Due to the know large amount of repetitive DNA in the maize genome in conjunction with the fact that maize is a diplodized tetrapoloid there have been two stages in the sequencing of the maize genome. The first was an effort to determine the most cost-effective method to determine the nucleotide sequence for the entire genome by examining a small piece. The National Science Foundation funded two sequencing projects in maize that will test the sequencing strategies employed for large plant genomes, using maize as an example.
The first project was awarded to the Consortium for Maize Genomics. They tested two strategies, methyl-filtration and high-Cot selection, as a method to exclude repetitive DNA from the input to sequencing. The consortium members are The Donald Danforth Plant Science Center, TIGR, Purdue University, and Orion Genomics. The underlying premise is that knowing the nucleotide sequence of the gene-space will be sufficient.
The second project was awarded to Jo Messing at Rutgers University along with Rod Wing and Cari Soderlund from the University of Arizona. They proposed to use a modified BAC-by-BAC sequencing strategy. They have sequenced about 20 Mb of maize genome represented in 140 maize BAC clones. Sequencing will be carried out at the Whitehead Institute/MIT Center for Genome Research.
The Arizona Genomics Institute has sequenced about 450,000 BACend clones which will aid in aligning BAC sequences to the genetic map using co-linearity of these sequences with the rice genomic sequence. Also a FPC map was produced by the Arizona Genomics Institute.
The results of the two preliminary genome sequencing efforts showed that the BAC-by-BAC approach was the only method suitable for reasonable quality data. Thus an interagency grant from the NSF, the USDA and the DOE funded the 3 year project to sequence the B73 cultivar at the Washington University Genome Sequencing Center. The first draft release was announced on February 28, 2007 at the 50th Maize Genetics Conference.
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