Maize Agarose FPC Map

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Major release of maize FPC. 19 July 2005 - 721 contigs. In this release, we made more use of maize-rice synteny and maize-maize duplication to anchor more contigs, adjust contig orientations, and fine-tune the genetic positions of contigs previously roughly anchored by IBM-neighboring markers.

The Maize Mapping Project (MMP: University of Missouri - Columbia, University of Georgia - Athens, and University of Arizona) was awarded NFS grant #9872655 to map the Zea mays cv. B73 genome. This site provides:

Additional information is at the MMP project site and maizeGDB.

FPC Status The manual editing has been led by Fusheng Wei, who worked in conjunction with Ed Coe et al. to confirm the anchoring of contigs to chromosome. For determining false positive and false negative joins, he used: (1) the agarose fingerprints, (2) markers, (3) the HICF FPC map funded by NSF grant #0211851 (PI: Messing), and (4) synteny between maize and rice funded by NSF grant #0115903 (PI: Paterson).

The first release of maize FPC was on 7/26/01. Manual editing began on 4/15/03. All releases are logged in the status table. Given a genome size of 2500 Mb and an average clone length of 150kb, we have approximately 17x coverage of clones. 414 contigs have been assigned to chromosomes. The total contigs span approximately 2148 MB, and the contigs assigned to chromosomes span approximately 1839 MB.

Contig Sizes
Date Clone Marker Anchor Contig Single >199 199:100 99:50 49:25 24:10 9:3 =2
4/15/03 291569 15422 1478 4518 14035 272 691 874 679 592 675 735
10/25/04 292201 19291 2019 760 16271 366 94 56 34 20 48 142
7/19/05 292519* 19291# 2021 721 16583 354+ 80 48 32 18 47 142
* The number of clones has increased as we automatically add sequenced clones to FPC as they get submitted to Genbank.
# See explanation of anchors and markers below.
+ Greater than 1000 = 76    999:800 = 44    799:600 = 47    599:400 = 68    399:200 = 119

WebAGCoL tools Back to top

WebFPC Java display of the Maize FPC contigs
WebChrom view maize chromosomes
WebBSS Feature Disabled
WebFcmp compare fingerprints
GBrowser FPC GMOD genome browser.
FTP A tar file the FPC files. Requires FPC V7.2*
username: ftp password: agiftpguest

* FPC V7.2 allows a marker to belong to any number of clones. The maize FPC has repeat markers that hit over 1000 clones. In order to load this file, you must download the new FPC executable. If you would like the bands, sizes and gel files also, please send us email and we will create one for you (it will be big!). Notes on FPC file: See rules for an explanation of the contig chromosome remark.

Information Back to top

Assembly: The clones are digested with HindIII, run on an agarose gels, band-called using Image, and automatically assembled using FPC.

  • Two clones overlap if they share at least N markers and have a cutoff less than M, using the following (N, M) pairs: (0, 1e-12) or (1, 1e-11) or (2, 1e-10) or (3, 1e-09).
  • The DQer reassembles all contigs that have > 5 Q clones using a more stringent cutoff. It tries 1e-13, 1e-14 and 1e-15. As soon as the number of Qs goes below 5, it splits the contigs into multiple ones. If it cannot reduce the number of Qs by a 1e-15, it leaves it alone.
  • Manual editing was performed as described under status.
  • The metric of a FPC contig is the CB (consensus band) unit. If the length of a contig is N CB units, then its approximate length in base pairs is N * 4900. The 4900 was calculated as the average size restriction fragment as follows: A total of 20 sequenced BACs that had corresponding fingerprints were downloaded from Genbank. The average size of all sequenced BACs was divided by the average number of fingerprinted bands, which resulted in an average band size of 4900. Since the number of bands were taken from the real fingerprint and not the simulated fingerprint, this average size takes into account missing bands.

Clone Description: One library was created at CUGI, funded by the MMP grant (NSF #9872655, PI: Coe), and the other is the CHORI-201 library created at Pieter de Jong's lab (NSF #9975618, PI: Messing).

Marker and Anchor Description: Markers are from Andrew Paterson's lab at University of Georgia - Athens, Ed Coe's lab at University of Missouri - Columbia and a Dupont/MMP/Incyte Partnership.

