UC San Diego

Plants produce an extraordinary array of molecules that guide physiological function, environmental responses, and developmental decisions1,2. Metabolomics has emerged as a powerful approach for characterizing this biochemical diversity, providing opportunities to relate metabolic variation to plant function3,4. Despite the utility of metabolomics, understanding how metabolites contribute to plant physiology remains challenging due to difficulties in metabolite identification, functional characterization5,6, tissue distribution, and biosynthetic origins3. A central challenge in plant physiology is connecting metabolite measurements to biological function, as this requires accurate characterization of chemical features, cellular localization, and physiological effects4,6. This dissertation integrates complementary mass spectrometry-based metabolomics with experimental plant physiology approaches to identify and characterize plant metabolites that contribute to ecological adaptation, crop performance enhancement, and developmental function. Specifically, using gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography-mass spectrometry (HPLC-MS), and mass spectrometry imaging (MSI) the studies presented in this dissertation reveal relationships between metabolite composition and localization to functional traits such as stress resilience and tissue growth. Chapter 1 outlines the use of an untargeted GC-MS metabolomics approach to examine relationships between metabolite composition and plant resource use-strategies across diverse California plant species. Correlation analyses demonstrated that specific metabolites are associated with key functional traits, including water use efficiency and photosynthetic rate. These results indicate certain chemical phenotypes are correlated with distinct physiological strategies in Californian native plants. This cross-disciplinary work demonstrates that specialized metabolites are integrated components of plant ecological strategies, providing a metabolomic perspective on the plant economics spectrum and advancing understanding of the links between plant physiology and drought adaptation. Chapter 2 details investigation into the role of benzoxazinoids in maize root development. Mass spectrometry imaging (MSI)-based spatial metabolomics identified a series of benzoxazinoids as conserved metabolic features of the maize root apical meristem across multiple genotypes, implicating these specialized metabolites in root development7. Phenotypic analyses of wild-type and benzoxazinoid deficient mutant plants supported a role for benzoxazinoids in regulating root system architecture through the formation and elongation of seminal roots – embryonically-derived roots that are important for seedling establishment. Treatment with one benzoxazinoid, 6-methoxy-2-benzoxazolinone (6-MBOA), was sufficient to increase seminal root formation on its own, suggesting that this molecule has an endogenous role establishing new seminal roots. Transcriptomic analysis further identified gene expression changes associated with 6-MBOA treatment in seminal roots, providing insight into molecular pathways underlying benzoxazinoid-mediated root growth. Notably, the transcriptomic response was consistent with a developmental role for 6-MBOA treatment, as it did not induce expression of classic defense genes. Overall, these results expand the known biological functions of this metabolite class beyond plant defense and lay the foundation for further exploration of their roles as developmental regulators. Collectively, this dissertation demonstrates how complementary mass spectrometry approaches can link metabolite organization to plant growth strategies, environmental responses, and developmental processes. These findings advance understanding of plant specialized metabolism while illustrating the utility of metabolomics for revealing the functional roles of metabolites across multiple scales of plant biology. These results have important implications for understanding the basic biology of plant growth and development, as well as developing new strategies for ecosystem restoration and agriculture.