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Background <p>Rice is a primary 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 nitrogen use efficiency (NUE) in rice for this complex polygenic trait, which remains largely unexplored.</p> Methods and results <p>In the present study, 20 promising novel genes identified earlier were first characterized in silico, followed by expression analysis in different tissues and growth stages under N-optimal and N-stress conditions in the contrasting rice genotypes N22 (poor NUE) and IR64 (superior NUE). We observed some special features in different genes, like the absence of essential coding sequences (ATG or stop codons), untranslated transcripts (lncRNAs), overlapping gene sequences, and genes with antisense transcripts. 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 was observed at the seedling stage and downregulation during the reproductive stage.</p> Conclusion <p>Apart from functional proteins, nitrogen stress-responsive genes in rice also transcribe into lncRNAs, some of them showing allelic variation across genotypes. These genes are regulated by light and hormone-responsive promoter elements under nitrogen stress. This study improves the understanding of important N-stress responsive genes and alleles in the two contrasting genotypes. The present study aims to identify promising genes with unique features for their functional validation, and for supporting the molecular breeding programs to develop rice lines with improved NUE.</p>

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Major genic factors influencing nitrogen response in rice revealed through in-silico characterization and expression dynamics of a set of novel candidate genes

  • 期刊论文

  • 发表日期：

    2025年10月14日

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  • Jeet Roy,
  • Ankur Poudel,
  • Sagnik Chanda,
  • Antara Das,
  • Amitha Mithra Sevanthi,
  • Jayanthi Madhavan,
  • Viswanathan Chinnusamy,
  • Pranab Kumar Mandal

摘要

Background

Rice is a primary 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 nitrogen use efficiency (NUE) in rice for this complex polygenic trait, which remains largely unexplored.

Methods and results

In the present study, 20 promising novel genes identified earlier were first characterized in silico, followed by expression analysis in different tissues and growth stages under N-optimal and N-stress conditions in the contrasting rice genotypes N22 (poor NUE) and IR64 (superior NUE). We observed some special features in different genes, like the absence of essential coding sequences (ATG or stop codons), untranslated transcripts (lncRNAs), overlapping gene sequences, and genes with antisense transcripts. 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 was observed at the seedling stage and downregulation during the reproductive stage.

Conclusion

Apart from functional proteins, nitrogen stress-responsive genes in rice also transcribe into lncRNAs, some of them showing allelic variation across genotypes. These genes are regulated by light and hormone-responsive promoter elements under nitrogen stress. This study improves the understanding of important N-stress responsive genes and alleles in the two contrasting genotypes. The present study aims to identify promising genes with unique features for their functional validation, and for supporting the molecular breeding programs to develop rice lines with improved NUE.