Location: Corn Insects and Crop Genetics Research
Project Number: 5030-21000-072-000-D
Project Type: In-House Appropriated
Start Date: Apr 10, 2023
End Date: Apr 9, 2028
Objective:
Objective 1: Improve maize trait analysis (e.g., drought and cold tolerance, disease and pest resistance), germplasm development, genetic studies, and breeding through stewardship of maize genomes, pan genomes, genetic data, and phenotype data.
Goal 1.A: Bring in reference-quality genome assemblies of domesticated maize outgroups that include stress-resilient varieties and connect gene-model and genome-browser pan-gene relationships between these genomes and domesticated maize.
Goal 1.B: Represent and integrate maize diversity through hosting maize genomes, pan-genomes, graph information, and whole-genome sequencing data.
Objective 2: Identify and curate key datasets (e.g., 3-D protein structure, pangenome gene functions) that will serve to enhance maize functional genome annotation with an emphasis on the targeted curation of traits related to abiotic and biotic stress and climate change.
Goal 2.A: Integrate maize stress-response expression and trait data with MaizeGDB genomes and functional genome annotation tools.
Goal 2.B: Integrate 3-D gene model protein structures across maize genomes, compare them within a pan-gene framework, and create gene function predictions based on protein structure similarity.
Objective 3: Develop infrastructure to integrate, add value to, and visualize multi-omics data sets, enable comparative genomics, facilitate genome to phenome knowledge discovery, and provide analysis through artificial intelligence approaches and genomic discovery tools.
Goal 3.A: Provide comparative and pan-genome resources to understand diversity and organize genes and develop artificial intelligence approaches to facilitate exploration of the complex relationship between phenotype and genotype.
Objective 4: Provide community support services, build strategic partnerships, and provide database training and outreach activities for user communities and stakeholders.
Goal 4.A: Facilitate communication among maize researchers to support research community needs and create and leverage synergistic activities with other databases and plant research communities.
Approach:
The Maize Genetics and Genomics Database (MaizeGDB – http://www.maizegdb.org) is the model organism database for maize. MaizeGDB’s overall aim is to provide long-term storage, support, and stability to the maize research community’s data and to provide informatics services for access, integration, visualization, and knowledge discovery. The MaizeGDB website, database, and underlying resources allow plant researchers to understand basic plant biology, make genetic enhancement, facilitate breeding efforts, and translate those findings into products that increase crop quality and production. To accelerate research and breeding progress, generated data must be made freely and easily accessible. Curation of high-quality and high-impact datasets has been the foundation of the MaizeGDB project since its inception over 25 years ago. MaizeGDB serves as a two-way conduit for getting maize research data to and from our stakeholders. The maize research community uses data at MaizeGDB to facilitate their research, and in return, their published data gets curated at MaizeGDB. The information and data provided at MaizeGDB and facilitated through outreach has directly been used in research that has had broad commercial, social, and academic impacts. The MaizeGDB team will make accessible high-quality, actively curated and reliable genetic, genomic, and phenotypic description datasets. At the root of high-quality genome annotation lies well-supported assemblies and annotations. For this reason, we focus our efforts on benefitting researchers by developing a system to ensure long-term stewardship of both a representative reference genome sequence assembly with associated structural and functional annotations as well as additional reference-quality genomes that help represent the diversity of maize. In addition, we will enable researchers to access data in a customized and flexible manner by deploying tools that enable direct interaction with the MaizeGDB database. Continued efforts to engage in education, outreach, and organizational needs of the maize research community will involve the creation and deployment of video and one-on-one tutorials, updating maize Cooperators on developments of interest to the community, and supporting the information technology needs of the Maize Genetics Executive Committee and Annual Maize Genetics Conference Steering Committee.
