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Welcome to Panzea's Map viewer. Here you can view graphical map displays of all of the maize genes and markers used in our project that have known or estimated map positions.
Find the order and locaton of all Panzea genes, loci and markers on Chromosome 1
Find the order and location of only the Panzea markers on Chromosome 1
Find the order and location of only the Panzea candidate and random genes on Chromosome 1
See how Panzea markers on contig 11 of the physical map align with chromosome 1 by clicking here
Zoom in for a closer view of this alignment by clicking here
Construct your own custom CMap views, starting from the CMap viewer Quick Start page
Make your own comparative physical vs. genetic maps using the CMap matrix
The following map features are displayed in our CMap views. These relate either to the attributes of genes or loci, or to the type of marker:
Gene/Locus attributes:
Candidate Genes: genes chosen for study because of their suspected or known influence on a trait of interest
Random Genes: genes randomly sampled from an EST library without regard to, or prior knowledge of, their function
Marker Loci: loci selected for use as markers (e.g., SSRs)
Marker types:
Panzea sequences: these are stored and displayed as sequence alignments in Panzea
Panzea SNPs: validated SNP markers that we are using in our genotyping experiments
Panzea SSRs: mapped SSRs that we utilized in our previous NSF grant
IBM2 core markers: core markers that define the genetic bins on the IBM2 Neighbors map, provided here as reference points
Since numerous genes and loci are displayed on each chromosome or contig, and since a single gene or locus can contain numerous markers, it is usually necessary to zoom in quite closely on a genomic region of interest in order for all of the labels to be displayed. This is accomplished by using the magnification control at the bottom of each map ("- Mag +").
Clicking on one of the map labels will lead you to a CMap "Feature details page". The links provided in the "Cross References:" section of the feature details page lead either to a Panzea Molecular Diversity Search or Gene/Locus Search for that feature.
Both genetic and physical map displays are available. These displays are generated by the software CMap -- the Comparative Map Viewer which we have ported from Gramene. In addition to viewing a genetic map of each maize chromosome or a physical map of each contig, you may also use the CMap viewer to construct a comparative map showing how physical contigs align to the genetic map of the corresponding chromosome.
Our Panzea markers are displayed in two distinct map sets, one genetic and one physical:
The IBM2 2005 Neighbors genetic map is the current "state of the art" genetic map in maize. More information on this map and the loci it contains can be found at MaizeGDB. In our CMap viewer we display all of the "core markers" that define the genetic bins on this map, and the placement of all of our mapped Panzea genes and markers relative to these core markers. Most of our genes and loci were not genotyped in the mapping populations that were used to construct the IBM2 Neighbors map, but instead were placed on the genetic map according to the contig on which they occur in the physical map. These contigs had previously been placed upon the IBM2 Neighbors genetic map by virtue of containing other markers that were genotyped in the IBM2 mapping population. More information on this process can be found here. This integrated genetic and physical map (the iMap) was developed by the Maize Mapping Project.
The AGI FPC physical map was also generated by the Maize Mapping Project, and is displayed at the Arizona Genomics Institute website. FPC stands for Finger Print Contig assembly, which refers to the method by which hundreds of thousands of overlapping BAC clones were grouped into contiguous sequences (contigs), using DNA fingerprinting patterns on agarose gels. The current release of the AGI Agarose FPC map consists of 721 contigs, most of which have been placed onto one of the ten chromosomes of maize. Many of our Panzea genes and markers have been placed onto a unique contig -- these are displayed in our CMap views of the physical map.
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