## 3 Discussion
### Many DEGs and TFs Are Involved in the Synthesis of VACs in Pepper Fruits  
The expression of key genes in amino acids, fatty acids, MVA, and MEP metabolism are an essential factor affecting the formation of aldehydes, alcohols, and esters producing VACs [9; 14]. The Lipoxygenase pathway is the key pathway for the biosynthesis of straight-chain aldehydes, alcohols, and esters, including four-step enzymatic reactions, in which LOX, as the first step in the synthesis of straight-chain volatile fatty acid derivatives, has been proven to be able to catalyze the oxidation of polyunsaturated fatty acids in apples to produce volatile C6 aldehydes [40]. HPL catalyzes the conversion of LOX reaction products into aldehydes, and its silencing significantly reduces the production of C6 volatiles in olive [41], such as hexanol, hexanal, and (E)-2-hexanol. ADH catalyzes the reduction of straight-chain aldehydes in fruits to corresponding straight-chain alcohols, which has been proven to be closely related to the formation of watermelon C9 alcohols [42]. AAT catalyzes linear alcohols and acyl carrier proteins (ACPs) to form volatile straight-chain esters in many horticultural plants, such as flowers, fruits, and vegetables [6]. Our study identified 13 LOX, 1 HPL, 11 ADH, and 3 AAT genes with different expression patterns in pepper fruits of different varieties and developmental stages with similar trends to some volatile compounds, such as hexanal, (e)-2-hexanol, hexanoic acid-hexyl ester. This suggests that these DEGs may regulate the production of straight-chain volatiles in pepper fruit. Branched-chain esters are the most critical VACs in pepper fruits in this study, mainly produced by BCAAP. As the last enzyme in the BCAAP, the catalytic product branched-chain amino acid of BCAT provides a precursor for the synthesis of volatile branched-chain compounds [15]. Studies have shown that BCAT is related to the formation of branched-chain esters in fruits such as bananas [43], melons [16], and apples [29]. Another study on peppers showed that the accumulation of most branched esters was significantly positively correlated with the _CcBcat4_ gene [33]. Our study confirmed three differentially expressed BCAT, of which the expression pattern of _LOC107867296_ was consistent with the changing trend of 4-methylpentyl-8-methyl-nonanoate (Z39) content, indicating that it may play a key regulatory role in Z39. CXE is a key enzyme for the synthesis of branched-chain esters, which has been shown to hydrolyze flavor esters in peach [17], strawberry [44], and tomato [45]. In this study, 10 genes encoding CXE were identified, of which _LOC107867571_ and _LOC107859022_ encoding CXE gene decreased significantly in the breaking and maturation stages of pepper fruit, which may be related to the accumulation of volatile branched-chain esters in pepper fruit in the middle and late growth. Methyl salicate (Z11) produced by SAMT-catalyzed SA is the most important aromatic compound in pepper fruit [46]. We identified four SAMT-coding genes; however, their expression pattern is not completely consistent with the accumulation pattern of methyl salicate (MeSA), which indicates that the synthesis of MeSA in pepper fruit may be regulated by other factors that need further study. As the most important enzyme-producing terpene compounds and the gene family with diverse functions in plants [14], TPS directly participated in the synthesis of monoterpene, sesquiterpene, and carotenoid derivatives, the main VACs of HDL1 and GJ fruits. In our experiment, 16 genes encoding TPS were identified as having different expression patterns, which may be related to their functions and the diversity of substrates produced. In addition, we found many other key DEGs related to the synthesis pathway of volatile aromatic compounds, which may play an important role in regulating the synthesis of volatile aromatic compounds in pepper fruits. TFs play an essential role in the metabolism of aroma volatiles [47].