A COMPARISON OF MAIZE AND RICE GENOME MAPS

¹ National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, New Mexico 87505

² Department of Agronomy, University of Missouri, Columbia, Missouri 65211

³ Department of Crop Sciences, Crop Biotechnology Center, Texas A&M University, College Station, Texas 77843-2123

The focus of this project is genome map comparisons between maize and rice. Using NCGR's Comparative Genome Map Tool (prototype), collinear regions in maize and rice were studied via aligned chromosome maps for each genome together with two types of connections between mapped objects: Those based on hybridization data where the same probes have been mapped in both species, and those based on name and/or sequence similarity. Map datasets for maize and rice were downloaded via the Internet from MaizeDB and RiceGenes public databases. Common probe identification could be inferred because similar naming conventions are used for both species. Where investigators have deposited nucleotide sequences in public databases like GenBank and recorded their internationally standard sequence accession numbers with the mapped objects, the sequences could be obtained automatically and used for comparative mapping. For some probes, nucleotide sequences could be manually assigned, based on more tedious database search by species, followed by marker name scans in the annotation. Using BLAST to compare available probe sequences in maize vs. rice, the corresponding markers with similar sequences were connected on their respective chromosome maps. These results confirm known regions of collinearity between maize and rice and help validate the approach of in silico comparative mapping.