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Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection

ABSTRACT: We profiled the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain) by small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis.

ORGANISM(S): Glycine max

PROVIDER: GSE76636 | GEO | 2016/06/30

SECONDARY ACCESSION(S): PRJNA308211

REPOSITORIES: GEO

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Project description:Resistance (R) genes are very effective for disease control in plants. Current research shows that R genes predominantly function by inducing a hypersensitive reaction (HR), which results in localized cell death thought to restrict pathogen spread. Some R genes elicit a more atypical response where resistance is not associated with HR or the associated gene expression changes, termed extreme resistance (ER). The molecular regulatory mechanism underlying ER is largely unexplored. One of the few known, naturally occurring, instances of ER is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent strains of soybean mosaic virus (SMV). To discern the regulatory mechanism underlying the Rsv3-mediated ER reaction, we generated a gene regulatory network using transcriptomic data from a time course comparison of SMV-G7-infected resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. We identified putative interactions between transcription factors (TFs) regulating gene expression in hormone regulatory pathways, such as abscisic acid (ABA) and jasmonic acid (JA). This is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. We found significant enrichment for the G-box motif (“CACGTG”) among genes implicated in ABA- and JA-related activities. This motif is specifically recognized by MYC2, which is a master regulator of ABA and JA signaling. Our network identified a MYC2 TF encoded by Glyma.07G051500 as a putative transcriptional regulator whose expression was significantly down-regulated in L29. This correlated with the down-regulation of expression of genes involved in ABA and JA processes. Our results suggest an important function for Glyma.07G051500 in ABA and JA derived defense signaling. Additionally, our regulatory network found other putative TFs with differential expression, such as MYBs and ERFs, which may also be involved in regulating ABA and JA signaling for defense. The regulatory network presented here offers new insights into the regulation of the molecular defense mechanism underlying Rsv3-mediated ER against SMV.

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Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection

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