Phenolics are one of the major groups of plant specialized metabolites. Within the plant, these metabolites have important roles in growth, adaptation, and defense, influencing agronomic traits and environmental interactions. While the core phenolic biosynthesis pathway is well known, many of the factors involved in controlling and synthesizing derivatives of the core structures remain to be identified. The goal of the present work is to comprehensively identify genes involved in phenolic formation. In this dissertation, I describe a comprehensive analysis of the maize genome, which revealed key genes accounting for 70% of the total mRNA accumulation for phenolic genes across 95 tissues and stress treatments. This candidate phenolic gene compendium provides a valuable resource for future studies. Furthermore, I explored natural variation of several phenolic compounds in a maize diversity panel and identified inbred lines show high or low accumulation of specific compounds; in some cases, this variation reflects loss-of-function mutants. Metabolite correlations across the population confirmed known substrate-product relationships and revealed potentially novel enzymatic conversions. A metabolite-Genome-Wide Association Study (mGWAS) identified Single Nucleotide Polymorphisms (SNPs) linked to phenolic accumulation, including associations with multiple metabolites. From these SNPs, I tested candidate loci for potential involvement in the phenolic pathway. This research uncovers genetic factors influencing phenolic diversity in maize and underscores the potential of mGWAS in plant metabolic studies.
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