Document Type : Research Paper
Authors
1 Assistant Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
2 2. Associate Prof, Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran.
10.30473/cb.2024.71791.1973
Abstract
Sclerotinia stem rot (SSR), caused by the soil-borne fungus Sclerotinia sclerotiorum, adversely impacts seed quality in rapeseed (Brassica napus) causing a 10-20% reduction in crop yield. The biological control agent Pseudomonas chlororaphis PA23 can protect rapeseed from the deleterious effects of the hemibiotrophic fungus S. sclerotiorum by inducing systemic resistance. However, little is known about the molecular mechanisms underlying defense priming and its regulatory processes. In this study, we amid to identify the protein-protein interaction (PPI) networks, with a particular focus on potential hub genes, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and regulatory network analysis including hub genes promoter analysis and miRNA prediction in canola plants pre-treated by PA23 in the presence of S. sclerotiorum using transcriptome data. Using the computational algorithms of the CytoHubba plugin in the Cytoscape platform, nodes with the highest interactions within the gene network were identified as hub genes, which are mainly involved in the maintenance and retrieval of metabolic pathways and photosynthetic activities, controlling cellular oxidation/reduction (redox) status, biosynthesis of aromatic amino acids and plant hormones, activation of MAPK-mediated defense signals, regulation of sulfur assimilation and cysteine biosynthesis. Using clustering analysis based on the IPCA algorithm in the Cytocluster plugin, functional modules effective in defense priming against SSR infection were identified. These modules were primarily involved in the biosynthesis of aromatic amino acids and the production of defensive metabolites in the shikimate pathway. The promoter analysis of 5′UTR region of hub genes identified various cis-regulatory elements (CREs), such as auxin signaling-responsive motifs involved in regulating defense responses against S. sclerotiorum infection. Prediction of miRNAs targeting hub genes, using the web-based psRNATarget program, revealed that miRNAs belonging to the families miR172, miR395, miR6028, miR6029, miR6032, miR6035, miR166, miR156, miR396 and miR824 play key roles as regulatory elements in the gene expression network of hub genes. These findings can aid in establishing biological control systems for plant disease management and protection of agricultural systems, as well as in advancing the fundamental mechanisms for developing disease-tolerant varieties.
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