Identification of QTLS for NH4+ and NO3- use efficiency under water stress and non-stress conditions and expression analysis of glutamine synthetase and nitrate reductase in rice (Oryza Sativa L.)

Nitrogen (N) is one of the most critical inputs and the current average nitrogen use efficiency (NUE) in the rice field is approximately 33%, poorest among cereals. Predominant form of N in aerobic soils is nitrate (NO3-) while ammonium (NH4+) exists in anaerobic soils. Development of cultivars with improved NH4+ or NO3- use efficiency by harnessing inherent significant variability for NUE can be an important approach. Considering these facts, the present study was established with one hundred twenty two and selected thirty two recombinant inbred lines (RILs) of two indica genotypes, Danteshwari × Dagad deshi under three nitrogen forms and three environments. The trend analysis of NH4+-N and NO3--N dynamics revealed that NH4+-N concentration persisted more under anaerobic condition and NO3--N concentration under aerobic conditions. Three way-ANOVA showed high level of significance for variance components (G, N, E) and their interactions effects (GXN, GXE, NXE, EXNXG) for yield and NUE and their component traits. Mean performance of genotypes depicted higher values for agronomically important traits i.e. yield and NUE under NH4+ as compared to NO3--N and N0. The phenotypic and genotypic data was statistically analyzed for QTLs identification for yield and NUE traits. A total of 58 QTLs conferring the corresponding five traits were detected under three N forms and two environments. We also investigated the different members of AMT (Ammonium transporters), NRT (Nitrate transporters), GS (Glutamine Synthetase) and GOGAT (Glutamate Synthase) genes, involved in NUE and analyzed the expression pattern of each gene using gene-specific primer in young rice seedlings. Collectively, OsGln1;1, OsGln1;2, OsGln1;3, OsGln2, OsGlt1 and OsGlt2 manifested different and reciprocal responses to nitrate and ammonium supply. The activity of enzymes NR, NiR, GS and GOGAT was significantly affected by NH4+and NO3- treatment. These results assist us to identify NH4+ and NO3- responsive cultivars which could be used for cultivation and/or used as parent’s in future breeding program to produce better nitrogen use efficiency varieties under water stress and non-stress conditions.