Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L

• Published in: Scientific reports 2024-07, Vol.14 (1), p.15839-15, Article 15839
• Main Authors: Eshaghi, Mahsa, Rashidi-Monfared, Sajad
• Format: Article
• Language: English
• Subjects: 631/114; 631/114/2114; 631/61; Biosynthesis; Biosynthetic Pathways - genetics; Co-regulation networks analysis; Crocus - genetics; Crocus - metabolism; Crocus sativus; Ecotypes; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene regulation; Gene Regulatory Networks; Genes; Hub TFs; Humanities and Social Sciences; Medicinal plants; Metabolites; multidisciplinary; Plant Proteins - genetics; Plant Proteins - metabolism; Protein biosynthesis; Science; Science (multidisciplinary); Secondary Metabolism - genetics; Secondary metabolites; Transcription Factors - genetics; Transcription Factors - metabolism; Zinc finger proteins
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-65870-z

Saffron ( Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation ( P