Maize Data For Biology, Breeding, and Genomics: The PanMaize Gramene Database

Authors: Gladman, Nicholas

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/29/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Gramene database (http://www.gramene.org) is an integrated resource for comparative genome and functional analysis in plants. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species - including maize - thus enabling powerful comparisons across species. During this workshop, it will be demonstrated how to query the available data at Gramene through our versatile search interface to help users search, interpret and explore public data through gene-focused views of genomic context, phylogenetic trees, gene expression profiles, pathways, and cross-referenced resources. Molecular biologists, geneticists, and genomicists wiIl find value in the expansive phylogenetic trees and incorporated homology views and information for genes and gene families of interest. These features are also integrated with greater-detailed web pages that host easy-to-access sequence information, ontologies, and a genome browser application that contain permanent expression and variation information as well as the ability to load custom browser tracks to assist in users' genomic experimentation. One of the more powerful features of Gramene and its pan-genome subsites is the curation of natural and EMS-induced variant population data within certain species; users can query gene models for disruptive variants and identity which respective population and individual germplasm contain these single nucleotide polymorphisms or structural variants. Additionally, the search interface allows geneticists and breeders to query a broad swath of public data for available gene models within species, including QTLs, ontologies, and metabolic pathway affiliations. In recent years, Gramene has positioned itself as a pan-genome resource dedicated to the study of individual crop groups (e.g., maize, rice, sorghum, and grape). The Gramene Maize pan-genome site (https://maize-pangenome.gramene.org) hosts a total of 39 maize genomes including 3 assembly versions of B73, 25 NAM founders, Ab10, and 4 European genomes, plus 7 outgroups, and maize-centric gene trees, in addition to gene expression profiles and pathway associations for B73. All of these data are available for download via a FTP site and can be queried in bulk with multiple filters through the GrameneMart portal. Gramene is supported by USDA-ARS (1907-21000-030-00D) award.