Missouri provides us with the file of markers, that get loaded into FPC. 2333 markers are associated with loci, and each has a remark stating its associated locus. 1991 loci are associated with markers, and each has a remark stating its associated marker. Both sets are now in FPC and the loci are the genetic markers. The following provides a description of the marker names:

  • Markers starting with "mito" are mitochondrial DNA; "chloro" are chloroplast DNA.
  • Markers starting with "Cent" and "CENT" are centromere-related; "pMTY" are telomere-related.
  • Marker "pZmR1" is a ribosomal probe; "185bp" is a knob heterochromatin probe.
  • Markers ending in "_ov" are overgos to Unigenes from the DuPont/MMP/Incyte Genomics partnership: CL* identifies clusters assembled from public EST sequences; PCO* public sequences combined with DuPont sequences (Unigene Cornsensus deposited in GenBank); dd* anonymous clusters assembled by DuPont (sequences are not available); si* public singletons that did not cluster with DuPont sequences.
  • SOG markers are overgos from the Paterson lab, derived from probes that have been mapped in maize and other grasses.
  • Anchors that are multiple copy have been split into two. The anchor retains the original name, and the un-anchored copy has a .A suffix.
  • There is one marker called HICF. This is used to link each pair of clones that is bridged by an HICF clone. We know that the pair of clones is close (within 150kb), and probably overlap but we cannot guarantee it.
  • Summary of markers: eMrk 19, STS 1633, Locus 2865, RFLP 66, REP 10, OVERGO 14717.
In the Marker box of WebFPC, search for any of the above groups by adding a "*" to the end, e.g. "mito*" will show you all the mitochondrial DNA.

Sequence clones description:

  • Tiling Clones - Clones selected for sequencing have been indicated in FPC as Tile. These clones are shown in Orange in FPC, and remarked by the group who selected the clone for sequencing. Once the clone is submitted to Genbank, its status changes to that of the sequencing state. See maize status for a table of submitted clones.

  • SD clones - We nightly download maize sequences from Genbank, run a simulated digest on them, and have them placed in the same position as its highest hitting clone (which should be the original clone if all is well). The SD clone is highlighted Blue and the original clone is highlighted Gray.

Requests and contacts Back to top

  • Markers - This is to request that you consider contributing probe:BAC address data that will advance the genetic and physical mapping of the genome of maize. Please see http://www.maizemap.org for the status of the project, and for the data that are being assembled.

    The following data contributions will be most valuable:
    Probe Name
    Probe Type (e.g., cDNA, genomic, SSR, overgo)
    Primers
    GenBank Accession
    BAC addresses and library (e.g., HindIII, EcoRI, or MboI filters)
    Bibliographic citations if any

    Copy number on Southern blots, Genetic map location(s), Northerns, sequence subclone results, etc., would be appreciated but are not essential to this purpose.

    In return, we will credit you for any data you provide.

    We would be most pleased to have from you citations of your publications that made use of the filters, or of any of the data from the Maize Mapping Project. Email to coee@Missouri.edu

  • Contig merges - If you have evidence of two contigs that can be merged, email to fushengw@ag.arizona.edu.

  • Suggestions - We have developed the WebAGCoL tools funded by USDA-IFAFS grant #11180 titled Web Resources for the Computation and Display of Physical Mapping Data. If there are additional web based features you would like to see, email to will@agcol.arizona.edu.

    References Back to top

    Gardiner J, Schroeder S, Polacco ML, Sanchez-Villeda H, Fang Z, Morgante M, Landewe T, Fengler K, Useche F, Hanafey M, Tingey S, Chou H, Wing R, Soderlund C, Coe EH. (2004) Anchoring 9,3971 maize expressed sequence tagged unigenes to the bacte rial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiology 134:1317-1326.

    Coe E, Cone K, McMullen M, Chen S, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, Soderlund C, Wing R (2002). Access to the maize genome: an integrated physical and genetic map. Plant Physiology 128:9-12.

    K. Cone, M. McMullen, I Vroh Bi, G. Davis, Y. Yim, J. Gardiner, M. Polacco, H. Sanchez-Villeda, Z. Fang, S. Schroeder, S. Havermann, J. Bowers, A. Paterson, C. Soderlund, F. Engler, R. Wing, and E. Coe, Jr. (2002) Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map Plant Physiololgy. 130:1598-1605.

    Y. Yim, G. Davis, N. Duru, T. Musket, E. Linton, J. Messing, M. McMullen, C. Soderlund, M. Polacco, J. Gardiner, and E. Coe, Jr. (2002) Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization. Plant Physiololgy. 130:1686-1696.

    • Email comments to www@genome.arizona.edu