Phytohormonal regulation of Solanum lycopersicum development at the systems level

Abstract

Plant growth, development, and environmental adaptation are orchestrated by an intricate network of phytohormone pathways. These pathways, while often studied individually, operate as an interconnected system, the phytohormone system, whose emergent properties cannot be fully understood through single-hormone perspectives. Dissecting the behavior of this system is essential for both fundamental plant biology and agricultural applications and is the primary focus of this dissertation. Chapter 1 provides a conceptual and historical foundation, reviewing prior studies that investigated the dynamics of phytohormone signaling networks. This chapter also highlights methodological advances, and emerging computational frameworks. Chapter 2 presents an experimental comparison of three distinct phytohormone extraction methods. These methods were systematically evaluated in their ability to reduce matrix effects and maximize recovery efficiency across six major phytohormone classes from Solanum lycopersicum (tomato) fruit and leaf tissue. Chapter 3 describes phytohormone profiles of multiple tomato organs, including fruit, leaves, flowers, and roots, across their development. The phytohormone profiles developing fruit were further assessed and used to construct statistical models, intended to inform on the role of different pathways, at each stage of fruit development or in transition from one stage to the next. Finally, Chapter 4 synthesizes the findings of the preceding chapters, offering critical reflections on experimental design, technical limitations, and interpretive challenges inherent to phytohormone research. This chapter underscores that future investigations will benefit from explicitly investigating the phytohormone system as a dynamic and adaptive regulatory network rather than a collection of linear pathways. Together, this dissertation increases ability to interrogate and conceptualize the phytohormone system. It provides both tools and theoretical perspectives that move phytohormone biology closer to a holistic understanding of how plants regulate growth and development. Such advances will ultimately inform efforts to engineer crops with improved resilience, productivity, and developmental precision.