## 2 Results
### The Expression Changes of Key Genes in the Biosynthesis Pathway of VACs
ACC: acetyl-CoA carboxylase; MAT: malonyl-CoA ACP transacylasse; FabH: 3-ketoacyl ACP synthase II; KAR: ketoacyl ACP reductase; DH: 3-hydroxyacyl ACP dehydratase; ER: 2.3-trans-enoyl ACP reductase; FaB: 3-ketoacyl ACP synthase; SAD: stereate ACP desaturase; OTE: oleate-ACP thioesterase; FAD: oleate and linoleate desaturase; LOX: lipoxygenase; HPL: hydroperoxide lyase; ADH: alcohol dehydrogenase; AAT: alcohol acyl transferase; AOS: allene oxide synthase; AOC: allene oxide cyclase; OPR: 12-oxophyllotonicoate reductase; OPCL: OPC-8:0 CoA ligase 1; ACX: acyl-CoA oxidase; MFP: enoyl-CoA hydratase; JMT: jasmonic acid carboxyl methyltransferase; AK: aspartate kinase; ASADH: aspartate semialdehyde dehydrogenase; HSK: homoserine kinase; TS: threonine synthase; TD: threonine deaminase; ALS: acetolactic synthetase; AHIR: acetohydroacid isomeroreductase; DHAD: dihydroxy acid dehydratase; BCAT: branched-chain aminotransferase; PD: pyruvate decarboxylase; ALDH: aldehyde dehydrogenase; CXE: carboxylesterase. Methyl salicate (Z11, MeSA) is widely found in various fruits and vegetables, often exhibiting green and minty aromas. In this experiment, MeSA mainly accumulated significantly and was the primary characteristic VACs of pepper fruits at the green stage. We detected 12 DEGs involved in MeSA synthesis, including 3 genes encoding DAHP synthase, 3 genes encoding AroE, 1 gene encoding MSK, 1 gene encoding ICS and 4 genes encoding SAMT, most of these genes had higher expression levels (Figure S9 and Table S6) at green stages. Moreover, comparing CTJ with the other three pepper varieties, we found that one gene encoding DAHP synthase (_LOC107864268_ and _LOC107849647_), were significantly more expressed at breaking and mature stages, which was consistent with the accumulation pattern of MeSA, indicating that these genes have a significant regulatory role in the MeSA biosynthesis in pepper fruit. A total of 20 volatile terpene compounds were detected in this experiment, mainly consisting of monoterenes and sesquiterpenes. As shown in Figure 7 and Table S6, our transcriptome data identified 49 differentially expressed genes involved in MVA and MEP pathways. 1-Deoxy-D-xylulose 5-phosphate synthase (DXS), 3-hydroxy-3-methyl-glutaryl-CoA synthase (HMGS), and 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) are considered to be the critical rate-limiting enzymes in the MVA and MEP pathways. In this study, we identified three differentially expressed DXS genes, three HMGs, and five HMGCRs. Although the number of these gene families was small, their expression levels have changed significantly in pepper fruits of different samples, which may play an important role in accumulating terpene compounds in pepper fruits. As the last key enzyme for the synthesis of terpen, 16 TPSs were identified, most of which were significantly expressed at the green stage, and the expression of _LOC107868331_, _LOC107846955_, _LOC107877838_, and _LOC10784047_ was more prominent, indicating that they play a more critical role in the synthesis of terpene aromatic compounds. The expression level of _LOC107878220_ (TPS) was significantly higher in the fruits of GJ at the breaking and maturation stages than in the other three varieties, which was consistent with the accumulation pattern of T4 (himachali-2,4-diene) in the four pepper varieties. In this experiment, five genes encoding carotenoid cleavage dioxygenase (CCD) were identified, which may be involved in regulating the formation of \(\alpha\)-ionone in pepper fruit.