Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring transcriptome Responses to Drought

Abstract

Climate change poses a significant threat to agriculture, particularly in regions where increased drought periods, abnormal heat, and intensified pest pressure threaten crop productivity. Viticulture, as one of the most economically important crops, is highly vulnerable to these challenges. Understanding the molecular mechanisms underlying drought responses in grapevines is essential for developing innovative molecular breeding strategies aimed at enhancing drought tolerance, improving cultivar resilience, and promoting agricultural sustainability. In this context, transcriptomic meta-analyses have proven valuable for uncovering global regulatory trends, gene co-expression networks and conserved biological responses across diverse conditions. As part of this study, 1107 public transcriptomic datasets from Illumina (631 runs) and ABI SOLID (476 runs) platforms were searched, reclassified and reanalyzed in the latest T2T genome assembly, in order to construct condition, cultivar and tissue-specific gene expression atlases associated with drought stress in grapevine. To facilitate exploration of this data, a web-based application, the Hydric Stress Atlas App (https://plantaeviz.tomsbiolab.com/vitviz/hydric_atlas/), was developed, as part of the Vitis module within the PlantaeViz platform. Together with this tool, we generated a whole-genome co-expression network using the same datasets (https://plantaeviz.tomsbiolab.com/vitviz/networks/non_agg_gcns/T2T/hydric_stress_TI/). This water stress condition-dependent GCN allows to explore and visualize gene co-expression relationships related to stress and identify network hubs holding novel drought stress regulators. We manually curated experimental metadata, and enabled the classification of transcriptomic data by cultivar, tissue, and drought tolerance. Finally, candidate genes associated with drought tolerance were identified via network topology analysis. These genes can be further used as molecular markers, or characterized via gene editing or cisgenesis, providing insights into their molecular roles in drought tolerance. This resource contributes to a deeper understanding of grapevine drought responses, offering a pathway for sustainable viticulture and innovative biotechnological solutions to address climate-related challenges.