Natural Variation in Maize Shikimate Dehydrogenase Alters Enzyme Activity and Kernel Homoserine Accumulation

Abstract Metabolic diversity in maize kernels determines nutritional quality and end-use value. Therefore, understanding its genetic basis is essential for crop improvement and elucidating plant metabolic regulation. Here, we integrated metabolite profiling with metabolite-based genome-wide association studies (mGWAS), structural modeling, enzyme kinetics, and genome-scale metabolic simulations to identify genetic determinants of kernel metabolite variation in 265 maize inbred lines. Profiling of 57 metabolites revealed inter-genotypic variation, with homoserine among the most variable metabolites. mGWAS identified 62 locus–trait associations implicating 788 candidate genes, including 154 encoding metabolic enzymes. A major association for homoserine mapped to the shikimate dehydrogenase gene Sad1 on chromosome 10. Four tightly linked coding-region SNPs, including three non-synonymous variants, defined two Sad1 haplotypes associated with differential homoserine accumulation, independent of gene expression variation. Structural analysis and recombinant enzyme assays showed that these substitutions occur within catalytic and cofactor-binding domains and alter catalytic efficiency. Genome-scale metabolic modeling indicated that variation in SAD1 activity influences plastidial oxaloacetate availability for aspartate and homoserine biosynthesis through redox-coupled flux via the malate-oxaloacetate shuttle. Together, our results indicate that Sad1 allelic variation alters enzyme function and amino acid accumulation, linking the shikimate pathway, redox metabolism, and amino acid biosynthesis in maize kernels.