Transcriptional Insights Suggest Altered Ripening Progression and Sugar Regulation in Japanese Indigenous Wine Grape Vitis sp. cv. Koshu

<i>Vitis</i> sp. cv. Koshu is an important Japanese indigenous wine grape cultivar. However, it possesses challenging traits for winemaking, including large berries and low sugar content. To explore the transcriptional profile associated with these characteristics, we conducted a comparative transcriptome analysis of the berry flesh of Koshu and Chardonnay at 10 days after the onset of véraison. A total of 5534 differentially expressed genes were identified, revealing a distinct transcriptional profile in Koshu. The expression patterns in Koshu suggest an altered ripening progression, characterized by the marked downregulation of the ripening marker <i>Grape Ripening-Induced Protein 22-like</i> (<i>GRIP22-like</i>) and the upregulation of photosynthesis-related genes. Despite its large-berry phenotype, cell wall-loosening genes were suppressed in Koshu, leading to the hypothesis that its size may reflect cell division in the early growth stage rather than cell expansion during ripening. Its low-sugar phenotype appears to be associated with multiple factors, including the suppression of key sugar accumulation enzyme genes, such as <i>sucrose synthase 2</i> (<i>SS2</i>) and <i>sucrose-phosphate synthase 1</i> (<i>SPS1</i>), the upregulation of <i>Early Response to Dehydration 6-like</i> (<i>ERD6-like</i>) genes, which encode putative vacuolar glucose exporters, and the suppression of cell wall-loosening genes, suggesting a potential biophysical limitation on sugar storage. This study provides the first detailed transcriptomic resource for Koshu berry and identifies key candidate genes for future breeding strategies to improve this unique cultivar.