Chloroplast-related pathways involved in grapevine drought responses

Abstract

Water scarcity is an increasing constraint for viticulture in Mediterranean regions, making the identification of molecular mechanisms underlying drought tolerance a key objective for grapevine breeding and management. While transcriptomic studies have revealed strong cultivar-dependent responses, the regulatory networks supporting these differences remain poorly characterized.

This study investigated drought-responsive transcriptional regulation in six Portuguese Vitis vinifera L. cultivars grown under field conditions and subjected to contrasting irrigation regimes (irrigated vs. rainfed). At the end of the ripening period, leaf samples were collected from three biological replicates per cultivar and irrigation regime. Total RNAwas sequenced using paired-end Illumina sequencing. RNA-seq data was analyzed using a combination of cultivar-specific differential expression analysis and weighted gene co-expression network analysis (WGCNA) performed across all cultivars.

The gene co-expression module most strongly correlated with the rainfed condition was predominantly composed of genes encoding proteins localized to chloroplasts and thylakoids, although not directly enriched in photosynthesis-related biological processes. Guided by this pattern, cultivar-specific responses were explored to assess how chloroplast-associated responses were manifested at the cultivar level.

Pronounced cultivar-dependent differences were observed in the regulation of chloroplast-related genes under water deficit. Cultivars exhibiting broader transcriptional responses showed a markedly higher proportion of up-regulated genes associated with chloroplasts and thylakoids. Photosynthesis-related biological processes were exclusively detected among up-regulated genes in four of the six cultivars, with no photosynthesis-associated down-regulation. These included core components of photosystem II and photosystem I, light-harvesting complexes, electron transport and NDH complex elements. Consistent with the WGCNAmodule, additional up-regulated genes were involved in thylakoid architecture and photosystem assembly, chloroplast gene expression and protein synthesis, protein folding and quality control mechanisms, redox regulation and oxidative stress control.

These findings support a conceptual framework in which chloroplasts act not only as sites of photosynthesis but as metabolic centers that integrate environmental signals and coordinate cellular responses to water stress through adjustments in photosynthetic capacity, structural organization, protein homeostasis, and antioxidant defenses. The identification of both conserved chloroplast-centered responses and cultivar-specific regulatory patterns provides valuable insights for grapevine breeding strategies aimed at improving drought tolerance in Mediterranean viticulture.

Funding

This work is funded by National Funds through FCT – Foundation for Science and Technology under the Project UID/05183/2025 and under the PhD scholarship 2024.00814.BDANA.

Acknowledgements

The authors acknowledge the R&D unit MED – Mediterranean Institute for Agriculture, Environment and Development (https://doi.org/10.54499/UID/05183/2025) and the Associate Laboratory CHANGE – Global Change and Sustainability Institute (https://doi.org/10.54499/LA/P/0121/2020), and the project BioGrapeSustain, Vine&Wine – SubProject Proposal – Project 81 Agenda Mobilizadora: Driving Sustainable Growth Through Smart Innovation (Reference C644866286-00000011).