2006 Annual Report 4d.Progress report. This report serves to document research conducted under a reimbersible agreement between ARS and the Department of Plant Pathology, Kansas State University. Additional information may be found in the report for the parent CRIS 6645-22000-015-00D. Microsatellite markers closely linked to a gene in wheat conferring resistance leaf rust and stripe rust were identified. Resistance to leaf rust and stripe rust has been short-lived in wheat cultivars world-wide due to high levels of variability in the pathogen populations. The appearance of new races of both leaf rust and stripe rust has lead to epidemics in parts of the U.S. in the past several years. The gene Lr46/Yr29 has provided partial resistance to both pathogens that is non-race specific for more than 30 years. Deployment of this gene in U.S. wheat cultivars has been complicated by the presence of other resistance genes that provide high levels of resistance that is often short-lived. Sequencing of wheat BAC clones identified with markers developed as part of this project identified microsatellite sequences that are tightly linked to the resistance gene. The newly developed microsatellite markers will be more easily utilized than previously reported markers in high-throughput marker-assisted selection of plants carrying Lr46/Yr29. This research was conducted in collaboration with the Department of Plant Pathology at Kansas State University and the ARS Plant Science and Entomology Research Unit.