Characterization of Resistant and Susceptible Responses to Phialophora gregata in Soybean using RNA-Seq

Breeding for pathogen resistance is an important objective to improve and protect soybean yields. In 2010, 14.4% of total soybean yield was suppressed by diseases. Brown stem rot (BSR), caused by the fungus Phialophora gregata, reduces yield by as much as 38%. To date, three dominant BSR resistance genes have been identified: Rbs1, Rbs2, and Rbs3, however the gene networks regulating defense responses to BSR remain unknown. Further, identifying resistant germplasm by genotyping or phenotyping remains difficult due to complexities of soybean/P. gregata interactions. To better understand resistance mechanisms, we conducted RNA-Seq of P. gregata infected and mock infected leaf, stem, and root tissues of both a resistant (PI 437970, Rbs3) and a susceptible (Corsoy 79) soybean genotype. Samples were collected one-week post infection. Our bioinformatic analyses focused on treatment, genotype, and treatment by genotype effects on gene expression. Our results indicate that resistant and susceptible genotypes respond differently when infected with P. gregata. Further, regardless of infection, the resistant and susceptible genotypes differ in their innate defense responses. These data indicate that molecular markers could be developed to allow identification of resistant and susceptible individuals at 1 week post infection, four weeks earlier than current protocols. Given that Rbs3 has been mapped to soybean chromosome 16, the RNA-Seq data was also used to generate novel SNPs within the Rbs3 locus that could be used for fine mapping Rbs3. Virus induced gene silencing (VIGS) was also used to characterize the candidate resistance genes and downstream defense responses.