Organic acids are the core of fruit flavor quality and cell metabolism, but a comprehensive review of their metabolism and regulatory networks in fruit trees is still limited. Here, we systematically summarized the biosynthesis, degradation and transport of major organic acids in fruits of horticultural crops. We focused on the distribution and molecular regulation of organic acids in citrus, pome fruits, stone fruits, grapes and tropical–subtropical fruits, and emphasized the regulation of transcription factors, epigenetic modifications and environmental signals. We also evaluated the progress of various omics strategies for dissecting organic acid metabolism and identifying key regulatory genes. Finally, we discuss the current research gaps and propose future directions for multi-gene editing and molecular design breeding. This review provides a theoretical framework for improving fruit flavor quality and breeding excellent varieties.

Phenolic compounds are critical components that determine the processing quality of wine grapes, and their accumulation is jointly affected by environmental conditions and genotype. However, the respective contributions of production site and cultivar, as well as the response differences in various phenolic components to environmental changes, remain unclear in northern China. In this study, three major red wine grape cultivars (Vitis vinifera L. cvs. Marselan, Cabernet Franc, Cabernet Sauvignon) were sampled from three typical producing areas, including Turpan, the Hexi Corridor, and Huailai in 2024. Botanical characteristics, quantitative agronomic traits, physicochemical indexes, and five phenolic components in berry skins and seeds were determined with three biological replicates. A general linear model (GLM) was used to quantify the effects of production site and genotype on berry quality, and principal component analysis (PCA) and Pearson correlation analysis were performed to explore the relationships between quality indicators. Our results indicate that clear quality differences were observed among the three studied production sites, which were the main source of variation in this dataset, accounting for 65.7% to 82.1% of total variance across most traits. Three distinct regional patterns were observed: grapes from Xinjiang had the highest sugar content, those from Gansu had the highest phenolic levels, and those from Zhangjiakou were richest in anthocyanins. The responsiveness of individual phenolic components to ecological conditions varied markedly, with anthocyanins being the most sensitive, followed by proanthocyanidins, tannins, total phenolics, and flavonoids. Marselan maintained a stable genotypic advantage in proanthocyanidin accumulation across all three sites, with skin levels 12.5–230.5% higher than other cultivars under the same growing conditions. Additionally, a potential tissue-specific association between cluster weight and phenolic components was preliminarily observed: higher cluster weight was associated with lower concentrations of late-accumulating anthocyanins and proanthocyanidins, but did not negatively affect total phenolics and tannins that form in early fruit development. Based on the above results, preliminary suggestions for cultivar–site matching were provided for reference. This study provides preliminary baseline data for cultivar selection and viticultural management in northern China, pending further multi-year validation.

To dissect the genetic trends of phenolic compounds in wine grapes and identify key regulatory genes for epicatechin (EC) synthesis, this study used an F1 population derived from ‘Pinot Noir’ × ‘Marselan’ as material. SSR molecular markers were used to verify the authenticity of hybrid offspring, and genotyping by target sequencing (GBTS) combined with genome-wide association study (GWAS) was employed to locate EC-related loci. The candidate gene VvCHR5 was then cloned, subjected to expression analysis, and functionally validated through Agrobacterium-mediated transient overexpression in grape berries. The results showed that 281 true hybrids were identified from 305 progeny, with a true hybrid rate of 92.13%. In F1 seeds, proanthocyanidins showed moderately high inheritance, and total flavonoids tended toward intermediate-to-low inheritance. Seeds were the main site of tannin accumulation, with C, EC, and EGC as the core monomers. GWAS detected three EC-related SNP loci distributed on Chr1, Chr6, and Chr12, and candidate genes such as VvCHR5 were identified. Transient overexpression of VvCHR5 significantly promoted EC accumulation in ‘Muscat Hamburg’ seeds. On day 4 after injection, EC increased to approximately 15 times the level of the empty vector control; on day 8, it remained significantly higher than the control, with an increase rate of approximately 326.72%. These findings suggest that VvCHR5 may affect EC accumulation by altering carbon flux within the flavonoid metabolic pathway, providing loci, genes, and materials for molecular breeding of phenolic quality in wine grapes.