A Comparative Transcriptomic Study Reveals Temporal and Genotype-Specific Defense Responses to Botrytis cinerea in Grapevine

Grapevine (<i>Vitis vinifera</i> L.), a globally significant crop, is highly susceptible to <i>Botrytis cinerea</i>, the causative agent of gray mold disease. This study investigates transcriptomic responses to <i>B. cinerea</i> in tolerant and susceptible grapevine genotypes using RNA sequencing (RNA-seq). Differentially expressed genes (DEGs) were identified at three time points (T1, T2, T3), highlighting both genotype-independent and genotype-specific responses. Early-stage infection (T1) revealed rapid and robust activation of defense pathways in both genotypes, though the tolerant genotype showed enhanced modulation of metabolic processes by T2, prioritizing secondary metabolism and stress adaptation over growth. In contrast, the susceptible genotype exhibited less coordinated metabolic reprogramming, with delayed or weaker activation of key defense mechanisms. Gene Ontology and KEGG analyses identified critical pathways, including phenylpropanoid biosynthesis-like lignin metabolism, <i>MAPK</i> signaling, as well as candidate genes such as <i>WRKY</i> transcription factors and enzymes involved in cell wall fortification and antifungal compound biosynthesis. Genotype-specific responses emphasized metabolic flexibility as a determinant of resistance, with the tolerant genotype exhibiting superior resource allocation to defense pathways. These findings provide insights into the molecular basis of grapevine resistance to <i>B. cinerea</i>, offering potential targets for breeding or genetic engineering to enhance resilience and reduce fungicide dependency.