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 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 the O. sativa assemblies from TIGR V4 and IRGSP V4 as well as the indica assembly from BGI.

O. sativa (TIGR V4) Ordered Maps



Clone 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


Contig View
  rufipogon nivara glaberrima punctata minuta officinalis alta australiensis coarctata brachyantha ridleyi granulata
Chr. 1 38 36 36 72 188 67 23 52 138 50 24 39
Chr. 2 31 22 28 50 137 59 20 31 98 33 66 33
Chr. 3 33 29 23 52 171 54 23 39 119 38 69 49
Chr. 4 47 35 37 36 99 37 20 22 96 19 48 28
Chr. 5 38 34 23 34 94 43 5 22 69 26 42 19
Chr. 6 38 37 32 32 86 39 3 21 66 22 32 21
Chr. 7 37 24 32 27 84 29 11 18 60 22 40 13
Chr. 8 39 28 32 29 64 26 8 14 64 18 27 14
Chr. 9 34 27 24 20 60 22 12 9 49 15 17 9
Chr. 10 33 30 25 14 54 30 7 13 39 15 21 14
Chr. 11 42 35 32 23 106 125 4 8 32 6 9 3
Chr. 12 37 31 37 21 63 20 6 14 45 10 21 8


Clone and Contig View
  rufipogon nivara glaberrima punctata minuta officinalis alta australiensis coarctata brachyantha ridleyi granulata
Chr. 1 2,347 3,356 1,959 822 1,261 684 141 453 1,709 522 161 254
Chr. 2 2,133 3,126 1,687 657 1,163 594 109 314 1,341 472 462 224
Chr. 3 2,031 3,115 1,819 825 1,373 608 134 400 1,774 631 508 401
Chr. 4 1,491 2,306 1,328 497 865 411 159 297 1,089 321 365 194
Chr. 5 1,434 2,026 1,222 422 667 405 34 202 793 275 287 133
Chr. 6 1,512 2,000 1,103 408 645 363 17 163 863 222 210 127
Chr. 7 1,337 1,914 1,049 375 566 284 64 147 673 194 255 94
Chr. 8 1,277 1,782 1,001 319 398 227 46 128 633 141 175 113
Chr. 9 943 1,361 886 316 436 244 60 138 523 174 124 63
Chr. 10 935 1,168 769 240 368 243 76 119 503 151 143 89
Chr. 11 1,096 1,439 831 231 611 1,029 16 43 250 40 43 19
Chr. 12 1,015 1,365 754 226 447 174 28 94 372 74 127 41


Indica (BGI) Ordered Maps



Clone View
  rufipogon nivara glaberrima punctata minuta officinalis alta australiensis coarctata brachyantha ridleyi granulata
Chr. 1 2,007 2,782 1,746 701 1,054 592 130 385 1,497 427 334 224
Chr. 2 1,932 2,701 1,477 574 985 502 75 254 1,130 423 390 186
Chr. 3 1,881 2,475 1,625 674 1,170 534 106 344 1,537 547 421 352
Chr. 4 1,266 2,012 1,061 427 774 362 60 267 897 265 313 153
Chr. 5 1,283 1,756 1,157 360 572 345 59 152 680 201 237 112
Chr. 6 1,252 1,607 922 345 526 297 15 117 693 161 165 95
Chr. 7 1,230 1,850 899 325 440 245 37 119 595 154 197 76
Chr. 8 1,051 1,462 810 259 315 170 22 92 490 89 135 104
Chr. 9 858 1,313 750 263 358 227 37 123 462 142 103 42
Chr. 10 813 945 622 204 282 198 47 101 384 101 126 82
Chr. 11 723 1,020 558 178 177 148 28 26 203 31 23 17
Chr. 12 767 1,011 507 190 354 171 10 71 284 48 85 40


Contig View
  rufipogon nivara glaberrima punctata minuta officinalis alta australiensis coarctata brachyantha ridleyi granulata
Chr. 1 46 40 41 67 180 63 23 50 131 44 49 42
Chr. 2 33 26 35 48 130 56 18 27 100 41 62 35
Chr. 3 38 42 32 47 169 50 23 39 117 38 66 53
Chr. 4 42 36 29 33 99 37 16 28 86 20 48 25
Chr. 5 45 42 37 32 97 46 9 19 70 23 41 18
Chr. 6 46 40 34 31 81 40 3 21 62 18 31 18
Chr. 7 38 28 32 26 73 29 9 16 65 19 33 13
Chr. 8 44 36 35 28 57 23 5 12 55 12 25 16
Chr. 9 34 24 25 22 60 25 9 10 48