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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Research Project #425427

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

2017 Annual Report


Objectives
Over the next 5 years the project will focus on the following specific objectives as part of the long-term purpose to synthesize, display, and provide access to small grains genomics and genetics data for the research community and applied users. Objective 1: Annotate wheat, barley and oat whole genome sequences in collaboration with the crop research communities and integrate with genetic, physical, and trait maps. • Sub-objective 1.A. - Contribute to wheat genome annotations and incorporation of small grains annotations into GrainGenes. • Sub-objective 1.B. - Collaborate in integrating small grains genetic, physical, and trait maps. • Sub-objective 1.C. - Modifying GrainGenes with enhanced user tools in accessing genomic and mapping data. Objective 2: Integrate genotyping and phenotyping results from the Triticeae Coordinated Agricultural Project (T-CAP) including the T3 database, the National Small Grains Collection and GRIN database, and Gramene, to enhance support for trait analysis by association mapping and trait improvement by genomic selection. • Sub-objective 2.A. - Collaborate in developing common standards describing phenotypes and traits across species. • Sub-objective 2.B. - Convert data from GRIN, ARS Genotyping Laboratories, and the small grains Regional Field Nurseries to GrainGenes database formats. • Sub-objective 2.C. – Modify the GrainGenes schema to accommodate increased data volume and utilization. Objective 3: Collate, analyze, and present trait data from wheat, barley and oat communities to facilitate the genetic improvement of target traits and trait gene isolation. • Sub-objective 3.A. - Collate data on target traits. • Sub-objective 3.B. - Implement tools and interfaces for map displays. Objective 4: Maintain existing and develop new user community outreach. • Sub-objective 4.A. - Solicitation of user community input. • Sub-objective 4.B. - Training and education for use of GrainGenes resources. Objective 5: Facilitate the use of genomic and genetic data, information, and tools for germplasm improvement, thus empowering ARS scientists and partners to use a new generation of computational tools and resources [NP301, C2, PS2A].


Approach
1) Contribute to the annotation of whole genome sequences of wheat, barley, and oats in collaboration with the research community along with other national and international small grains genomics efforts. 2) Incorporation of genomic sequences and maps (genetic, physical, trait) into GrainGenes. To include integration of maps from multiple sources and related data sets already represented within GrainGenes. 3) Integrate genotyping and phenotyping data into GrainGenes. To include collaborating the GRIN, Gramene, and the Triticeae T-CAP project. 4) Modify the GrainGenes web site with enhanced user tools for accessing data, implement tools and interfaces for enhanced map displays, and modify the GrainGenes database schema to accommodate larger data sets. To include a complete rewrite and redeign of the GrainGenes web site and databases. 5) Enhanced research community outreach through regular solicitation of user community input, development of social medium tools for data access and user training, and develop formal training manuals and training manuals for GrainGenes users.


