Co-Expression Networks in Sunflower: Harnessing the Power of Multi-Study Transcriptomic Public Data to Identify and Categorize Candidate Genes for Fungal Resistance

• Published in: Plants (Basel) 2023-07, Vol.12 (15), p.2767
• Main Authors: Ribone, Andrés I, Fass, Mónica, Gonzalez, Sergio, Lia, Veronica, Paniego, Norma, Rivarola, Máximo
• Format: Article
• Language: English
• Subjects: Analysis; Annotations; Arabidopsis thaliana; Automation; Biological activity; Cell division; co-expression networks; Crop diseases; Disease resistance; Diseases and pests; Food security; Food supply; Fungal diseases of plants; fungal pathogens; Fungi; Gene expression; Genes; Genetic aspects; Genetic research; Genomes; Genomics; Helianthus annuus; Identification and classification; Machine learning; Medical research; Medicine, Experimental; Meta-analysis; Modules; Network analysis; Pathogens; Physiological aspects; Plant diseases; Plant genetics; Plant immunology; plant pathology; Plant tissues; Proteins; Quantitative trait loci; Sunflowers; Transcription factors; Transcriptomes; Transcriptomics; WRKY
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12152767

Fungal plant diseases are a major threat to food security worldwide. Current efforts to identify and list involved in different biological processes are more complicated than originally thought, even when complete genome assemblies are available. Despite numerous experimental and computational efforts to characterize gene functions in plants, about ~40% of protein-coding genes in the model plant L. are still not categorized in the Gene Ontology (GO) Biological Process (BP) annotation. In non-model organisms, such as sunflower ( L.), the number of BP term annotations is far fewer, ~22%. In the current study, we performed gene co-expression network analysis using eight terabytes of public transcriptome datasets and expression-based functional prediction to categorize and identify involved in the response to fungal pathogens. We were able to construct a reference gene network of healthy green tissue (GreenGCN) and a gene network of healthy and stressed root tissues (RootGCN). Both networks achieved robust, high-quality scores on the metrics of guilt-by-association and selective constraints versus gene connectivity. We were able to identify eight modules enriched in defense functions, of which two out of the three modules in the RootGCN were also conserved in the GreenGCN, suggesting similar defense-related expression patterns. We identified 16 WRKY genes involved in defense related functions and 65 previously uncharacterized now linked to defense response. In addition, we identified and classified 122 previously identified within QTLs or near candidate reported in GWAS studies of disease resistance in sunflower linked to defense response. All in all, we have implemented a valuable strategy to better describe genes within specific biological processes.