New crop plants suited to growth in semi-arid environments will be fundamental to the future of agriculture. The interactions between nitrogen supply and water availability that determine yield and quality in crops grown in semi-arid environments are being elucidated. Tools for analyzing the metabolic changes associated with enhanced nitrogen assimilation under drought have been genrated. Maize (Zea mays) and other crop plants have altered metabolic profiles caused by in planta expression of the bacterial glutamate dehydrogenase (EC 220.127.116.11) encoding transgene, a modified gdhA. The change in glutamate concentration has profound effects on plant metabolisms. The metabolic changes resulted in phenotypic changes that included increases in mean plant biomass production in dry soils, tolerance to the herbicide phosphinothricin, tolerance to both severe and mild water deficit and resistance to rotting necrotrophs including carcinogenic Aspergillus flavus contaminations. Leaves had higher nutritional value and higher yield indicating improved NUE and WUE. Sporulation of A. flavus was inhibited and the abundance of 747 fungal transcript altered suggesting the GDH maize was not supporting normal fungal growth. Cancer incidences due to toxin contamination can potentially be reduced by 50%. There were about 283 metabolites in roots, 98 metabolites in leaves and 56 metabolites in ears that changed abundances. The altered metabolites and proteins provided biomarkers for these valuable. See patents 5,998,700; 6,329,573; and pending.