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

Abstract

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, 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 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h 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 defence 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 datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence 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. Abstract. Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, 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 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h 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 defence 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 datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription...

Identification of Novel Genomic Loci Associated with Soybean Shoot Tissue Macro and Micronutrient Concentrations

“…The lowest number of candidate genes was identified for B and Mn (two each) and the highest for Fe (13). For all 56 unique candidate genes identified in this study, a gene ontology (GO) Enrichment analysis was conducted in Soybase (http://www.soybase.org, accessed 18 May 2018) (Morales et al, 2013) with the gene model and data mining and analysis option. Of the 56 genes, 55 had one or more GO classification, whereas one gene was not found in any GO classification.…”

Resistance against Sclerotinia sclerotiorum in soybean involves a reprogramming of the phenylpropanoid pathway and up‐regulation of antifungal activity targeting ergosterol biosynthesis

“…gov/pz/portal.html#!bulk?org=Org_Gmax) while soybean chloroplast (https://www.ncbi.nlm.nih.gov/nuccore/91214122) and mitochondrion (https://www.ncbi.nlm.nih.gov/nuccore/476507670) sequences were used from NCBI. The statistically significant DEGs ( P ‐value < 0.01; log 2 FC > 1 or <−1) of the R versus S comparison were used to identify enriched Gene ontology (GO) terms using the Soybase GO term enrichment tool (https://www.soybase.org/goslimgraphic_v2/dashboard.php) (Morales et al ., ).…”

“…We focus the reminder of this manuscript on direct comparisons between resistant and susceptible soybean lines, to single out potential processes associated with resistance to S. sclerotiorum in soybean. Soybean gene locus IDs identified through the DEG analysis were used to perform gene ontology (GO) enrichment analysis using the Soybase gene model data mining and analysis tool (Morales et al, 2013). A false discovery rate (FDR) value of 0.05 was used to identify significantly regulated GO biological processes, and individual GO processes were considered in this analysis if they were significantly enriched in at least one of the time points used (Table S3 and Figure 2).…”

“…The statistically significant DEGs (P-value < 0.01; log 2 FC > 1 or <À1) of the R versus S comparison were used to identify enriched Gene ontology (GO) terms using the Soybase GO term enrichment tool (https://www.soybase. org/goslimgraphic_v2/dashboard.php) (Morales et al, 2013).…”

Field‐grown soybean transcriptome shows diurnal patterns in photosynthesis‐related processes

“…Gene ontology (GO) annotations were downloaded from SoyBase (https://soybase.org/; (Grant, Nelson, Cannon, & Shoemaker, 2009)), and to identify GO terms that were overrepresented among DE genes, Fisher's exact test with a Bonferroni p-value correction was applied through the tool on SoyBase (Morales et al, 2013). Dominant diurnal transcription patterns among DE genes were identified with k-means clustering of log 2 (TMM) values in SAS PROC FAS-TCLUS.…”