HIGH DENSITY COMPARATIVE MAPPING VIA SEQUENCE MATCHING

¹ Dept of Plant Breeding, Cornell University, Ithaca, NY 14853 USA
² USDA ARS WRRC, Albany, CA 94710-1105 USA
³ USDA ARS, Cornell University, Ithaca, NY 14853 USA

Given a model species for which the entire genome is sequenced, how can that information be used to map and identify genes of a large genome species (LGS)? One approach is to sequence previously mapped probes or generate new ESTs for the LGS, map a fraction of them in the LGS, and cross-reference both mapped and un-mapped sequences by sequence matching using BLAST searches against the model species. The utility of this approach was assessed using sequence matching of previously mapped clones. We used DNA sequence analyses of oat and barley cDNA clones in BLAST searches and identified a large number that matched rice EST sequences which had previously. We compared rice chromosome locations of the oat and barley cDNAs that matched the mapped rice ESTs according to BLAST. Nine of our oat or barley probes were both mapped in rice by Southern analysis and matched a rice EST that was mapped by Southern analysis. Out of those 9 matches, 5 of the rice chromosome locations were similar for the cDNA and the EST while the other 4 mapped to different chromosomes. We then used our comparative maps for maize, barley and wheat to predict the map location of those clones as well as other oat and barley cDNA-probed loci in rice. Six matching rice ESTs were available for maize and 18 were available for barley and wheat. In maize 4 out of 6 matched the predicted location and for wheat/barley, 12 out of 18 matched the predicted location.