Multi-omics dissection of molecular and metabolic drivers of pineapple fruit flesh translucency

Fruit flesh translucency is a major physiological disorder that severely compromises pineapple quality, yet its molecular basis remains insufficiently understood. To address this gap, we performed integrated transcriptomic and metabolomic analyses comparing translucent and healthy fruits of the cultivar ‘MD2’. Transcriptomic and metabolic reprogramming revealed that sugar transporters were markedly down-regulated, accompanied by enhanced glycolysis, organic acid turnover, and amino acid biosynthesis, leading to local accumulation of soluble sugars and polyols and increased osmotic potential. Coordinated cell wall degradation, membrane phospholipid remodeling, and reduced aquaporin expression impaired water homeostasis, thereby promoting extracellular fluid accumulation. Concurrent activation of antioxidant defense and stress-responsive transcription factors indicated intensified oxidative stress, while brassinosteroid, jasmonate, and calcium signaling appeared to modulate these metabolic and structural responses. Collectively, these findings provide a comprehensive molecular framework for understanding pineapple translucency and offer potential molecular targets and practical insights that could inform breeding and management strategies to mitigate this disorder and improve fruit quality.