Enhanced pan-genomic resources at the maize genetics and genomics database

Authors: Cannon, Ethalinda; Portwood, John; HAYFORD, RITA - Orise Fellow; HAYLEY, OLIVIA - Orise Fellow; GARDINER, JACK - University Of Missouri; Andorf, Carson; Woodhouse, Margaret

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/13/2024
Publication Date: 4/5/2024
Citation: Cannon, E.K., Portwood II, J.L., Hayford, R.K., Hayley, O.C., Gardiner, J.M., Andorf, C.M., Woodhouse, M.R. 2024. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics. 227(1). https://doi.org/10.1093/genetics/iyae036.
DOI: https://doi.org/10.1093/genetics/iyae036

Interpretive Summary: Maize, a crucial global crop, exhibits tremendous genetic variety, making a single reference genome insufficient for comprehensive research and application. Researchers at the Maize Genetics and Genomics Database (MaizeGDB) have expanded their resources by integrating all available genome sequences from maize and related grass species and creating a pan-genome data center. The data center provides information and tools that facilitate the ability to analyze and visualize maize genetic data, providing researchers with improved access to genetic information and a deeper understanding of maize diversity. This can accelerate improvements in maize breeding and research, aiding efforts to enhance crop yield, disease resistance, and climate adaptability, which are crucial for global food security.

Technical Abstract: Genetic diversity within species limits the usefulness of a single reference genome. A pan-genome encompasses the entirety of genetic sequences found in a collection of genomes within a species. For a species like Zea mays, which has a particularly diverse and complex genome, this presents significant challenges in data presentation, analysis, and visualization. MaizeGDB has expanded to include the genic subset of the Zea pan-genome in a new data center. This data center provides information and a variety of browsing and visualization tools to explore pan-genes in Zea that were calculated by the pipeline Pandagma. The pan-genes are also linked to the extensive data within MaizeGDB's gene model pages, including expression, insertions, proteomic data, protein structures, and classical genetic information. The pan-gene dataset includes the Zea mays genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. Together, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.