The biological improvement of fertilizer nitrogen use efficiency (NUE) is hampered by the poor characterization of the phenotype and genotype for crop N response and NUE. In an attempt to identify phenotypic traits for N-response and NUE in the earliest stages of plant growth, we analyzed the N-responsive germination, respiration, urease activities, and root/shoot growth of 21 Indica genotypes of rice (Oryza sativa var. indica). We found that N delays germination from 0 to 12 h in a genotype-dependent and source-dependent manner, especially with urea and nitrate. We identified contrasting groups of fast germinating genotypes such as Aditya, Nidhi, and Swarnadhan, which were also least delayed by N and slow germinating genotypes such as Panvel 1, Triguna, and Vikramarya, which were also most delayed by N. Oxygen uptake measurements in the seeds of contrasting genotypes revealed that they were affected by N source in accordance with germination rates, especially with urea. Germinating seeds were found to have endogenous urease activity, indicating the need to explore genotypic differences in the effective urea uptake and metabolism, which remain unexplored so far. Urea was found to significantly inhibit early root growth in all genotypes but not shoot growth. Field evaluation of 15 of the above genotypes clearly showed that germination rates, crop duration, and yield are linked to NUE. Slow germinating genotypes had longer crop duration and higher yield even at lower N, indicating their higher NUE, relative to fast germinating or short duration genotypes. Moreover, longer duration genotypes suffered lesser yield losses at reduced N levels as compared to short duration genotypes, which is also a measure of their NUE. Together, these results indicate the potential of germination rates, crop duration, urea utilization and its effect on root growth in the development of novel phenotypic traits for screening genotypes and crop improvement for NUE, at least in rice.

Zinc malnutrition is a major issue in developing countries where polished rice is a staple food. With the existing significant genetic variability for high zinc in polished rice, the development of biofortified rice varieties was targeted in India with support from HarvestPlus,

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Considering the importance of organic farming and growing demand for organically produced foods, field studies were conducted for 5 years (2004-05 to 2009-10) on a black clayey vertisol soil at the Directorate of Rice Research, Hyderabad, to study the influence of organic and conventional farming systems on productivity, grain quality, soil health and economic returns of super fine rice varieties. Two main plot treatments, with and without plant protection, and four sub plot treatments viz., Control; 100% inorganics; 100% organics; and 50% inorganics+50% organics (integrated nutrient management, INM) were imposed. During wet season, grain yields under 100% inorganics and INM were near stable (4.7-5.5 t/ha) and superior to organics by 15-20% during the first two years, which improved with organics (4.8-5.2 t/ha) in the later years to comparable levels with inorganics, while it had taken five years during dry season. Moderate improvement in nutritional quality was recorded with organics, especially in brown rice. There was a significant improvement in soil physical, fertility and biological properties with organics, which resulted in further improvement in soil quality indices. The sustainability index of the soil was maximum with organics (1.63) compared to inorganics (1.33), after five years of study. The soil organic carbon (SOC) stocks were higher with organics by 44 and 35%, compared to conventional system during wet and dry seasons, respectively, after five years of study. The carbon sequestration rate was also positive with organics (0.97 and 0.57 t/ha/yr during wet and dry seasons, respectively), compared to conventional system that recorded negative SOC sequestration rate (-0.21 and-0.33 t/ha/yr during wet and dry seasons, respectively). Benefit cost ratio was less with organics in the initial years and improved later over inorganics by fifth year.

With the priority of the low input sustainable rice cultivation for environment friendly agriculture, NUE of rice becomes the need of the hour. A set of 472 rice genotypes comprising landraces and breeding lines were evaluated for two seasons under field conditions with low and recommended nitrogen and >100 landraces were identified with relative higher yield under low nitrogen. Donors were identified for higher N uptake, N translocation into grains and grain yield under low N. Grains on secondary branches, N content in grain and yield appears to be the selection criterion under low N. Through association mapping, using minimum marker set of 50 rice SSR markers, 12 genomic regions were identified for yield and yield associated traits under low nitrogen. Four associated genomic regions on chromosomes 5, 7 and 10 were fine mapped and QTL for yield under low N were identified from the marker delimited regions. Three candidate genes viz., 2-oxoglutarate /malate translocator (Os05g0208000), alanine aminotransferase (Os07g0617800) and pyridoxal phosphate-dependent transferase (Os10g0189600) from QTL regions showed enhanced expression in the genotypes with promising yield under low N. Marker assisted selection using SSR markers associated with three candidate genes identified two stable breeding lines confirmed through multi-location evaluation.