The goal of this proposal is to generate a map of the chromosomes of maize based on cytological features that will integrate information from existing genetic maps with new cytological and physical data. In general, this new map will be created by using three dimensional fluorescent in situ hybridization (3-D FISH), deconvolution light microscopy, and computerized image analysis to place genetically mapped genes onto the cytological map of maize. Genetic maps are based on the percent recombination between genes. Genetic maps report the linear order of genes and the amount of recombination between linked genes, but do not contain information on cytological distance or number of base pairs between genes. Cytological maps are created by determining the position of any visible structure on a chromosome as viewed through a microscope. The position is usually reported as a percentage of total chromosome arm length. Physical maps reflect DNA sequence data, and show the position of DNA motifs relative to an absolute scale in base pairs. For example, a map of overlapping sequenced clones forming a contig is a physical map.
The cytogenetic map will be created by using 3-D FISH to place genetically mapped genes onto the cytological map of maize. Meiotic pachytene chromosomes will be utilized as the basis of the map since they are 10X longer than mitotic chromosomes and display excellent cytology. Several cytological features such as the heterochromatic knobs and prominent chromomeres will be genetically mapped. Chromosome specific bar codes, based on repetitive sequences, that will allow unambiguous determination of each region on every chromosome, will also be developed. The cytological position of highly repetitive DNA elements, as well as the gene positions, will be determined to allow the discovery of regions of the chromosomes that are gene rich or gene-poor. To utilize sequence data in the map, base pair distances between markers will be integrated into the map as these data are determined by other groups. This will make it possible to determine relationships between physical, cytological and genetic distances; i.e., the relationships of base pairs to microns to centimorgans in different parts of the genome.
This map will provide biological information about the global positions of genes, the global organization of repetitive elements, position of recombination events, and will possibly shed light on the process of meiotic homologous pairing. It could be used for ordering large insert clones, for integration of the several genetic maps of maize, and for the genetic placement of markers that cannot be mapped genetically. This technology will be generally applicable to other grasses and could be used in a comparative approach to study grass genome evolution. In general, this publicly available map will be used to arrange and manage a large amount of genome data, and will provide biologically relevant information to the plant genome community.
