Uniform, undamaged ‘Fengyuanhong’ apricot fruits at the commercial ripening stage were collected and immediately transported to the laboratory. The fruits were subjected to the following treatments: A concentration of 1 μL·L_-1 1-MCP (Macklin Biochemical Technology Co., Ltd., Shanghai, China) was applied by airtight fumigation for 24 hours; a concentration of 30 mg·kg⁻¹ ethephon (Macklin Biochemical Technology Co., Ltd.) was used to soak the apricot fruits for 20 min, followed by air drying and subsequent airtight storage for 24 hours; and a blank airtight treatment was used as the control. All the treated samples were placed in foam boxes and stored at 25 °C with 70% relative humidity. Sampling was conducted at 0, 2, 4, 6, 8, 10, and 12 days posttreatment. A destructive sampling approach was adopted, in which a distinct set of at least 20 fruits was collected for analysis at each time point. No fruit measured at a given time point was reused in subsequent sampling events. A portion of the fruits was used for relevant physiological measurements, while the remainder was rapidly dissected snap-frozen in liquid nitrogen, and stored at −80 °C for subsequent analysis. Three biological replicates were performed for each treatment group.

The color difference values of the apricot fruits at different time points were measured using a CR-400 colorimeter (Konica Minolta, Japan) (three biological replicates, five fruits per replicate). CIELAB software was used to measure the L*, a*, b*, and h* values. The L* value represents lightness from black (L*=0) to white (L*=100), a* indicates the green (−) to red (+) spectrum, b* represents the blue (−) to yellow (+) spectrum, and h° denotes the hue angle, which ranges from 0° to 360° with specific color associations; different angles correspond to different colors. Usually, 0° (or 360°) is defined as red, 90° as yellow, 180° as green, and 270° as blue. Fruit firmness was measured using a fruit hardness tester (GY-2). The weight of individual apricot fruits from each treatment was determined using an electronic balance.

The soluble solids content was measured using a handheld refractometer (Atago, Japan, PAL-1). The concentrations of fructose, glucose, sorbitol, sucrose, malic acid, citric acid, quinic acid, shikimic acid, and oxalic acid were analyzed by high-performance liquid chromatography (HPLC; Thermo Scientific UltiMate 3000 system) following the chromatographic column specifications and detection methods described by Cheng et al. (2018), where 5.0 g of fruit flesh was weighed into a 5 mL grinding tube with zirconium oxide beads for homogenization, transferred to a 50 mL centrifuge tube and diluted to 10 mL with ultrapure water, subjected to an 80 °C water bath for 30 min with vortex mixing every 10 min, followed by 30 min of ultrasonic extraction (with one repetition of this water bath-ultrasonic cycle), then centrifuged at 12,000 rpm for 30 min at 4 °C, and finally filtered through a 0.22 μm aqueous membrane with the filtrate stored in amber vials for HPLC analysis (Cheng et al., 2018).

The sugar components were analyzed using a mobile phase consisting of acetonitrile (with 1% ammonia water) and water (85:15, v/v) at a flow rate of 0.2 mL/min, with the column temperature maintained at 45 °C, an injection volume of 2 μL, and a run time of 18 minutes, employing an ELSD detector with the nebulizer gas pressure set at 25 psi, drift tube temperature at 55 °C, and spray chamber temperature at 25 °C, using a UPLC ACQUITY BEH amide column (1.7 μm, 2.1×100 mm), whereas the organic acid components were analyzed with standard curves established from reference standards and their corresponding peak areas and 0.02 mol/L potassium hydrogen phosphate buffer (pH adjusted to 2.4 with phosphoric acid) as the mobile phase at a flow rate of 0.5 mL/min. The quantification of both the sugar and organic acid components was achieved by calculations against standard curves established from reference standards and their corresponding peak areas. The information of sampling time points for all experiments are provided in Supplementary Table 1.

Total RNA was extracted from frozen apricot fruit pulp following the protocol of the E.Z.N.A.^® Plant RNA Kit (Omega Bio-tek, USA). RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, USA), and concentration and purity were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). RNA samples that satisfied the following quality criteria were classified as high-quality and used for subsequent library preparation: an OD260/280 ratio between 1.8 and 2.2, an OD260/230 ratio ≥ 2.0, an RNA integrity number (RIN) ≥ 6.5, a 28S:18S ribosomal RNA ratio ≥ 1.0, and a total RNA quantity exceeding 10 µg.

