielded maps related to phenotypic traits for disease resistance and grain quality, allowing GrainGenes to document its progress before it initiates a new phase of research associated with the newly formed Triticeae CAP. Similarly, integrated maps of barley were placed on GrainGenes from population studies. Final maps summarizing the barley CAP were also loaded as it has now joined the efforts supporting the Triticeae CAP project. Collaborations with the oat community yielded the first major advance in oat expressed sequence tags and assisted in the design of single- nucleotide-polymorphism (SNP) probes for the differenting oat germplasm. Probe design and screening serves as first steps in establishing a marker- assisted selection system for association mapping studies to improve key traits in oat; mapping studies are now underway in North America and are expanding to be a global effort. Collaborations to generate maps with groups working on forage grasses were also initiated, and preliminary maps are in preparation before publication. Comparative maps allowed collaborators 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. Major progress was made toward transferring The Hordeum Toolbox (THT) to the GrainGenes project as the barley CAP closed. The importance of using molecular markers to track phenotypic and genotypic data for agronomic and plant quality traits in breeding lines was a capital point in this study, and is being carried forward with the combined wheat and barley CAP projects know as the Triticeae CAP (TCAP). Collaborations with programming developers continues to improve data tool development. Enhancements have been made toward importing/exporting data, specialized curation tools, and display of genotyping data. Software improvements have occurred under the GrainGenes, THT, and T3 databases. The feasibility for using expanded genome and data software were also tested as a platform to view data in a different perspective. The website for the US Wheat and Barley Scab Initiative, www.scabusa.org, was enhanced with additional features and redesign. The �FHB Alerts� regions were reconfigured and an administrative interface was created to manage the FHB Alert subscriptions; these updates were advertised by poster at a recent barley conference. Web site forms and server-side processing scripts used for authorized credit processing, database registration and procedure ordering, a tool vital towards organizing project activities, was updated. The USWBSI server was updated, and the scabsmart.org web-site was integrated into this resource. Accomplishments 01 Integrating genetic and physical maps with developing genomic sequences. The combination of additional genome sequence resources and the improvements in computer technology have led to improved ways for the researcher to access information. Efficient access to maps of small grai crop genomes is critical to grain crop improvement. Several species of t Triticeae, mainly wheat and barley, and some of the related species are actively being sequenced and studied. Progress made within the GrainGene project have aided in providing data in a user-friendly way. GrainGenes continues to serve the research community in providing resources to deposit and analyze data, and to develop a platform to provide the data the public. A wealth of genetic maps and accompanying data are currently available for wheat, barley, oat and grass species and for forming the foundation for discoveries for the GrainGenes-associated species.
Impacts
(N/A)
Publications
- You, F., Huo, N., Deal, K., Gu, Y.Q., Luo, M., Mcguire, P., Dvorak, J., Anderson, O.D. 2011. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. Biomed Central (BMC) Genomics. 12:59.
- Oliver, R.E., Lazo, G.R., Lutz, J.D., Rubenfield, M.J., Tinker, N.A., Anderson, J.M., Wisniewski-Morehead, N.H., Adhikary, D., Jellen, E.N., Maughan, P.J., Brown Guedira, G.L., Chao, S., Beattie, A.D., Carson, M.L., Rines, H.W., Obert, D.E., Bonman, J.M., Jackson, E.W. 2011. Model SNP development based on the complex oat genome using high-throughput 454 sequencing technology. Biomed Central (BMC) Genomics. 12:77.
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report 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. 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). 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. Accomplishments 01 Integrating genetic and physical maps with developing genomic sequences. Increasing numbers of small grains genomic and expressed sequence tag (E sequences will be maximally utilized only when integrated with availabl genetic and physical maps of these species. As genomic sequencing and physical mapping of Triticeae scale up, there is a need to integrate thi 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 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 no includes a short list of the most important maps which will aid users wh are not familiar with the full range of maps available.
Impacts
(N/A)
Publications
- 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.
- 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.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report 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. 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). Significant Activities that Support Special Target Populations The entire website for the US Wheat and Barley Scab Initiative was converted into a module style PHP administrated website, adding efficiency toward adding updates to the website. A system for online submission of research proposals also allows submitters and reviewers to track proposals through the approval process with secure access to the files they have access to. Curator processing of small grains research information allowed genetic and physical maps to be integrated into the GrainGenes resource. For barley, diversity SNP consensus maps for pilot and extended projects, and two additional population studies were added. For wheat, new marker technologies including DArT, SSR, and MAS (expressed STSs/SSRs) have added new maps, including one from the wheat CAP project, and an updated map from the NSF-funded wheat physical mapping project. Additional maps included a rye consensus map and a 21 linkage group map for hexaploid oat. Assistance was also provided to Brachypodium and switchgrass research projects to build development maps which will be incorporated into future database resources. Advancements were made toward improving administrative interfaces for the database and software tools. Recently a web-based interface was developed to provide a database conversion and administration tool for the Comparative Map Viewer (CMap, http://wheat.pw.usda.gov/cmap) data, a critical interface for viewing map data. Most of this data is extracted from the GrainGenes database, with the rest provided by curator input. This interface greatly streamlines a routine operation in database maintenance. Weekly updates of the GrainGenes database have been facilitated by modifications applied to the "ggupdate" processing protocol to streamline database administration steps. Technology Transfer Number of Web Sites managed: 7
Impacts
(N/A)
Publications
- Anderson, O.D., Gu, Y.Q., Kong, K., Lazo, G.R., Wu, J. 2009. Structure of the omega-gliadin gene family. Functional and Integrative Genomics. 9: 397-410.
- Matthews, D.E., Lazo, G.R., Anderson, O.D. 2009. Plant and Crop Databases. In: Somers, D.J., Langridge, P., and Gustafson, J.P., editors. Plant Genomics: Methods and Protocols. New York, NY: Humana Press. P. 243-262.
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report 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. 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). Significant Activities that Support Special Target Populations The project has developed a system for online submission of research proposals to be considered for funding by the US Wheat and Barley Scab Initiative. The system provides submitters and reviewers with secure access to the files they have access to, and tracks proposals through the approval process. The Genomic Diversity and Phenotype Connection (GDPC, www.maizegenetics. net/gdpc) can connect to and extract data from several disparate relational databases using different schemas. A GDPC adapter has now been built that works with the Wheat CAP database described above, allowing the user to retrieve SSR and SNP molecular allele data for a desired set of germplasm accessions and markers. Recently a web-based interface has been developed to provide a database conversion and administration tool for the Comparative Map Viewer (CMap, http://rye.pw.usda.gov/cmap) data. Most of this data is extracted from the GrainGenes database, with the rest provided by curator input. This interface greatly streamlines a routine operation in database maintenance. NP 301 Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statements A: Genome Database Stewardship and Informatics Tool Development, B: Structural Comparison and Analysis of Crop Genomes, and C: Genetic Analyses and Mapping of Important Traits. Technology Transfer Number of New Patent Applications filed: 1 Number of Web Sites managed: 6
Impacts
(N/A)
Publications
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