RNA regulatory landscapes in fleshy fruits: From regulation mechanisms to quality design

Fruit quality is a complex trait shaped by developmental programs, metabolic networks, and environmental responses; yet, the RNA-level regulatory processes that determine functional outputs remain insufficiently integrated and underexplored. In this review, we provide an integrated overview of RNA-mediated regulatory mechanisms underlying fleshy fruit quality formation, focusing on five major layers, including RNA modification, organellar RNA editing, alternative splicing, long non-coding RNAs, microRNAs, and their crosstalk. We summarize their molecular modes of action and discuss how these regulatory mechanisms shape diverse quality traits, including fruit morphology, pigmentation, flavor, texture remodeling, ripening progression, and postharvest performance. Furthermore, we highlight emerging strategies for harnessing RNA-mediated regulation to improve and maintain fruit quality, including RNA-centered multi-omics integration, AI-driven design of RNA regulatory elements, and precision of RNA-level manipulation. We propose that deciphering and manipulating post-transcriptional regulatory codes will provide a conceptual and technological framework for shifting fruit improvement from empirical selection toward rational RNA-guided quality design, with broad implications for crop improvement, nutritional enhancement, and sustainable postharvest management.