Considering water and labor crises, area under direct seeded rice cultivation has increased. With the direct seeding during the early seedling stage the rice crop is very sensitive to water stress and nutrient deficiencies. The availability of nutrients is highly influenced by water status. Over the years, we have critically observed that under direct seeded condition at seedling stage if drought occurs the plants suffer more because of nutrient deficiency rather than water deficiency. The continued plant growth and development under changed rhizosphere depends heavily on availability of nitrogen and other nutrients (P, Fe and S) and the ability of the root system to absorb these nutrients efficiently and use in metabolism under their changed forms. Rice has evolved and adopted for efficient utilization of ammonical form of nitrogen, while nitrate from is less efficiently used at least during seedling and early vegetative phases. Most of the genotypes (except a few) we evaluated exhibited extremely low level of "Nitrate transporter" and "Nitrate Reductase" activities which are key factor and enzyme in absorption and utilization of nitrate form of nitrogen. Therefore, the identification of lines with greater nitrate use efficiency, mainly because of more efficient High Affinity Transporters, increased expression of nitrate reductase and nitrite reductase along with ammonium transporters and GS and GOGAT will certainly have key role in N efficiency of rice genotypes particularly under water stress conditions. In study 1, one hundred twenty two and selected thirty two recombinant inbred lines (RILs) of two indica genotypes, Danteshwari × Dagaddeshi were evaluated under three nitrogen forms and three environments (Irrigated, Rainfed and Terminal stage drought) along with root studies under soil filled glass rhizotrons at IGKV, Raipur, for generation of phenotypic data. The genotypic data of 162 SSR and HvSSR based markers were developed and used for identifying QTLs for agronomically complex trait i.e. NUE. The phenotypic and genotypic data was statistically analyzed for QTLs identification for yield & NUE traits using QTL Cartalographer. QTLs for nitrate and ammonical use efficiency varied significantly. A presence of QTL clusters between HvSSR 1-87(38.9 cM) to HvSSR 1-89 (40.6 cM) on chromosome 6, RM 449 (81.9 cM) to RM5 (9.4 cM) on chromosome 5, HvSSR 9-25 (14.6cM) to HvSSR 9-27 (15.5cM) on chromosome 9 and RM 434 (57.7 cM) to RM 410 (64.4 cM) on chromosome 5 signifies important genomic regions associated with evaluated traits under different conditions and will be useful in marker assisted breeding for NUE in rice. In study 2, we investigated the different members AMT (Ammonium transporters), NRT (Nitrate transporters), GS (Glutamine Synthetase) & GOGAT (Glutamate Synthase) genes, involved in NUE and analyzed the expression pattern of each gene using gene-specific primer in young rice seedlings by quantitative real time PCR, revealing a distinct expression pattern of these genes. Collectively, OsGln1;1, OsGln1;2, OsGln1;3, OsGln2, OsGlt1 and OsGlt2 manifested different and reciprocal responses to nitrate and ammonium supply. The relationship of these genes / enzymes and its interaction with water stress will be presented during the conference.