Phenotypic, Physiological, and Gene Expression Analysis for Nitrogen and Phosphorus Use Efficienies in Three Popular Genotypes of Rice (Oryza sativa Indica)

Crop nitrogen (N) and phosphorus (P) use efficiencies (NUE/PUE) are important to minimize wastage and nutrient pollution, but no improved crop for both is currently available. We addressed them together in rice, in the view of its high consumption of NPK fertilizers. We analyzed 46 morphophysiological parameters for the N/P response in three popular indica genotypes, namely, BPT 5204, Panvel 1, and CR Dhan 301 at low, medium, and normal N/P doses. They include 18 vegetative, 15 physiological, and 13 reproductive parameters. The segregation of significantly N/P-responsive parameters correlating with NUE/PUE revealed 21 NUE, 22 PUE, and 12 common parameters. Feature selection analyses revealed the common high-ranking parameters including the photosynthetic rate at the reproductive stage, tiller number, root-shoot ratio, culm thickness, and flag leaf width. The venn selection using the reported NUE/PUE-related candidate genes in rice revealed five genes in common for both, namely <i>OsIAA3</i>, <i>OsEXPA10</i>, <i>OsCYP75B4</i>, <i>OsSultr3;4</i>, and <i>OsFER2</i>, which were associated with three of the common traits for NUE/PUE. Their expression studies using qRT-PCR revealed the opposite regulation in contrasting genotypes for <i>OsSultr3;4</i> and <i>OsEXPA10</i> in N-response and for <i>OsFER2</i> in P-response, indicating their role in contrasting N/P use efficiencies. Overall, CR Dhan 301 has the highest NUE and PUE followed by Panvel 1 and BPT5204 among the studied genotypes.