Progress Report
Objective 1: Genomic Assembly and Annotations Integration and Visualization: GrainGenes is communicating and working with genome assembly groups to be informed of developments and scheduling to bring assemblies and annotations of small grain crops and their wild relatives into GrainGenes. This year, we collaborated with the International Wild Emmer Wheat Genome Sequencing Consortium and visualized the sequence and annotations of wild emmer wheat (Zavitan) to place the first downloadable complete genome sequence and an associated genome browser on GrainGenes. Annotated releases of DNA sequence information from reference genomes for wheat, barley, and rye were placed into the JBrowse visualization tool. Objectives 1 and 2: Genetic, Genotypic, and Phenotypic Data Curation: Within the past year, several high-impact map sets have been added to the GrainGenes database. In addition, a multitude of other small grains papers were curated, thus contributing to the collection of genetic map, Quantitative Trait Loci, locus, gene, sequence, germplasm, and related data types that are stored in GrainGenes. Curation activities include: Marker Assisted Selection (MAS) Wheat data, National Small Grains Collection durum wheat stem rust data, durum wheat pre-harvest sprouting data, hexaploid oat consensus map markers, barley 9K iSelect single nucleotide polymorphism (SNP) data, tetraploid wheat consensus map markers, and wheat landrace consensus map. Objective 2: Enhanced Home Page for GrainGenes: The GrainGenes team has made extensive changes to the GrainGenes home page to improve content, ensure consistent visual communication, and provide means for user feedback and interaction. Changes include: adding links for data download, a GrainGenes mailing list, and tutorials. These changes increase the number of “Species Portals” and moves the links for the Annual Wheat Newsletter, Barley Genetics Newsletter and Oat Newsletter to the front page to give them more visibility; itemizes and date “GrainGenes Updates” entries, creating “Quick Links,” and putting a “Feedback” button on the header of each page to improve communication with our users to open direct communication channels with them, with a 24-hour response time to assure them their feedback is valued. GrainGenes has housed sequence databases for many projects; access to over sixty databases has been organized into a single navigable page. Objective 3: Genetic Maps and Visualization: Several genetic maps were uploaded onto GrainGenes including the hexaploid oat consensus map, tetraploid wheat consensus map, and wheat landrace consensus map. The hexaploid oat consensus map was created from 12 biparental recombinant inbred line (RIL) populations. A total of 19 parents were used in the crosses in order to represent the diversity of North American hexaploid oat germplasm. Over 16,000 markers were mapped, with 7,202 markers forming a framework consensus. Tetraploid Wheat Consensus Map was assembled using genotypic data of 13 tetraploid wheat mapping populations including 1928 lines (1773 RILS and 155 doubled haploids). Eight elite Triticum (T.) durum x T. durum populations, three T. durum x T. dicoccum populations, and two T. durum x T. dicoccoides populations were used to construct the map. A total of 29,719 markers are in the consensus map available in GrainGenes (including 26,626 SNPs and 791 single sequence repeats), half of which were present in at least two component maps. The consensus map and thirteen biparental component maps are also available to view in CMap. Wheat Landrace Consensus Map, viewable in CMap, contains 21 linkage groups corresponding to the chromosomes of hexaploid wheat and includes over 2,400 genetic loci. A total of 85545 SNP markers from a 600,000-member genotyping array were positioned into the reference scaffolds under development for the rye genome. In our five-year plan, we had proposed to implement GBrowse Linkage Disequilibrium viewer and Haploview connection to show genetic marker relationships. Our interactions with our users showed they would be better served by using the CMap genetic map visualization tool and enriched genetic marker pages on GrainGenes to accomplish the same goal. We have implemented these modifications. Objective 4: Public Outreach: We created an area on our front page for updates to increase the reach of GrainGenes updates, attract new users and inform them about tools we offer, and broadcast new data curated at GrainGenes. Job postings and scientific articles of interest to the small grains community were shared by GrainGenes. Such public outreach efforts help GrainGenes to continue to be a hub for small grains communication and a knowledge resource. Training: Several new approaches have been implemented to provide training on the use of the GrainGenes database and its tools. A GrainGenes YouTube Channel was created (https://wheat.pw.usda.gov/GG3/tutorials). So far, three training videos have been posted; navigating the GrainGenes homepage, a database browser demo, and a demo on obtaining DNA sequences from markers. PDF slides converted from the video tutorials are also offered, as well as slides on how to use the Genome Browser, CMap, and the Quick Queries tools. In addition to serving as a centralized repository for small grains data, GrainGenes continues to provide excellent service to the small grains research communities by providing a digital platform for other repositories and community newsletters. The Triticeae Toolbox (T3), an ARS project previously funded by the Triticeae Coordinated Agricultural Project (CAP) and continuing under the WheatCAP project, which hosts genotypic, phenotypic, and pedigree data for small grains, and provides researchers a suite of web-based tools to analyze raw data (https://triticeaetoolbox.org); USDA-ARS Small Grains Genotyping Labs, the website describing the four ARS genotyping labs in the U.S. and used for information, links, and data transfer to their users through the FTP server (https://wheat.pw.usda.gov/GenotypingLabs); and, Oat Global, a strategy forum driven by the leaders of the public and private oat community at large. This year, GrainGenes successfully re-formed its international Liaison Committee consisting of five wheat, oat and barley breeders and molecular biologists. The GrainGenes team prepared a status report, and organized a web meeting that included committee members and observers from USDA National Institute of Food and Agriculture, Agriculture and Agri-Food Canada, and Oat Global. The Liaison Committee chair prepared a report that provides strategic guidance from the stakeholders for the 2018-2023 five-year GrainGenes project plan currently being drafted and reviewed.


Accomplishments


Review Publications
Walsh, J., Schaeffer, M.L., Zhang, P., Rhee, S., Dickerson, J., Sen, T.Z. 2016. The quality of metabolic pathway resources depends on initial enzymatic function assignments and level of manual curation: A case for maize. BMC Systems Biology. 10:129.
Sen, T.Z., Braun, B., Schott, D., Portwood II, J.L., Schaeffer, M.L., Harper, E.C., Cannon, E.K., Andorf, C.M. 2017. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bax031.
Wang, Y., Xu, L., Gu, Y.Q., Coleman-Derr, D.A. 2016. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics. 32(22):3469-3470. doi:10.1093/bioinformatics/btw507.