RNA-seq Reveals Differential Responses in <i>Vitis vinifera</i> Cultivars Protected by Distinct Biocontrol Agents Against <i>Neofusicoccum parvum</i> Bt67

Botryosphaeria dieback (BD) is a worldwide grapevine trunk disease constituting a serious threat to sustainable grapevine production, especially in the context of climate change. Effective treatments to control BD are still lacking, prompting the exploration of new non-chemical alternatives. Among these, biocontrol agents (BCAs), such as <i>Trichoderma</i> spp. and <i>Bacillus</i> spp., are described as promising. This study aimed to thoroughly investigate the physiological changes in grapevines induced by two BCAs, <i>Bacillus subtilis</i> (<i>Bs</i> PTA-271) and <i>Trichoderma atroviride</i> (<i>Ta</i> SC1), which are used to protect two cultivars from <i>Neofusicoccum parvum</i> Bt67 (Np-Bt67) infection. Using nontarget transcriptomic analysis (RNA-seq) and validation by qRT-PCR, this research offers novel insights into the molecular responses associated with Np-Bt67 infection in Chardonnay and Tempranillo cultivars in relation to the protective mechanisms conferred by each BCA. RNA-seq revealed that the cultivars showed no common transcriptional changes upon pathogen challenge. In Chardonnay, changes were mainly related to terpene/carotenoid pathways, whereas in Tempranillo, they mostly related to amino acid transport and photosynthesis. Following the inoculation of protective BCA, changes were also distinct between the infected cultivars: <i>Bs</i> PTA-271's protective effect against infection in Chardonnay was mainly related to the phenylpropanoid pathway and secondary metabolic processes, whereas that of <i>Ta</i> SC1 for Tempranillo correlated with more metabolic changes. Consecutive validation by qRT-PCR provided markers indicating grapevine susceptibility versus protection against Np-Bt67, some of which are shared by both cultivars. These markers could offer valuable tools for monitoring the health status of grapevine toward <i>N. parvum</i>.