RNA-seq transcriptome libraries were constructed from 1 µg of total RNA per sample using a standard mRNA-seq workflow. Polyadenylated mRNA was enriched with oligo(dT) magnetic beads and then fragmented. First- and second-strand cDNA synthesis was performed, followed by end repair, adenylation of 3’ ends, and ligation of indexed adapters. The resulting cDNA libraries were size-selected (200–300 bp) on a 2% low range ultra agarose gel and amplified for 15 cycles with Phusion High-Fidelity DNA Polymerase (New England Biolabs, USA). Library concentration and size distribution were quantified with a TBS380 fluorometer (Turner BioSystems). Finally, paired-end sequencing (2 × 150 bp) was carried out on an Illumina NovaSeq 6000 platform (Illumina, USA) by Shanghai BIOZERON Biotech. Co., Ltd., following the manufacturer’s standard protocols.

Quality assessment and preprocessing were first performed on the raw sequencing data, where FastQC software was used to evaluate the quality metrics (including sequence quality distribution, GC content, and adapter contamination) of the original FASTQ files, after which Trimmomatic was used to remove low-quality sequences and adapter contaminants to obtain high-quality clean reads for downstream analysis. The preprocessed RNA-seq data were subsequently aligned to the ‘Jintaiyang’ reference genome (https://www.rosaceae.org/Analysis/10254125) using HISAT2 with the parameter ‘--dta’, after which the alignment results were sorted and indexed using SAMtools to generate BAM files for subsequent analyses (Jung et al., 2007).

Transcriptome assembly and expression quantification were performed using StringTie2, followed by differentially expressed gene (DEG) screening and statistical analysis with the DESeq2 package in R, while the WGCNA package in R was employed to construct gene co-expression networks (criteria: average read count >10, fold change >2, adjusted p<0.05) with a soft threshold power β=12 to identify co-expression modules and analyze their phenotypic correlations. Finally, Cytoscape was used for network visualization of key modules to elucidate gene co-expression relationships and topological structures.

Putative downstream target genes of the transcription factors (TFs) were identified using a co−expression network constructed with WGCNA (v1.71). Genes exhibiting a connection weight of ≥ 0.08 to each target TF were extracted as initial candidates. For each candidate gene, a 2 kb genomic region upstream of the translation start site was retrieved. These promoter sequences were scanned for the presence of known binding motifs of ERF and MYB transcription factors using the cis−regulatory element database integrated in plantTFDB (https://planttfdb.gao-lab.org/prediction.php). Candidate genes harboring the corresponding TF−binding motifs in their promoters were retained for further analysis. Finally, functional annotation of the filtered candidate target genes was performed using eggnog−mapper (emapper−2.1.13) with the eggNOG database (version 5.0.2).

To experimentally validate the transcriptome sequencing results, 8 key DEGs were selected for qRT–PCR analysis. The qRT-PCR method was performed with slight modifications based on the protocol previously described by Wu et al. (2017). First-strand cDNA was synthesized from 1 μg of total RNA using a PrimeScript RT reagent kit (Takara, China). qRT–PCR was conducted on a QuantStudio 5 real−time PCR system (Applied Biosystems, USA) in a 20 μL reaction mixture containing 10 μL SYBR Premix Ex Taq II (Takara), 0.8 μL each of forward and reverse primers (10 μM), 2 μL cDNA template, and 6.4 μL ddH₂O. The amplification protocol consisted of initial denaturation at 95°C for 30 s, followed by 40 cycles of denaturation at 95°C for 5 s and annealing/extension at 60°C for 30 s. All reactions were carried out in triplicate. The actin gene of apricot was employed as the internal reference for normalization. Relative expression levels were calculated using the 2^−ΔΔCt method, and statistical significance between treatment and control groups was assessed by Student’s t−test (*P < 0.05). The sequences of the primers used are provided in Supplementary Table 2.

Treatment of mature ‘Fengyuanhong’ apricot fruits with 1-MCP or ethephon resulted in markedly divergent effects during 10 days of storage, with phenotypic observations performed every two days (Figure 1). The apricot fruits of the control group retained marketable quality—characterized by a bright orange–yellow color and the absence of decay—until day 8. While the visual appearance, particularly color development, of 1-MCP-treated fruits did not differ markedly from that of the control during the initial storage phase (e.g., through day 4), the treated fruits preserved these quality attributes until day 10, demonstrating a significant extension of shelf life. In contrast, ethephon treatment significantly accelerated the aging of apricot fruits. After the completion of all the treatments (i.e., day 0), the fruits in the ethephon group exhibited brown coloration, whereas those in both the control and 1-MCP groups retained their green color (Figure 1). The fruits treated with ethephon had completely rotted by day 8, and their color changed from green to yellow. With increasing storage time, the intensity of the yellow color increased (Figure 1).

