The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits Some QTLs and genes related to maize yield as well as root traits have been identified. Characterizing growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. Scientists identified 1555 genes to respond to nutrient treatments, in one or both tissues. Integrating genetic analysis, gene co-expression, and functional annotation revealed two candidate genes controlling genotype-water-nitrogen interactions, affecting both leaf width and grain yield. Genes involved in abscisic acid biosynthesis and bZIP, NAC, and WRKY transcription factors participated in maize response to water and nitrogen conditions. It suggested that application of pure organic N likely induces N-deficiency response in maize plants, with a consequent increase in physiological N utilization efficiency due to up-regulation of key genes involved in N remobilization processes.