The International Oryza map alignment project: a golden path to unlock the genetic potential of the wild relatives of rice

The availability of close comparative systems provides one with the ability to address basic and applied questions within a robust phylogenetic framework. After completion of the rice genome in 2004, our consortium set out to create a closed experimental system for the genus oryza which contains 23 species (2 cultivated species; 10 distinct genome types; 6 diploid & 4 polyploid species; 3.6 genome size variation; wide distribution & habits) under the rubric – the International oryza Map Alignment Project (I-OMAP: www.omap.org). The wild relatives of rice contain a virtually untapped reservoir of agriculturally important genes that could be used to improve the world’s most important food crop. The core I-OMAP resource is composed of 17 deep-coverage BAC libraries, 13 BAC fingerprint/end sequenced physical maps aligned to the rice reference genome, and 9 chromosome 3 short arm sequences. These physical maps serve as entry points to virtually any region of the collective oryza genome for interrogation (e.g. Adh1, Moc1, hd1, Cen8), as well as scaffolds to guide reference genome assembly. In November 2009 the I-OMAP consortia developed a plan to generate high-quality reference genome sequences for representatives of all 14 diploid oryza species, and the outgroup leersia perrieri, by mid 2011. Our goal is to provide the highest quality reference genome sequences as possible, which can then be used as resequencing templates to capture allelic diversity, and structural variation for functional and evolutionary studies. Recent analyses of the I-OMAP system will be presented, along with an update of the communities’ efforts to generate RefSeqs for all diploid oryza: including the newly completed oryza glaberrima (West African cultivated rice) RefSeq.