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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 (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:
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 |
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 |
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