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    Welcome to MaizeGDB!

    MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.

    MaizeGDB is a founding member of AgBioData, a consortuim of agriculture-related online resources which is committed to making agriculture-related research data FAIR.

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    Maize Genetics Meeting

    The 68th Annual Maize Genetics Meeting will be held from February 26th - March 1st, 2026 at the Maritim Hotel, Cologne, Germany.

    The 67th Annual Maize Genetics Meeting was held from March 6th - 9th, 2025 at the Union Station, St. Louis, Missouri, USA.


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  • Genomes
    Representative genome - B73
    Zm-B73-REFERENCE-NAM-5.0
    Zm-B73-REFERENCE-GRAMENE-4.0
    B73 RefGen_v3
    B73 RefGen_v2
    B73 RefGen_v1
    BAC-based B73

    W22 genome assemblies
    Zm-W22-REFERENCE-NRGENE-2.0
    Genome assembly collections
    Amaizing genomes
    European Flints
    Pan-Andropogoneae
    NAM parents
    Highland-lowland genomes
    Chinese inbred founder lines


    Visualizations
    Whole genome views of B73 and NAM founders
    Karytypes of 14 inbred lines
    Karytypes of Mo17 and B73

    Complete collection of genome assemblies

  • Tools

    Featured tools at MaizeGDB

    A resource to BLAST your sequence against maize genomes and annotations.
    A data warehouse to access genomic, proteomic, and literature data for maize.
    A platform to compare gene and protein expression data across multiple genomes.
    A set of comprehensive metabolic pathway resources for maize.

    New tools at MaizeGDB


    Fusariuim Protein Toolkit     A set of tools and datasets to explore the functions and structures of the Fusarium proteome.

    Phylostrata     Phylostratigraphy determines the level of evolutionary conservation of a given protein.

    PanEffect     PanEffect: A tool to explore the variant effects across the maize pan-genome.

    SNPversity 2.0     A tool to access large-scale maize genetic variation data.

    Foldseek Search     Fast comparisons of large protein structure sets.

    Other tools at MaizeGDB

    • SNPversity 2.0
      • SNPversity: A tool to access large-scale maize genetic variation data.
    • TYPSimSelector
      • TYPSimSelector: A tool that sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa).
    • PanEffect
      • PanEffect: A tool to explore the variant effects across the maize pan-genome.
    • Bin viewer
      • Bin Viewer: A tool to explore data in regions defined by genetic bins.
    • GenomeQC
      • GenomeQC: A tool to assess the quality of genome assemblies and annotations.
    • Maize Feature Store
      • MFS: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications.
    • Pedigree Viewer
      • Pedigree Viewer: A tool to visualize maize pedigree data and networks.
    • PAST
      • PAST: A tool that assigns your SNPs to genes and your genes to metabolic pathways.
    • Genome Context Viewer
      • GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
  • Data Centers

    A-I

    • Alleles/Polymorphisms
    • SNPs/Traits
    • Expression
    • Gene/Gene Models
    • Gene Products
    • Genomes
    • Images
    • Insertions

    L-Z

    • Loci + QTL
    • Maps
    • Metabolic Pathways
    • Molecular Markers
    • Mutants & Phenotypes
    • Pan-genes
    • References
    • Stocks
    Archived data centers
  • Explore MaizeGDB
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Home> Metabolic Pathways

Metabolic Pathways at MaizeGDB
CornCyc is comprehensive metabolic pathway resources developed using the Pathway Tools Software Suite in collaboration between MaizeGDB, the Plant Metabolic Network (PMN) (CornCyc). MaizeGDB curators performed literature-based manual annotation for both resources. MaizeCyc is a comparable tool that was once supported here, but no longer is. Comparisons between CornCyc and MaizeCyc can be found below.

While CornCyc and MaizeCyc are generated using the same Pathway Tools Software Suite to generate their respective data sets, they differ in the number of pathways, enzymes, and enzymatic reactions. This is mainly due to their respective methods of assigning enzymatic function. You can find more information about both resources in the "Information and Tutorials" section below.

RefGen_v4 (Zm00001d gene models)

CornCyc_logo
CornCyc at MaizeGDB
CornCyc at PMN

RefGen_v3 (5b+ gene models)

CornCyc_logo
CornCyc at MaizeGDB

Information and Tutorials
  • Comparison of CornCyc and MaizeCyc resources
  • How to install Pathway Tools and visualize Cyc resources locally
  • How to visualize your RNA-seq data using Pathway Tools interface at MaizeGDB
  • Video Tutorial on metabolic pathways at Gramene

Downloads
  • MaizeCyc paper and Supplementary materials
  • MaizeCyc resource files for local installation (see the Pathway Tools installation directions above)
  • CornCyc resource files for local installation (see the Pathway Tools installation directions above)
  • Example data from Sekhon et al, Plant Journal, 2011
  • Go terms associated with gene models.

External Links
  • Plant Metabolic Network
  • Gramene
  • Webinars at BioCyc

Contact us!
You can help MaizeGDB! Let us know if you have experimental evidence about a metabolic pathway and its genetics by using the feedback button at the top of the page.

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