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Maize Genome

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Maize Genome Sequencing Project

Corn (Maize) is a major crop in the U.S., a main source of global food supply, and an important model system for basic biological research. Knowledge gained from maize can also be used to improve its relatives such as sorghum, wheat, rice, switchgrass and Miscanthus At AGI, we have been working on the maize genome since 1998. In the Maize Mapping Project, we built a BAC-based maize agarose physical map and an integrated genetic and physical map. In the maize sequencing pilot project, we constructed a maize high information content fingerprint (HICF) physical map and sequenced the ends of all BACs in the physical map. Extensive manual editing of the agarose map was performed. In July 2005, we released a sequencing-ready maize physical map. In November, 2005, The Maize Sequencing Consortium was formed and awarded to sequence the maize genome. The Maize Genome Sequencing Project provided a maize reference genome sequence with finished high quality sequence in low copy regions. Co-PIs of the sequencing consortium are:

Richard Wilson, Washington University at St. Louis
Sandra Clifton, Washington University at St. Louis
Rod A. Wing, Arizona Genomics Institute
Doreen Ware, Cold Spring Harbor Laboratory
Lincoln Stein, Cold Spring Harbor Laboratory
Richard McCombie, Cold Spring Harbor Laboratory
Robert Martienssen, Cold Spring Harbor Laboratory
Patrick Schnable, Iowa State University
Srinivas Aluru, Iowa State University

In February, 2008 at the 50th Maize Genetic Meeting, the Maize Sequencing Consortium announced the draft sequence of the maize genome. Click to see original Image in a new window Since then, extensive work has been done to finish the remaining clones, improve the physical map, anchor the sequence to the genetic map, build an AGP (A Golden Path) to generate maize pseudomolecules, and to annotate the genome. Please visit the official project website for details. On March 20, 2009, AGI released an updated maize integrated genetic and physical map, consisting of 440 contigs. Please click here to check the quality of each contig, including order and orientation information. Please visit our maize FPC ftp site to download the file . The sequenced BACs are highlighted in red on the FPC map. The AGP and pseudomolecules for the 10 maize chromosomes and the unanchored contigs (chr0) are available for download. We also released the maize minimum tiling path (MTP) for the sequencing project. This MTP will link the pseudomolecules to physical contigs. In the MTP website, when you click the clone name, it will show you the best hits of the clone to other clones in the sequencing project. The BES2BAC column indicates the sequence similarities of the BES of this clone to the sequenced BAC on its left or right end. A simple click will lead to the sequence alignment.


Maize Full Length cDNA Project The complete set of maize FLcDNA clones are available from the AGI Resource Center

Maize Physical Map


Maize B73 RefGen_v2 Downloads
The complete list of maize FLcDNA clones
FPC ftp site
MTP, Clone list
Sequences of Genetic Markers, the major genetic and physical changes, including the anchoring quality of each contig, are in this table

Maize B73 RefGen_v1 Downloads
FPC ftp site
HICF FPC ftp site
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Files linked to this article
File name Published on Hits
Download this file B73RefGen_v2QualityChanges.xls
The anchoring (genetic or optical) quality of each contig and substantial physical position changes
2010/3/31 2290
Download this file MTP_Pseudo_v2_Clones
Clone list
2010/3/31 1748

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A portion of AGI's material is based upon work supported by the National Science Foundation under Grant Number 102620.