Metabolomic and Transcriptomic Analyses Provide Insights into Metabolic Networks During Kiyomi Tangors Development and Ripening

Flavor formation in citrus fruit is governed by complex and dynamic changes in primary and secondary metabolism during development and ripening. Here, we integrated metabolomic, hormonal, and transcriptomic analyses to elucidate the regulatory landscape underlying soluble sugar and organic acid metabolism in ‘Kiyomi’ citrus fruit. A total of 1679 metabolites were identified, revealing stage-specific reprogramming of metabolic pathways, including a sharp decline in citric acid after 90 days after flowering (DAF) and peak accumulation of sucrose at 180 DAF. Hormonal profiling showed that abscisic acid (ABA) progressively accumulated from 120 to 210 DAF, while 1-aminocyclopropane-1-carboxylic acid (ACC) peaked at 120 DAF and declined thereafter, suggesting distinct and temporally coordinated roles in ripening regulation. Transcriptomic profiling uncovered widespread temporal shifts in gene expression, with the most pronounced changes occurring between 180 and 210 DAF. Co-expression network analysis identified gene modules associated with sugar and acid accumulation, and highlighted transcription factors from the ERF, MYB, NAC, and HSF families as candidate regulators of ripening-related metabolic transitions. These findings provide a comprehensive framework for understanding the coordinated molecular and metabolic programs underlying flavor development in non-climacteric citrus fruit and offer candidate genes for the genetic improvement of fruit quality.