Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Allele Mining
            

PROSPECTS FOR ASSOCATION MAPPING IN RICE: THE CASE OF XA5

¹ Institute for Genomic Diversity, Cornell University, 130 Biotechnology Buildling, Ithaca, NY, 14853, USA

² Department of Plant Breeding, Cornell University, 418 Bradfield Hall, Ithaca, NY 14853, USA

Linkage disequilibrium mapping and association mapping have the potential to augment the use of genetic resources collections by linking molecular diversity with traits. Developed for use in medical genetics, association mapping has been used successfully in maize to identify a suite of polymorphisms it the Dwarf8 gene that association with variation in flowering time (Thornsberry et al., 2001). Because of the rapid decay of linkage disequilibrium around maize genes (Remington et al., 2001), association mapping is appropriate for testing candidate genes, but its utility in highly selfing organisms has not been established. In this study, linkage disequilibrium and association testing were used to evaluate polymorphisms in the candidate region for a bacterial blight resistance gene in rice. xa5 is a recessive gene conferring race-specific resistance to bacterial pathogen Xanthomonas oryzae pv. oryzae. We sequenced 13 short segments spanning the 70 kb candidate region in 114 rice accessions. Plant were scored for resistance to Xanthomonas oryzae pv. oryzae. Five additional loci spanning 45 kb adjacent to the candidate region were sequenced in the subset of 60 rice accessions showing a resistant phenotype. Random markers were used assess population structure. The data was analyzed to determine the significance of population structure, the extent of linkage disequilibrium, and the association of polymorphisms with resistance. An understanding of the extent of linkage disequilibrium in rice will allow us to make predictions about the resolution of association studies.