2006 Annual Report 4d.Progress report. This report serves to document research conducted by ARS under a trust agreement between ARS and University of Arkansas. Additional details of research can be found for the parent CRIS 6203-21430-005-00D Application of Rice Genomics to Develop Sustainable Cropping Systems for the Gulf Coast. The major goal of the RiceCAP project is to bridge an ever-widening gap between molecular biology efforts in rice research and applied aspects of rice breeding to develop high value rice cultivars for commercial production in the U.S. The RiceCAP project includes applied and basic rice scientists from 14 different institutions from 12 states. Research progress has been made in developing the several rice mapping populations to identify QTL associated with milling yield and sheath blight resistance, identification of a large array of polymorphic microsatellite molecular markers to evaluate these segregating populations, the initiation of functional analysis of candidate genes directly controlling complex traits, and the development of informational and instructional posters, presentations, and modular displays for various outreach and educational efforts. Data were collected on the milling yield population evaluated at three locations for some 133 traits believed to impact milling quality. Tillering, whole milling, total milling, percent pre-brokens, and induced fissuring among the segregating families were poorly correlated between the two growing locations. However, most grain dimension (length, width, thickness, etc.) traits and amylose content were highly correlated between the locations. These results indicate that grain dimension traits are quite stable over locations, whereas other factors influencing milling yield are very sensitive to the environment. Factors associated with grain ripening and post-harvest handling appear to have a large impact on whole milling yield. Other traits, hypothesized to have a significant impact (heading, tillering, grain dimension, etc.) on whole milling yield, were not very influential. However, segregation distortion in the population resulted in relatively few of Cypress alleles being present in the population, which limited our ability to detect their impact on milling quality. Brown spot (BS) symptoms were observed at one location offering the opportunity for identifying QTL associated with this disease. Leaves from each of the segregating families were scanned using an image analysis system to determine the percent of the leaf area that was diseased. RT0034 was observed to be very susceptible to brown spot (40% of blades diseased) as compared to Cypress (7%). About half of the population had 30% or more of the leaf blades diseased. There was a moderate correlation of heading date with BS disease (r=0.47), suggesting that later flowering lines had a greater build up of disease symptoms before they were harvested. A preliminary analysis identified two potential QTL associated with brown spot susceptibility. Additional mapping populations for milling yield and sheath blight resistance are being developed for evaluation over the next two years.