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     Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea; Zea mays

The maize nuclear genome is thought to be amphidiploid - a fusion of two diploid genomes (Helentjaris T, Weber D, Wright S, 1988) - or allopolyploid - (Wilson et al. 1999) with knob heterochromatin. The knob heterochromatin has been characterized as a duplication of a 185-bp element (Peacock WJ et al. 1981) and a 350-bp element (Ananiev EV et al. 1998) with the amount of duplication varying up to 3 to 4 orders of magnitude between different races of corn. This leads to a wide range of genome sizes among corn. The minimum size is estimated to be 2400 Mbp with a high proportion of repetitive DNA.

Contemporary US corn crops are the consequence of introgressing various traits into a group of corn varieties. Examination of the pedigrees shows that each is a mixture, in differing proportions, of two ancestral maize strains: northern flint and southern dent [(Allard RW. 1999); (Doebley et al. Econ Bot 1988 42:120-131)]. With the application of inexpensive tools to precisely perform genotypic analysis (Matsuoka Y et al. 2002) the initial findings were confirmed and expanded (Liu K et al. 2003). This investigation was expanded to examine the genetic relationships between individual local populations of different corn land races (Vigouroux Y et al. 2005). The conclusion is that there are five maize land races which arose from independent efforts across the Americas following a single domestication of maize (Matsuoka Y et al. 2002).

At a NSF sponsored workshop it was decided that sequencing maize genes and placing them on a cross-referenced physical-genetic map is important to improving the agronomic characteristics of the plant. Due to the known large amount of repetitive DNA in the maize genome in conjunction with the fact that maize is a diploidized tetraploid there have been questions regarding the efficacy of alternative strategies for sequencing of the maize genome. One proposed approach was to sequence individual BAC clones from a tiling path defined by combining genetic and physical mapping. Another focused on the non-repetitive (gene-rich) sequences while a third examined the most cost-effective method to determine the nucleotide sequence for the entire genome by examining a small portion. The National Science Foundation funded three sequencing projects in maize that tested the sequencing strategies for large plant genomes, using maize as an example. The first project funded under the NSF Plant Genome Initiative, toward genetic and physical mapping, was awarded to Ed Coe and colleagues at the University of Missouri along with Rod Wing of the University of Arizona and Andrew Paterson of the University of Georgia. The question under test for maize was whether fingerprinted BACs could be assembled into contigs and pseudochromosomes. By combining genetic and physical strategies they derived a high-resolution genetic map; constructed and fingerprinted 450,000 BACs and assembled them into contigs; and anchored assemblies onto the genetic map, integrating the physical elements in genetic map order. These data and materials were staged for subsequent selection of a minimum tiling path and BAC-by-BAC sequencing, once the feasibility of this approach was demonstrated.

The test project for non-repetitive sequences 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 test project for sequencing and examining a portion of the genome 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 the maize genome represented in 140 BAC clones. Sequencing was carried out at the Whitehead Institute/MIT Center for Genome Research.

The Arizona Genomics Institute has sequenced about 450,000 BAC ends which 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.

Fourteen genetic maps and one physical map are available in Map Viewer. Detailed information for the maps is available in the BioProject database. As data for other maps are requested or new map data are made available, these maps will be displayed.

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