Integrated genetic and functional analyses reveal PEPC and cMDH as antagonistic regulators of grape acidity
Abstract
Breeding grape cultivars with optimized acidity is a priority for climate resilience, yet identifying causal regulators of malate metabolism remains challenging due to the complexity and long generation time of whole-vine functional studies. Multiple molecular and genetic studies, including QTL mapping, have highlighted the cytosolic malate dehydrogenase (cMDH) and phosphoenolpyruvate carboxylase/carboxykinase (PEPC/PEPCK) pathways as primary candidates for malate regulation. To dissect their specific roles, we integrated comparative transcriptomics with rapid functional characterization.
Compared to V. vinifera cultivars, high-malate wild species (V. riparia, V. cinerea) exhibited a distinct expression signature during ripening, characterized by elevated PEPC and reduced cMDH expression. To translate these findings to causal evidence, we utilized grape-derived cell cultures as a rapid reverse-genetics platform. Wild-type cultures reproduced the sugar-malate dynamics and coordinated expression of malate metabolic and transport genes characteristic of pre-veraison berries, supporting their suitability for functional studies of malate regulation.
Stable overexpression (OE) lines exhibited clear and opposing effects. PEPC OE increased malate accumulation by 47–50 % and enhanced biomass, while inducing PEPCK expression, linking these enzymes as highlighted by transcriptomic (PEPC) and QTL (PEPCK) analyses. Metabolite profiling revealed shifts in organic acids and amino acids, consistent with enhanced carbon flux into malate biosynthesis. In contrast, cMDH OE reduced malate levels by 25–30 % and increased sugars, mirroring the metabolic shift characteristic of berry ripening.
PEPC and cMDH emerge as antagonistic “push–pull” regulators of the malate-sugar balance and as promising targets for modulating fruit acidity under climate change. Gene-function validation remains a major bottleneck in grape genetics, particularly in the era of genome editing. Our results demonstrate that grape-derived cell cultures provide a rapid, valuable strategy for establishing gene-trait relationships and prioritizing editing targets prior to whole-vine transformation.
Acknowledgements
US-Israel Binational Agricultural Research and Development (BARD) Fund, project No. IS-5601-23D.
Issue: GBG 2026
Type: Oral
Authors
1 Dept. of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization – Volcani Institute, Israel
2 Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
3 Institute of Plant Sciences, Agricultural Research Organization – Volcani Institute, Israel
4 Albert Katz International School for Desert Studies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Israel
5 The French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Israel
6 Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
7 Department of Food Science, Cornell University, Ithaca, NY 14853, USA