Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

Authors: MORALES, AGUIDA - Universidade Federal De Vicosa; O`Rourke, Jamie; VAN DE MORTEL, MARTIJN - Iowa State University; Schneider, Katherine; BANCROFT, TIMOTHY - Iowa State University; BOREM, ALUIZIO - Universidade Federal De Vicosa; Nelson, Rex; NETTLETON, DAN - Iowa State University; BAUM, THOMAS - Iowa State University; Shoemaker, Randy; Frederick, Reid; ABDELNOOR, RICARDO - Embrapa; Pedley, Kerry; WHITHAM, STEVEN - Iowa State University; Graham, Michelle

Submitted to: Functional Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/11/2013
Publication Date: 7/15/2013
Citation: Morales, A., O'Rourke, J.A., Van De Mortel, M., Schneider, K., Bancroft, T., Borem, A., Nelson, R., Nettleton, D., Baum, T., Shoemaker, R.C., Frederick, R.D., Abdelnoor, R.V., Pedley, K.F., Whitham, S.A., Graham, M.A. 2013. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. Functional Plant Biology. DOI:10.1071/FP12296.

Interpretive Summary: Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, has now spread to every major soybean producing country in the world. Yields losses as high as 80% have been reported. To understand the molecular basis of resistance, we have examined the expression of ~37,000 soybean genes following infection with P. pachyrhizi. Analyses compared gene expression over a seven day timeline in resistant (carrying the Rpp4 resistance gene) and susceptible soybean lines infected or mock-infected with rust. Genes expressed early in the timeline are likely basic defense genes while genes expressed later are likely involved in Rpp4-mediated resistance. Our analysis identified 4,136 genes expressed in response to P. pachyrhizi infection in the resistant line and 4038 expressed in the susceptible line. We compared these differentially expressed genes to microarray analyses performed in Rpp2 and Rpp3 resistant genetic backgrounds. Surprisingly, only 54 genes were expressed in all three genetic backgrounds (Rpp2, Rpp3 and Rpp4). These genes will provide targets for future studies designed to assess their role in ASR resistance.

Technical Abstract: Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to P. pachyrhizi, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a twelve-day time course. Surprisingly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 hours after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defense responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression data sets were compared to microarray data previously generated for Rpp2 and Rpp3-mediated defense responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.