# Transcriptional Regulatory Networks Oscillate Seasonal Plasticity of Fruit Metabolism in Melon
## 1 Introduction  
Melon (_Cucumis melo_), a member of the _Cucurbitaceae_ family, is a global fruit crop of great economic importance, with an estimated annual yield of more than 30 million tons worldwide \"[[http://www.fao.org/faostat/](http://www.fao.org/faostat/)]([http://www.fao.org/faostat/](http://www.fao.org/faostat/))\" (accessed on 15 November 2023). The most important traits of melon for consumer acceptance are its sweet, refreshing flesh and flavor [1]. To date, these traits have been extensively studied independently from a genetic or metabolic perspective [2, 3, 4, 5]. These concerned fruit quality traits are susceptible to being influenced by the environment, such as temperature, light, or other factors [6, 7, 8]. Typically, winter/spring and summer/autumn cropping cycles are used mainly to meet the requirements of annual melon production, resulting in seasonally variable fruit quality.  
Seasonal turnover is the dominant environmental fluctuation that organisms experience during their lifetime [9, 10]. Both temperature and photoperiod are generally considered to be the two reliable cues for the response of plant development to environmental seasonality [11]. The combination of temperature and day length in natural habitats has shaped the adaptation to seasonal environments of the perennial plant _Arabidopsis hallerisubsp. _Gemmifera_, and its seasonal dynamics of the transcriptome elucidate the molecular mechanisms of environmental responses and demonstrate how plants utilize multiple types of environmental information to adapt to seasonal environmental changes [12]. Developmental plasticity in various traits is often observed to be seasonally controlled, as they evolve in a seasonal context. For example, many phenological events in plants, such as flowering, fruiting, budding, bud formation, and growth arrest [13; 14]. In addition to the visible phenological events, physiological changes such as photosynthetic activity and metabolic changes also occur [12]. However, our current understanding of how molecular mechanisms govern the seasonal operation of plants as a whole remains limited. Understanding how environmental conditions regulate the biosynthesis of these specialized metabolites is essential for fruit development. Many existing studies have primarily focused on the relationship between environmental factors and plant growth, and the understanding of the interaction between fruit development caused by environmental cues and fruit quality is relatively preliminary and fragmented. Fruits are the plant organs with the most abundant metabolites; therefore, metabolomics provides an opportunity to study the metabolic processes involved in fruit quality development [15]. High-throughput screening of phenylalanine patterns through GC- or UPLC-MS allows to correlate metabolite patterns to transcriptional profiles in an organ- or tissue-specific manner in the absence of phenotypes [16]. This method may uncover the effects of individual genes in the phenylpropanol pathway on other metabolic pathways [17].  
Our study unveiled a strong correlation between metabolic and transcriptomic changes during fruit development under seasonal conditions. Employing an innovative approach to data mining, we utilized machine learning methods to iteratively cluster melon fruit transcriptome data. Through association studies linking key metabolites to protein interaction networks, we elucidated the molecular mechanisms influencing fruit quality under varying seasonal growth conditions. Furthermore, we identified central regulatory genes responsive to environmental changes. This collaborative regulatory network defined by highly correlated metabolites, referred to as \"hub\", serves as a promising target for future high-throughput screening in breeding. This approach offers a comprehensive understanding of the transcriptional regulatory networks mediating the seasonal plasticity of fruit metabolism in melons.