OMAP - 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 rice genome and can be viewed through the Gramene Genome Browser.



Unordered FPC Maps
SpeciesMap Set Name 
Oryza altaFPC OA_BB Jul 2006View
Oryza australiensisFPC OA_CB Dec 2006View
Oryza brachyanthaFPC OB__B Jun 2007View
Oryza coarctataFPC OC__B Dec 2006View
Oryza granulataFPC OG_AB Apr 2006View
Oryza glaberrimaCurated FPC OG_BB Feb 2006View
Oryza minutaFPC OM__B Sep 2006View
Oryza officinalisFPC OO__B Jun 2007View
Oryza punctataFPC OP__B May 2007View
Oryza ridleyiFPC OR_AB May 2007View
Oryza nivaraCurated FPC OR_BB Feb 2006View
Oryza rufipogonCurated FPC OR_CB Feb 2006View


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 rice based on BES alignments to rice in conjunction with the assembly of wild rice clones in fingerprint contigs. Detailed maps showing correspondences between the wild rice chromosomes and rice 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. These methods have been applied to Gramene's annotated version of the O. sativa assembly from TIGR.

O. sativa (TIGR) Ordered Maps



Clone and Contig View
  rufipogon nivara glaberrima punctata minuta officinalis alta australiensis coarctata brachyantha ridleyi granulata
Chr. 1 2,309 3,320 1,923 750 1,073 617 118 401 1,571 472 137 215
Chr. 2 2,102 3,104 1,659 607 1,026 535 89 283 1,243 439 396 191
Chr. 3 1,998 3,086 1,796 773 1,202 554 111 361 1,655 593 439 352
Chr. 4 1,444 2,271 1,291 461 766 374 139 275 993 302 317 166
Chr. 5 1,396 1,992 1,199 388 573 362 29 180 724 249 245 114
Chr. 6 1,474 1,963 1,071 376 559 324 14 142 797 200 178 106
Chr. 7 1,300 1,890 1,017 348 482 255 53 129 613 172 215 81
Chr. 8 1,238 1,754 969 290 334 201 38 114 569 123 148 99
Chr. 9 909 1,334 862 296 376 222 48 129 474 159 107 54
Chr. 10 902 1,138 744 226 314 213 69 106 464 136 122 75
Chr. 11 1,054 1,404 799 208 505 904 12 35 218 34 34 16
Chr. 12 978 1,334 717 205 384 154 22 80 327 64 106 33


Unordered FPC Maps
SpeciesMap Set Name 
Oryza rufipogonCurated FPC OR_CB Feb 2006View
Oryza nivaraCurated FPC OR_BB Feb 2006View
Oryza glaberrimaCurated FPC OG_BB Feb 2006View
Oryza altaFPC OA_BB Jul 2006View
Oryza granulataFPC OG_AB Apr 2006View