Major Genic Factors Influencing Nitrogen Response in Rice Revealed Through in-silico Characterization and Expression Dynamics of a Set of Novel Candidate Genes

Background Rice is a vital cereal and staple food worldwide. Although rice cultivation requires a large amount of nitrogenous fertilizer, its nitrogen use efficiency (NUE) is only 20–50%. Therefore, in addition to soil and fertilizer management, it is crucial to improve the genetic potential of rice for this complex polygenic trait, NUE, which remains largely unexplored. Methods and results In the present study, 20 promising novel genes identified earlier were primarily characterized in silico, followed by expression analysis in different tissues at various growth stages under optimal and stress nitrogen conditions in the contrasting rice genotypes N22 (poor NUE) and IR64(superior NUE). We observed interesting features of these genes, such as the absence of essential coding sequences (ATG or stop codons), untranslated transcripts (lncRNAs), overlapping gene sequences, and genes on complementary strands. Due to this complexity, the functions of these genes are yet to be determined. Expression profiling under nitrogen stress showed upregulation in both vegetative and reproductive stages in N22, while in IR64, upregulation occurred at the seedling stage and downregulation during reproductive stages. Conclusion Apart from functional proteins, nitrogen stress-responsive genes in rice also transcribe into lncRNAs, with some showing allelic variation across genotypes. These genes are regulated by light- and hormone-responsive promoter elements under nitrogen stress. This study improves understanding of alleles in contrasting genotypes and their nitrogen deprivation response. Ultimately, it aims to identify promising genes with unique features for functional validation, supporting molecular breeding programs to develop rice lines with improved nitrogen use efficiency.