Teosinte alleles enhance nitrogen assimilation and seed protein in maize.

During maize (Zea mays L.) domestication, seed protein content sharply declined1,2. In plants, glutamine and asparagine levels are closely correlated with protein content3,4. Asparagine is synthesized from glutamine, a process catalysed by asparagine synthase5. Teosinte harbours a superior haplotype of asparagine synthase 4 (ASN4)2. Here, we report that teosinte also possesses a superior haplotype gene promoting glutamine synthesis. We identify and clone teosinte high protein 3 (THP3), which encodes glutamate-oxaloacetate transaminase 1 (GOT1), a key enzyme involved in nitrogen assimilation and carbon-nitrogen balance. The superior THP3-T allele, subjected to negative selection during domestication, has natural variations that boost both its expression and enzymatic activity. Overexpressing THP3-T, but not the modern THP3-B allele, significantly increases seed protein, representing altered carbon-nitrogen composition. Pyramiding THP3-T with THP9-T (the latter encoding asparagine synthase 4 (ASN4)) synergistically elevates both seed and whole-plant protein in elite hybrids while maintaining yield. Our findings demonstrate a powerful strategy for crop improvement by reintroducing beneficial rare alleles disfavoured during domestication from wild relatives.