# Transcriptional Regulatory Networks Oscillate Seasonal Plasticity of Fruit Metabolism in Melon
## 4 Discussion  
Seasonal change is the most important source of environmental variation worldwide. Organisms respond to specific combinations of multiple seasonal signals under natural conditions to robustly control and produce optimal phenotypes, which may be independent of other evolutionary and developmental effects [27]. In particular, in response to a variety of external stimuli and changes in environmental conditions, plants intensively produce diverse specialized plant metabolites, which in turn leads to variations in fruit quality [28]. In resisting environmental stressors, various specialized metabolites produced by the phenylpropanol biosynthesis pathway play a major role [29; 30]. Currently, omics analysis combined with phenotype has been used in many crops to study the effects of plant-environment interactions on agronomic traits. For example, a combination of methylomics and transcriptome analysis was used to study flower bud formation in apple (_Malus domestica_ Borkh.) [31]. In the study of various abiotic stresses, transcriptome data can be used to reveal the molecular mechanism of tomato drought resistance [32]. Combined with the metabolic level, the adaptation mechanism of olive seedlings to a high-salinity environment was studied [33]. The transcriptional response of Chinese cabbage leaves under heat stress was analyzed using scRNA-seq [34]. And in the context of biological stress, the transcriptome was used to analyze mechanisms of resistance to powdery mildew in pumpkin [35]. In addition, the combination analysis of metabolome and transcriptome has been widely used in melon, mainly involving peel color [36], flavor [37], fruit firmness [38], soluble sugar and organic acid [39], and other aspects affecting melon quality. In our study, we analyzed a massive time-series transcriptome and metabolome set from seasonal cultivation conditions and identified several hub genes that are associated with temperature, photoperiod, and carbohydrate assimilation capacity signal-mediated fruit quality during fruit development under seasonal cultivation conditions using machine learning. Phenylalanine is generated via the shikimic acid pathway. Therefore, the phenylpropanol metabolism pathway guides the metabolic flux from core (the primary metabolism) to specialized metabolism (the secondary metabolism) [36]; it is a precursor source of thousands of metabolites with multiple functions [30]. The metabolic branches of the phenylpropanol pathway generate end products including flavonoids, hydroxycinnamic acids and esters, hydroxycinnamic acid amides, and precursors of lignin, lignans, and tannins, as well as a variety of other aromatic metabolites such as coumarins and phenolic volatiles [37]. According to the chemical structures, phenylpropanol compounds can be divided into five categories, including flavonoids, monolignols, phenolic acids, stilbenes, and coumarins [30; 38]. Phenylpropanol homeostasis among different branches is maintained through metabolic flux redirection (MFR) regulation, demonstrating remark able complexity and high levels of plasticity in continuous developmental phases and responses to environmental stimulus and changes [39]. It can be seen that phenylpropanol metabolites are crucial for the development and survival of plants. In this study, we analyzed a large number of time series transcriptomics and metabolomics under seasonal planting conditions and found that the phenylpropanol pathway, especially the biosynthetic branches of monolignol and flavonoids, are key differential metabolic pathways. Through machine learning analysis, the core hub genes and their annotated functional pathways in each stage were identified, and the main regulatory pathways that formed the differences in each stage were identified, constructing a dynamic transcriptional regulatory network. As photosynthesis is the foundation of plant growth and development, it is regulated by various factors, not only by light, but also by temperature, which is one of the environmental factors limiting photosynthesis.