OMAP - The Oryza Map Alignment Project

The Oryza Map Alignment Project (OMAP) provides the first ever closed experimental system for understanding the evolution, physiology and biochemistry of a single genus in plants or animals. In this project, twelve deep coverage BAC libraries have been constructed and are representative of both diploid and tetraploid genomes from wild species of Oryza. These libraries were end sequenced and assembled into physical maps using DNA fingerprinting (FPC). Presently, three FPC maps have been manually edited (O. rufipogon, O. nivara, O. glaberrima) and are available in Gramene along with phase 1 maps from the other species. Additionally, over 1.4 million BAC end sequences (BES) from the twelve wild rice genomes have been aligned to the finished sequence of the O. sativa genome and can be viewed through the Gramene Genome Browser.

OMAP Ordered Maps

Using these data we can begin to address important biological questions on a whole-genome scale including elucidating patterns of conservation and divergence, genome rearrangement, evolution, domestication and gene regulation. To this end, we have constructed a synteny pipeline to align clones and contigs from the wild species to O. sativa based on BES alignments to O. sativa in conjunction with the assembly of wild rice clones in fingerprint contigs. Detailed maps showing correspondences between the wild rice chromosomes and O. sativa by the clones and contigs, clones alone, or contigs alone ordered along chromosomes are listed below. The methods for determining the clone and contig positions in the ordered maps are listed here.