MaizeGDB 2018: The maize multi-genome genetics and genomics database

Authors: Portwood, John; WOODHOUSE, MARGARET - Iowa State University; Cannon, Ethalinda; GARDINER, JACK - University Of Missouri; Harper, Elisabeth; Schaeffer, Mary; WALSH, JESSE - Oak Ridge Institute For Science And Education (ORISE); Sen, Taner; CHO, KYOUNG TAK - Iowa State University; BRAUN, BREMEN - Oak Ridge Institute For Science And Education (ORISE); DIETZE, MIRANDA - Iowa State University; DUNFEE, BRITTNEY - Iowa State University; ELSIK, CHRISTINE - Iowa State University; MANCHANDA, NANCY - Iowa State University; COE, ED - Retired Non ARS Employee; Sachs, Martin; Stinard, Philip; Tolbert, Joshua; Zimmerman, Shane; Andorf, Carson

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2018
Publication Date: 11/8/2018
Citation: Portwood II, J.L., Woodhouse, M.R., Cannon, E.K., Gardiner, J., Harper, E.C., Schaeffer, M.L., Walsh, J., Sen, T.Z., Cho, K., Braun, B.L., Dietze, M., Dunfee, B., Elsik, C.G., Manchanda, N., Coe, E., Sachs, M.M., Stinard, P.S., Tolbert, J.P., Zimmerman, S.A., Andorf, C.M. 2018. MaizeGDB 2018: The maize multi-genome genetics and genomics database. Nucleic Acids Research. 47(D1):D1146-D1154. https://doi.org/10.1093/nar/gky1046.
DOI: https://doi.org/10.1093/nar/gky1046

Interpretive Summary: MaizeGDB, the USDA-ARS maize genetics and genomics database, is a highly curated, community -oriented informatics service to researchers focused on the crop plant and model organism Zea mays. MaizeGDB facilitates maize research by curating and maintaining a database that serves as the central repository for the maize community. With the availability of more reference quality genomes for maize, MaizeGDB has become more sequence-centric, while still maintaining traditional maize genetics datasets. The research focus of the maize community has continued to evolve, making it necessary to continually redefine data access and data analysis tools. In this poster we present an overview of new services and data types provided by MaizeGDB. New genome sequences are incorporated into MaizeGDB and made accessible through the annotation/assembly pages, BLAST databases, and genome browsers. MaizeGDB is responsible for stewardship of the maize representative genome assembly, including the improvement of associations between the B73 gene models and gene models for all other assemblies. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data, download and compare gene expression data, visualize pedigree data, link genes with phenotype images, and enable flexible user specified queries. MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible.

Technical Abstract: Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at http://www.maizegdb.org.