Single-nucleus transcriptome analysis reveals spatial and cell-type-specific responses to sunburn in grape berries

Abstract Sunburn, a physiological disorder triggered by high temperature and intense light, severely impacts grape berry quality and yield. However, the underlying molecular mechanisms, particularly the cell-type-specific responses, remain poorly understood. Here, we combined physiological characterization with single-nucleus RNA sequencing to investigate the spatiotemporal dynamics of sunburn responses in grape berries under natural field conditions. The first single-nucleus transcriptomic atlas of grape berry was established, identifying three major cell types: exocarp, mesocarp, and vascular cells. Analyses revealed distinct yet coordinated transcriptional reprogramming across cell types, with vascular cells, exhibiting the highest sensitivity, enriched in signal transduction and transport functions; mesocarp cells activating photoprotection and metabolic homeostasis; and exocarp cells specializing in defense responses including cuticle and stilbene biosynthesis. Pseudotime trajectory and co-expression network analyses collectively uncovered a programmed spatiotemporal response pattern, with sequential activation initiating in vascular cells for signal perception, progressing through mesocarp cells for metabolic support, and culminating in exocarp cells for physical and chemical defense. Functional validation confirmed that the exocarp-specific stilbene synthase gene VvVINST1 significantly enhanced sunburn resistance through coordinated enhancement of stilbenoid accumulation, enzymatic antioxidant defense, and hormonal homeostasis in the exocarp. This multi-level integration of field phenotypes, physiological data, single-cell molecular evidence, and gene functional validation proposes a ‘cell-type-specific programmed response’ model for grape berry sunburn. These findings provide crucial insights and genetic resources for enhancing abiotic stress resistance in horticultural crops at single-cell resolution.