To evaluate the effects of 1-MCP and ethephon treatments on the physicochemical characteristics of apricot fruits, we first measured the surface color parameters using a colorimeter (Figures 2A–D). The results demonstrated that while 1-MCP treatment resulted in no significant differences in color indices compared with those of the control, ethephon treatment markedly altered fruit coloration during postharvest storage (Figures 2A–D). Specifically, ethephon treatment increased the L*, a*, and b* values by 0.96%–1.81% (P = 0.0039–0.1682), 19.85%–41.16% (P = 0.0031–0.0288), and 8.97%–10.52% (P = 0.0008–0.0056), respectively, but significantly decreased the h° value by 3.04%–5.02% during postharvest days 2–6 (Figures 2A–D). Further analysis of fruit firmness and fruit weight during storage (Figures 2E, F) revealed no significant differences in firmness between the 1-MCP-treated group and the control group, whereas compared with the control treatment, the ethephon treatment resulted in a significant reduction in firmness of 41.22%–63.97% (P = 0.0011–0.0092) during postharvest storage (Figure 2E). Additionally, compared with control fruits, ethephon-treated fruits presented significant decreases in per-fruit weight of 10.07% (P = 0.0060) and 9.16% (P = 0.0347) on storage days 0 and 2, respectively (Figure 2F).

To investigate the effects of 1-MCP and ethephon treatments on apricot fruit flavor quality, we analyzed the contents of soluble solids, sugars, and organic acids. The results demonstrated that both treatments significantly altered the soluble solids content during postharvest storage. Ethephon treatments increased the soluble solids content by 18.76% (P = 0.0082) and 15.59% (P = 0.0328), respectively, 0 and 4 days after treatment. The 1-MCP treatment increased the soluble solids content by 16.83%–21.57% (P = 0.0123–0.0396) 0–4 days after treatment, whereas the 1-MCP treatment decreased the soluble solids content by 11.88% (P = 0.0160) and 9.27% (P = 0.0314), respectively, 6 and 8 days after treatment (Figure 2G).

Significant variations were observed in the sugar and organic acid profiles among the treatments. Compared with the control treatment, the ethephon treatment increased the fructose content by 6.26% (P = 0.0023) and 108.33% (P = 0.0053) 0 and 6 days after treatment, respectively, but decreased it by 12.04% (P = 0.0093) 4 days after treatment, whereas the 1-MCP treatment reduced the fructose content by 27.88% (P = 0.0016) and 18.80% (P = 0.0219) 0 and 6 days after treatment, respectively (Figure 2H). Ethephon treatment increased the glucose content by 76.02% (P = 0.0076) 2 days after treatment, whereas 1-MCP treatment decreased it by 72.57% (P = 0.0018) 0 d after treatment (Figure 2I). With respect to sorbitol, 1-MCP treatment resulted in dynamic changes, with 39.71% (P = 0.0167) and 42.96% (P = 0.0129) decreases 0 and 4 days after treatment, respectively, but 41.01% (P = 0.0380) and 157.97% (P = 0.0007) increases 2 and 6 days after treatment, respectively, whereas ethephon treatment resulted in a 156.93% (P = 0.00002) increase 0 days after treatment (Figure 2J). The sucrose content decreased by 40.36% (P = 0.0027), 23.99% (P = 0.0429), and 26.89% (P = 0.0142) 0, 4, and 6 days after treatment with 1-MCP, respectively, whereas ethephon treatment increased it by 24.41% (P = 0.0104) 0 days after treatment (Figure 2K).

In terms of organic acids, ethephon treatment consistently reduced the malic and citric acid contents 2 and 4 days after treatment but they increased after 6 days (Figures 2L, M). 1-MCP treatment decreased the malic acid content by 36.12% (P = 0.0040) after 2 days but it increased by 14.08% (P = 0.0105) and 72.33% (P = 0.0015) after 4 and 6 days, respectively, whereas it dramatically increased the citric acid content by 276.34% (P = 0.0051) and 210.67% (P = 0.0008) after 6 and 8 days, respectively (Figures 2L, M). Quinic acid increased by 27.36% (P = 0.0040) and 140.01% (P = 0.0021) 0 and 6 days after ethephon treatment, respectively, whereas 1-MCP treatment caused a 58.29% (P = 0.0009) decrease 4 days after treatment, followed by 94.88% (P = 0.0025) and 119.30% (P = 0.0051) increases after 6 and 8 days, respectively (Figure 2N). The oxalic acid content decreased by 13.84% (P = 0.0343) after ethephon treatment (0 days), whereas 1-MCP treatment resulted in a 32.45% (P = 0.0109) decrease and a 13.22% (P = 0.0160) increase after 4 and 8 days, respectively (Figure 2O). The shikimic acid content decreased by 24.75%–31.85% (P = 0.0004–0.0375) in ethephon-treated fruits from 2–6 days, whereas 1-MCP treatment resulted in greater reductions of 43.69% (P = 0.0020) and 37.79% (P = 0.0007) after 2 and 4 days, respectively (Figure 2P).