Location: Crop Improvement and Genetics Research
Project Number: 2030-21000-024-000-D
Project Type: In-House Appropriated
Start Date: Apr 12, 2018
End Date: Apr 11, 2023
GrainGenes is an international, centralized crop database for peer-reviewed small grains data and information portal that serves the small grains research and breeding communities (wheat, barley, oat, and rye). The GrainGenes project ensures long-term data curation, accessibility, and sustainability so that small grains researchers can develop new, more nutritious, disease and pest resistant, high yielding cultivars. Objective 1: Accelerate small grains (wheat, oats, barley, and rye) trait analysis, germplasm analysis, genetic studies, and breeding by providing open access to small grains genome sequences, germplasm diversity information, trait mapping information, and phenotype data at GrainGenes. Goal 1A: Integrate small grains genome assemblies, pangenomes, and annotations into GrainGenes. Goal 1B: Integrate genetic, diversity, functional, and phenotypic data into GrainGenes with a genome-centric focus. Objective 2: Develop an infrastructure to curate, integrate, query, and visualize the genetic, genomic, and phenotypic relationships in small grains germplasm. Goal 2A: Develop methods and pipelines to link genetic, genomic, functional, and phenotypic information and to enhance genome-centric focus. Goal 2B: Implement web-based and computational tools to integrate and visualize genomic data linked with genetic, expression, functional, and diversity data. Goal 2C: Update database structure to align with community migration to a unified interface. Objective 3: Collaborate with database developers and plant researchers to develop improved methods and mechanisms for open, standardized data and knowledge exchange to enhance database utility and interoperability. Goal 3A: Collaborate with data and germplasm repositories and organizations to facilitate the curation, sharing, and linking of data. Goal 3B: Collaborate with community software development efforts to adopt database schema design and tool development. Objective 4: Provide community support and training for small grains researchers through workshops, webinars, and other outreach activities. Goal 4: Facilitate communication and information sharing among the small grains communities and GrainGenes to support research needs.
As a service project, the GrainGenes team does not perform hypothesis-driven research, but rather fulfills its long-term objectives by adding value to peer-reviewed data generated by others. It provides data curation, management and integration, long-term sustainability, and digital platforms as needed. Driven by stakeholder input, GrainGenes will maintain a central location for curated genomic, genetic, functional, and phenotypic data sets, downloadable in standardized formats, enhanced by intuitive query and visualization tools. Tutorial videos will be created to train small grains researchers on how to efficiently access and retrieve information from GrainGenes, and to show them different ways to reach and use multiple types of data to help develop better small grain crops. Objective 1: Our approach will be to (a) curate genomic, pangenomic, and diversity data into the GrainGenes database; (b) create gene model pages to aggregate and link genomic and genetic data at GrainGenes; (c) curate high-impact, peer-reviewed genetic, trait, phenotypic data into GrainGenes; (d) visualize more accurate genetic maps at GrainGenes; and (e) curate functional gene annotations. Objective 2: We will implement computational pipelines to (a) align genomic and genetic features between different genome assemblies; (b) assign gene function for small grain genomes; (c) facilitate data curation into the GrainGenes database; (d) visualize SNP data online; and (e) display pedigree information. In addition, we will implement and maintain genome browsers to display tracks for multiple genome assemblies and create a multi-species Basic Local Alignment Search Tool (BLAST) interface to allow users to align their sequences against small grains genome assemblies; in parallel, we will prepare for a new release of GrainGenes with an updated content management system. Objective 3: We will enhance links and data sharing between GrainGenes and the Triticeae Toolbox for small grains data, and collaborate with other data and germplasm repositories, groups, and organizations to facilitate the curation, sharing, and linking of data. Objective 4: We will (a) present GrainGenes tools and resources at conferences and site visits; (b) create training videos to teach our users how they can use GrainGenes more efficiently; (c) organize annual meetings between GrainGenes and the GrainGenes Liaison Committee to receive community feedback; and (d) maintain GrainGenes e-mail lists to facilitate communication among members of the small grains community.