2007 Annual Report 1a.Objectives (from AD-416) Characterize rice genome in order to develop useful molecular strategies to accelerate the production of improved rice germplasm. Molecular genetics, molecular cytogenetics and molecular plant pathology approaches will be used to address four integrated objectives:. 1)mapping and genomic analysis of disease resistance and end-use quality genes in rice for use by US rice researchers,. 2)introgressing novel disease resistance genes from the wild Oryza species into cultivated rice for use by US rice breeders and identifying genetic stocks for use by rice researchers,. 3)determining allelic variation of Pi-ta for identification of new sources of resistance; identifying the interaction components in the Pi-ta gene-mediated signal recognition and transduction pathways for precisely engineering resistance, and analyzing structural and functional relationships of AVR-Pita for predicting the stability of blast resistance in current cultivars, and. 4)identifying differentially expressed genes after rice is infected with either the rice blast fungus or sheath blight fungus in order to develop strategies that will improve resistance in enhanced rice germplasm. 1b.Approach (from AD-416) Develop molecular markers associated with the economically important traits of a) disease resistance, with emphasis on rice blast and rice sheath blight and b) end-use quality, with emphasis on starch biosynthesis, which will improve identification of these traits in rice germplasm and promote the usefulness of marker-asisted selection in developing improved rice germplasm. Molecular markers will allow more efficient incorporation of Oryza spp. DNA into cultivated rice and can be used to further identify Oryza spp., backcross progenies, RILs, and genetic stocks. Characterize the Pi-ta gene-mediated signal transduction pathways which will aid in the development of both conventional and novel strategies to improve blast resistance for US rice germplasm. Identify differentially expressed genes upon pathogen attack to enhance understanding of the molecular mechanisms of interactions of necrotrpohic fungal pathogen and host. This may lead to the development of molecular markers for marker-assisted selection. 4.Accomplishments Evolution of disease resistance genes in rice: Evaluating genetic sequence variability in cultivated, wild and weedy species of rice allows scientists to study gene evolution. Scientists at the Dale Bumpers National Rice Research Center at Stuttgart, AR determined the genetic sequence of the Pi-ta gene in 52 accessions derived from six rice species. Results indicate that the Pi-ta gene is an ancient gene which is found in wild, weedy relatives of cultivated rice that has undergone numerous mutations through evolution which have had no apparent affect. However, a recent mutation has resulted in a single amino acid change altering the protein produced by this gene to confer resistance to the fungus which causes blast disease in rice plants. Knowledge of the relationship between the structure and function of this gene will help geneticist to develop rice cultivars with durable resistance to diseases. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits) Phytotoxin is identified as a component of susceptibility to sheath blight disease in rice: Although sheath blight is an important disease of rice worldwide, effective methods for screening for resistance in rice germplasm have been lacking. Sensitivity to a phytotoxin derived from Rhizoctonia solani was shown to correlate with disease susceptibility by researchers at the Dale Bumpers National Rice Research Center in Stuttgart, AR. The phytotoxin method increased the accuracy of disease evaluations and will facilitate the identification of chromosomal regions associated with sheath blight resistance. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits) Identification of chromosomal locations of agronomic traits in rice: Mapping populations between cultivated rice and its two ancestral species, O. nivara and O. rufipogon, can be used to understand the evolution of important agronomic genes. At the Dale Bumpers National Rice Research Center in Stuttgart, AR a mapping population between the U.S. medium grain cultivar M-202 and an O. nivara accession (IRGC 100195) was evaluated for seedling vigor, and agronomic and grain quality traits. The chromosomal locations of genes (QTL) for these traits were identified and many corresponded to regions identified in other mapping populations. Validation of putative QTL is critical for precisely mapping important genes and eventually determining gene function. (NP301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2B: Structural Comparison and Analysis of Crop Genomes, and Problem Statement 2C: Genetic Analyses and Mapping of Important Traits) 6.Technology Transfer Number of non-peer reviewed presentations and proceedings 15 Number of newspaper articles and other presentations for non-science audiences 8 Review Publications Olsen, K.M., Caicedo, A.L., Jia, Y. 2007. The evolutionary genomics of weedy red rice in the U.S.A. Journal of Integrative Plant Biology. 49:811-816. Jia, Y., Coarrea-Victoria, F., McClung, A.M., Zhu, L., Liu, G., Wamishe, Y., Xie, J., Marchetti, M.A., Pinson, S.R., Rutger, J.N., Correll, J.C. 2006. Rapid determination of rice cultivar responses to the sheath blight pathogen Rhizoctonia solani using a micro-chamber screening method. Plant Disease. 91:485-489. Wang, Z., Redus, M., Jia, Y. 2005. Establishment of codominant marker for rice blast resistance gene pi-ta. Chinese Journal Rice Science. 19(6):483-488. Chen, C., Yun, K., Ressom, H., Mohanty, B., Bajic, V.B., Jia, Y., Yun, S., De Los Reyes, B.G. 2007. Reactive oxygen species trigger a regulatory module involved in the early responses of rice seedlings to cold stress. Biomed Central (BMC) Genomics. 18:175.