RNA-seq Reveals Differential Responses in Vitis vinifera Cultivars Protected by Distinct Biocontrol Agents Against Neofusicoccum parvum 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 Trichoderma spp. and Bacillus spp., are described as promising. This study aimed to thoroughly investigate the physiological changes in grapevines induced by two BCAs, Bacillus subtilis ( Bs PTA-271) and Trichoderma atroviride ( Ta SC1), which are used to protect two cultivars from Neofusicoccum parvum 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: Bs PTA-271’s protective effect against infection in Chardonnay was mainly related to the phenylpropanoid pathway and secondary metabolic processes, whereas that of Ta 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 N. parvum.