Maize Genomic Tools

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Maize Genomics Resource News

February 25, 2021: The genome assemblies and annotation for the five stiff stalk inbreds and annotation for B73 v4 are now available on the Maize Stiff Stalk Genomes and Annotation Data page.

September 4, 2020: We have generated PacBio chromosome-scale assemblies for five stiff stalk inbreds (B84, LH145, NKH8431, PHB47, PHJ40) and annotated these genomes along with B73 v4 using a custom annotation pipeline that included genotype-specific transcript evidence derived from five tissues (seedling shoot, seedling root, internode, endosperm, leaf) for each inbred. The genomes are available via a Jbrowse genome browser.

February 19, 2020: New tracks have been added to the JBrowse displaying Nanopore direct RNA sequencing reads and Stringtie2 assemblies of seedlings and kernels from B73 and W22.

August 15, 2019: A new track for UniformMu Release 9 for B73v4 has been added to the JBrowse. We would like to thank Dr. McCarty at UFL for providing the UniformMu Release 9 data.

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:
Zm00001d040431, Zm00001d013402_T004
Search terms:
phytochrome, kinase

Annotation Summary


Total Loci 39,324
Number 39,005
Gene Models 148,528
Average Gene Length 4,187 bp
Average Exons/Gene 9.2
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
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.