Location: Crop Improvement and Genetics Research
2023 Annual Report
Objectives
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, germplasm, genetics and genomics, and breeding data analysis and information by curating small grains genome sequences, germplasm diversity information, pangenomes, trait mapping information, and phenotype data into GrainGenes. Sub-objective 1.A: Integrate small grains genome assemblies, pangenomes, and annotations into GrainGenes. Sub-objective 1.B: Integrate genetic, diversity, functional, and phenotypic data into GrainGenes with a pangenome-centric focus. Objective 2: Develop computational and visualization tools to curate, integrate, and query the genetic, genomic, and phenotypic relationships in small grains germplasm, and deploy machine learning and artificial intelligence approaches to enhance functional annotations and discover biological interactions. Sub-objective 2.A: Develop methods and pipelines to link genetic, genomic, functional, and phenotypic information and to enhance pangenome-centric focus. Sub-objective 2.B: Implement web-based and computational tools to integrate and visualize genomic data linked with genetic, expression, functional, and diversity data. 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. Sub-objective 3.A: Collaborate with data and germplasm repositories and organizations to facilitate the curation, sharing, and linking of data. Objective 4: Provide community support and training for small grains researchers through workshops, webinars, and other outreach activities.
Sub-objective 4.A: Facilitate communication and information sharing among the small grain communities and GrainGenes to support research needs.
Approach
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. Objective 1: Our approach will be to (a) curate genomic, pangenomic, and diversity data into GrainGenes database; (b) create new genome browsers, 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 and structural annotations (gene ontology, enzymatic functions, protein structure). For Objective 2: we will (a) create better search indexing and linking for data discovery at GrainGenes; (b) implement computational pipelines to link and align genomic and genetic features between different genome assemblies and GrainGenes pages; (c) implement computational pipelines to link and align genomic and genetic features between different genome assemblies and GrainGenes pages; (d) implement pipelines to facilitate data curation into the GrainGenes database; (e) implement and maintain genome browsers that allow comparative viewing using JBrowse2; (f) implement and maintain genome browsers to display tracks for multiple genome assemblies; and (g) create a BLAST plug-in that can be easily installed in JBrowse instances to allow users to align their sequences against small grains genome assemblies from JBrowse. For Objective 3: we will (a) enhance links and data sharing between GrainGenes and the Triticeae Toolbox for small grains data; (b) collaborate with other data and germplasm repositories, groups and organizations to facilitate the curation, sharing, and linking of data; (c) improve data interoperability and data sharing with WheatIS; (d) coordinate with ARS databases MaizeGDB and The Triticeae Toolbox to establish distributed infrastructure to serve users faster and more reliably; and (e) actively participate in the AgBioData Consortium. For Objective 4: we will (a) present GrainGenes tools and resources in conferences and site visits; (b) create training videos to teach users how they can use GrainGenes more efficiently; (c) organize annual meetings between GrainGenes and the GrainGenes Liaison Committee to receive community feedback; (d) maintain GrainGenes and OatMail e-mail lists to help the communication among the members of small grain communities; and (e) maintain and provide digital platforms to small grain researchers as needed.
Progress Report
This report documents progress for project 2030-21000-056-000D, GrainGenes - A Global Data Repository for Small Grains, which started April 2023 and continues research from project 2030-21000-024-000D, GrainGenes: Enabling Data Access and Sustainability for Small Grains Researchers.
Accomplishments
