The characteristic green-note aroma of Chinese plum (Prunus salicina) is largely defined by C6 aldehydes and alcohols synthesized through the fatty acid pathway involving lipoxygenase (LOX), hydroperoxide lyase (HPL), and alcohol dehydrogenase (ADH). However, the LOX/HPL/ADH gene families and their potential contributions to C6 volatile formation remain poorly characterized in Chinese plum. Here, we integrated genome-wide identification with cultivar-level volatile profiling and RT–qPCR expression analyses to link candidate genes with C6 volatile accumulation. We identified 8 PsLOX, 3 PsHPL, and 13 PsADH genes and classified them into 2, 1, and 3 subfamilies, respectively. Conserved motifs/domains were shared within each family, whereas gene-structure variation suggested functional divergence; segmental duplication was the main driver of family expansion. To explore their functional relevance to aroma biosynthesis, five major C6 aldehydes and alcohols were analyzed in ten cultivars using solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC–MS), revealing substantial diversity in green-note composition. Combined with reverse transcription quantitative polymerase chain reaction (qRT–PCR) expression profiling, low PsADH2.7 expression was associated with high hexanal content, whereas elevated PsLOX5 and PsADH2.2 expression corresponded to increased 1-hexanol accumulation. High 2-ethyl-1-hexanol levels were linked to increased PsLOX4.1 and PsHPL1.3 but decreased PsADH1.2 expression. In addition, (Z)-3-hexen-1-ol abundance showed strong positive correlations with PsLOX3.1, PsHPL1.2, and PsADH2.6 expression. This integrated genomic and expression–metabolite analysis highlights candidate genes potentially involved in C6 aldehyde/alcohol biosynthesis underlying the green-note aroma of Chinese plum and provides genetic targets for aroma-oriented breeding.

Fruit volatile organic compounds (VOCs) are key determinants of plum flavor quality, and esters contribute strongly to the fruity aroma of ripe fruit. However, the molecular basis of cultivar differences in ester formation during ripening has not been systematically clarified. Here, we characterized pulp VOC profiles across ripening in three Chinese plum (Prunus salicina) cultivars (‘WeiWang’ (WW), ‘WeiDi’ (WD), and ‘KongLongDan’ (KLD)) and integrated transcriptome analysis with weighted gene co-expression network analysis (WGCNA) to identify genes associated with ester accumulation. HS-SPME-GC-MS identified 38 VOCs, mainly esters, aldehydes, and alcohols, with ‘WW’ showing the highest total VOC abundance. During ripening, esters became the predominant volatile class in ‘WW’ and ‘WD’, in agreement with their fruity sensory characteristics, whereas ‘KLD’ maintained a more balanced composition of fruity and green-related volatiles. Transcriptomic analyses highlighted Prunus salicina alcohol acyltransferase 3 (PsAAT3) as the most abundant AAT transcript in pulp and strongly induced in ‘WW’. Transient overexpression of PsAAT3 in the low-ester background increased butyl acetate and hexyl acetate by 4.8- and 2.2-fold, respectively. WGCNA further identified ester-associated modules and candidate transcription factors co-expressed with PsAAT3 (JA2L, HY5, NAC073, and PHL13). As a result, this study identifies PsAAT3 as a key determinant of high-ester aroma in Chinese plum and provide candidate targets for aroma improvement and flavor-oriented breeding.

Background: Fruit texture is a major component of plum quality, affecting both consumer acceptance and postharvest behavior. Pectin methylesterases (PMEs) play important roles in cell-wall pectin modification and are therefore likely to contribute to plum fruit texture development and ripening-associated softening. However, the PME gene family has not yet been comprehensively investigated in plum (Prunus salicina L.). Methods: In the present study, a chromosome-level plum genome was used to survey this gene family at the whole-genome scale. Phylogenetic relationships, chromosomal positions, exon–intron organization, conserved motifs, domain architectures, gene duplication, and cis-elements were analyzed. Four flesh texture traits were measured in 55 plum accessions to characterize texture variation and select two representative cultivars with contrasting flesh textures for further molecular analysis. Based on the clustering results, ‘WSCL’ and ‘FR’ were selected for expression profiling during fruit development and subsequent correlation analysis with texture traits. Results: A total of 46 PsPME genes were identified. Phylogenetic analysis classified them into four major subgroups. Structural analyses indicated an overall conserved family framework, although noticeable variation was retained among individual members. Dispersed duplication made the largest contribution to family expansion, and most duplicated pairs appeared to have evolved under purifying selection. Correlation analysis showed that PsPME20, PsPME22, and PsPME25 were significantly negatively correlated with flesh firmness, while PsPME20 was additionally linked to flesh compactness and flesh fragility. Conclusions: Overall, this study clarifies the structural and evolutionary characteristics of the PsPME family and identifies candidate genes that may contribute to texture differences in plum, offering a basis for future functional studies and breeding programs.