2012 Annual Report 1a.Objectives (from AD-416): 1. Use virus induced gene silencing (VIGS) to turn off candidate resistance genes in the Brown Stem Rot resistant genotypes. Test silenced plants for susceptibility to Brown Stem Rot. 2. Use Solexa transcript sequencing to determine which resistance genes in the Rbs3 locus are expressed preferentially in the resistant parent and correlate with Brown Stem Rot resistance. 3. Use the Williams 82 genome sequence to fine map Rbs3 in a population segregating for Brown Stem Rot resistance (BSR101 x PI437654, developed by Lewers et al. 1999). Develop SSR markers to be used for marker-assisted selection of BSR resistance. 1b.Approach (from AD-416): Our approach will identify candidate Brown Stem Rot resistance genes for Rbs3. We will leverage the Williams 82 genome sequences and use it to identify candidate genes from the resistant parents. We have compared sequence from the Williams 82 soybean genome to markers that have been used to map Rbs3. The region corresponding to Rbs3 has been bioinformatically screened for the presence of genes with similiarity to known resistance genes. The sequences of these R-genes has been used to develop Virus Induced Gene Silencing Constructs. These constructs will be tested on Brown Stem Rot resistant genotypes to determine if we can turn off resistance to Brown Stem Rot. This information will identify a cluster of genes responsible for resistance. To identify the actual genes, we will use solexa transcript sequences to compare Brown Stem Rot resistant and susceptible genotypes before and after infection with Brown Stem Rot. Significantly differentially expressed genes in the Rbs3 cluster will be candidates for Rbs3. In addition, we will use fine mapping to further define the candidate genes. 3.Progress Report: Plant mechanisms for controlling infection by Phiolophora gregata (the causal agent of Brown Stem Rot (BSR) in soybeans) are poorly understood. Unlike most soybean-pathogen systems, scoring resistance or susceptibility to BSR takes six to seven weeks. It is unclear if resistance is not induced until that time or if we are unable to detect early resistance by visual inspection. We have set up time course experiments to compare resistant and susceptible genotypes infected with P. gregata compared to mock-infected controls. Currently, we are isolating RNA from resistant and susceptible plants infected and mock infected with P. gregata over a large time course spanning 24 hours post-infect to 21 days post infection. RNA will be used for microarray analysis to determine when and how resistance occurs. The results will be used to improve our virus induced gene silencing approaching for identifying candidate resistance genes.