Unravelling the molecular mechanisms of vegetative-to-reproductive transition in Cynara cardunculus by RNA-Seq analysis.

Cynara cardunculus inflorescence plays a significant role in cheese manufacturing and human consumption due to the milk-clotting capacity and the production of edible immature capitula. Consequently, it is crucial to understand the complex cellular and molecular processes involved in the development of cardoon flowers. The current study used western wild cardoon in two developmental stages, vegetative and reproductive, to understand the molecular mechanisms mediating cardoon`s vegetative-to-reproductive transition. Transcriptome profiling identified 552 differentially expressed genes (DEGs) between vegetative and reproductive stages, with 321 upregulated in stage 4 (vegetative state) and 231 in stages 5/6 (reproductive state). Gene Ontology (GO) analysis revealed DEGs involved in biological processes such as oxidation-reduction, lipid metabolism, and defense responses. Metabolic pathways, including phenylpropanoid biosynthesis and anther/pollen development, were significantly enriched. Genes associated with lignin formation, flavonoid synthesis, and acetyltransferase activity were upregulated in the vegetative stage. At the same time, those related to flower development and sesquiterpene lactone biosynthesis were prominent in the reproductive stage. Transcription factors, including MADS-box and ethylene-responsive families, were critical in regulating developmental transitions. This study provides comprehensive insights into the morphological, chemical, and molecular dynamics of C. cardunculus across its phenological stages, underscoring the plant’s adaptability and potential for pharmaceutical and industrial applications. The findings highlight the importance of seasonal and developmental timing in optimizing the production of valuable secondary metabolites, such as cynaropicrin.