| The objectives of this research were to evaluate techniques for the rapid genetic characterization of cultivated rice (Oryza sativa L.) germplasm and to determine the genomic localization of the xa-5 gene for resistance to rice bacterial leaf blight (BLB).;Genetic and physical mapping were used to characterize the chromosomal region surrounding the xa-5 gene as a prelude to its positional cloning. Polymorphic molecular markers were identified in a parental survey of a nearly isogenic line cross. Recombination events around the gene were selected for by an efficient PCR-based screening of over one thousand F;Two physical contigs for the region were assembled based on bacterial (BAC) and yeast (YAC) artificial chromosome large-insert-clones. The BAC contig was constructed based on marker content and ISSR fingerprints of the individual clones. The interval with the targeted gene was spanned by a maximum of two BAC clones or either of two single YAC clones and the locus-specific estimates of the ratio of genetic to physical distance were very favorable for positional cloning.;The cloning of xa-5 should help to clarify some of the interesting central events of infection of rice by the BLB pathogen, Xanthomonas oryzae pv. oryzae, and will have implications for the study of recessive resistance genes in other pathosystems.;Three fingerprinting techniques, inter-simple sequence repeats (ISSR), amplified fragment length polymorphisms (AFLP), and fluorescently-labeled multiplexed microsatellites, were used to characterize varieties representative of the diversity of cultivated rice. These PCR-based genome scanning methods were able to identify Japonica versus Indica subspecies and to dissect finer levels of diversity. The ISSR analysis provided insights into the organization and frequency of different simple sequence repeats in the rice genome, while mapping of specific ISSR bands suggested that this technique produces many heritable markers useful for genetic analysis. |
