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

A study has uncovered how genetic differences in maize kernels affect their nutritional value and end-use quality. To unravel this genetic basis, researchers combined metabolite profiling with genome-wide association studies (mGWAS), structural modeling, enzyme kinetics, and genome-scale metabolic simulations in 265 maize inbred lines.

This analysis revealed significant variation among kernels in 57 metabolites, with homoserine standing out as one of the most variable compounds. Genome-wide association studies identified 62 associations between specific genetic locations and metabolite traits, implicating 788 candidate genes, including 154 that encode metabolic enzymes.

Among these, the shikimate dehydrogenase gene Sad1, located on chromosome 10, emerged as a key player. Four closely linked coding-region SNPs, encompassing three non-synonymous variants, defined two Sad1 haplotypes that led to varying homoserine levels, despite no differences in gene expression. Structural analysis and laboratory enzyme tests demonstrated that these substitutions occur within catalytic and cofactor-binding regions, thereby modifying the enzyme's efficiency.

Using comprehensive metabolic modeling, the team found that Sad1 activity fluctuations influence the availability of plastidial oxaloacetate, a crucial building block for amino acid synthesis like aspartate and homoserine. This redox-coupled flux occurs via the malate-oxaloacetate shuttle. In summary, this research highlights how Sad1 allelic variations impact enzyme performance and amino acid accumulation, thereby linking the shikimate pathway, redox metabolism, and amino acid biosynthesis in maize kernels.