2012 Annual Report 1a.Objectives (from AD-416): The objectives are to identify differentially expressed genes in Rpp2 and rpp2 gentoypes, and Rps8 and rps8 genotypes during post-infection response to Asian Soybean Rust and Phytophthora Root and Stem Rot pathogens, respectively. 1b.Approach (from AD-416): Soybean lines resistant (Rpp2) or susceptible (rpp2) to Asian Soybean Rust will be inoculated with the rust pathogen by collaborators in Brazil. Tissue samples will be collected at time zero, plus four other timepoints. RNA will be isolated from tissue representing each time point. Libraries will be made from each time point and provided to the cooperator. The cooperator will generate Solexa Digital Gene Expression data for each library. In addition, the cooperator will generate Solexa Whole Transcriptome Shotgun data from two pooled libraries representing resistant and sensitive lines. Soybean lines resistant (Rps8) or susceptible (rps8) to Phytophthora sojae will be inoculated with the Phytophthora pathogen. Tissue samples will be collected at time zero, plus three other timepoints. RNA will be isolated from tissue representing each time point. Libraries will be made from each timepoint and provided to the cooperator. The cooperator will generate Solexa Digital Gene Expression data for each library. In addition, the cooperator will generate Solexa Whole Transcriptome Shotgun data from libraries representing resistant and sensitive lines. The cooperator will generate a database of gene expression based on transcript counts and will provide this information to the ADODR. Differentially expressed genes will be overlain onto the soybean whole genome sequence and correlated with known positions of resistance genes. 3.Progress Report: RNA-Seq technology was used to identify differentially expressed genes in iron efficient and iron inefficient genotypes, grown hydroponically in iron sufficient and iron insufficient conditions. Root tissue was harvested at one hour, six hour, and 24 hours post-stress induction. RNA-Sequencing was conducted on RNA isolated from the root tissue. Sequence data has been returned to ARS PI and is currently being analyzed to identify differentially expressed genes involved in early stages of the soybean response to iron deficiency. Differentially expressed genes are compared to the soybean Gene Atlas to determine in which tissues specific genes are expressed. These analyses contribute to the whole genome annotation of the soybean genome sequence.