Maize Genomic Tools

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Maize Genomics Resource

Maize (Zea mays) is the most produced (as measured by tonnes) staple crop world-wide and has been the focus of intense breeding efforts to improve agronomic traits for centuries. However, the genetic basis of numerous phenotypes is still unknown and genomic tools provide a valuable resource to accelerate breeding efforts. To facilitate breeding and research efforts in maize, we analyzed publicly available transcriptomic data for the reference maize inbred, B73, and developed the Maize Genomics Resource (MGR).

Transcriptomic data from the developmental B73 gene atlas and several B73 abiotic and biotic stress experiments (for complete list see here) were aligned to the AGPv4 B73 genome assembly and gene expression was quantified using the Zm00001d.1 gene annotation. Differential and co-expression analyses were conducted, and orthologous genes were characterized. The data was also deployed to the Bio-Analytic Resource for Plant Biology (BAR) eFP browser and new AGPv4 views were developed. The MGR consists of a set of search and query tools to quickly access this information via a BLAST server, genome browser, and gene report pages. Bulk data are also available for download.

This work was funded by the Department of Energy Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494), the National Science Foundation Plant Genome Research Program (IOS- 1546657), and the Michigan State University Foundation.


When using data and analyses from the Maize Genomic Resource (MGR), please cite the following publication:

Quick Search

Gene ID:
Examples:
Zm00001d040431, Zm00001d013402_T004
    
Search terms:
Examples:
phytochrome, kinase
    

Annotation Summary

AGPv4

Total Loci 39,324
Chromosome
Number 39,005
Gene Models 148,528
Average Gene Length 4,187 bp
Average Exons/Gene 9.2
Unanchored
Number 319
Gene Models 1,141
Average Gene Length 3,900 bp
Average Exons/Gene 8.1

MSU Analyses

Total Loci 39,324
MSU Annotation
GO Annotation 21,914
Pfam Hit 28,862
InterPro Hit 35,638

Chromosomal Loci 39,005
Genes Expressed
FPKM > 1 29,414
FPKM > 5 26,404
Expression Analyses
Organ Specific 4,154
Stress Induced 7,704
WGCNA 13,590
Homology
Ortholog 29,246
Singleton 9,759

Maintenance Notice

Web pages may be unavailable or only partially functional during server maintenance, which is planned for the first Wednesday of every month.