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<p>The plant growth in potato largely depends on the availability of nutrients in the soil and related genomics of the plant. The present study aimed at unravelling the genomics of potato plant under nitrogen stress conditions. The study identifies and characterizes differentially expressed long non-coding RNAs (DE-lncRNAs), differentially expressed circular RNAs (DE-circRNAs) and alternative splicing (AS) events from shoot, root and stolon tissues of potato varietie Kufri Gaurav, under high and low regimes of nitrogen stress conditions and their roles in regulating genes associated with nitrogen use efficiency (NUE), growth-development and yield. A total of 269 DE-lncRNAs, 26 DE-circRNAs and 20,625 AS genes were identified from in silico studies. A few DE-lncRNAs were found targeting the nitrogen related genes such as L-asparaginase, ubiquitin fold modifier, while rest were involved in metabolic pathways and biosynthesis of secondary metabolites. A total of 12 DE-lncRNAs were validated by real-time qPCR and found to be involved in metabolic processes such as tuber formation, growth &amp; development, lipid homoeostasis, nitrogen-relocation. The competing endogenous RNAs (ceRNAs) acting as sponges for miRNAs were studied from interaction point of view. It was observed that 42 and 31 miRNA response elements (MREs) were present on DE-circRNAs and DE-lncRNAs respectively. Interestingly, five miRNAs involved in protein transport, iron homeostasis, adaptive growth etc. were predicted as absorbed by DE-lncRNA and DE-circRNAs simultaneously. The internal ribosomal entry sites (IRES) and AS genes regulating the nitrogen like mandelonitrile lyase, nitrate transporter, and carbon–nitrogen hydrolase were identified as likely contributors to crop nitrogen use efficiency (NUE) and yield. A user-friendly information system based on the findings was developed and made available at <a href="https://potatotransdb.rf.gd/">https://potatotransdb.rf.gd/</a> for potato breeders and geneticists. Our findings may help to understand the role of regulatory elements under nitrogen stress in potato and achieve the targets of improving agronomic traits through marker assisted breeding.</p>

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Noncoding RNAs and Splicing Variants Associated with Nitrogen Stress Tolerance: Insights into Growth and Development in Potato

  • 期刊论文

  • 发表日期：

    2026年5月26日

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  • Sarika Sahu,
  • Atmakuri Ramakrishna Rao,
  • Soumya Sharma,
  • Jagesh Kumar Tiwari,
  • Sanjeev Kumar,
  • Dwijesh Chandra Mishra

摘要

The plant growth in potato largely depends on the availability of nutrients in the soil and related genomics of the plant. The present study aimed at unravelling the genomics of potato plant under nitrogen stress conditions. The study identifies and characterizes differentially expressed long non-coding RNAs (DE-lncRNAs), differentially expressed circular RNAs (DE-circRNAs) and alternative splicing (AS) events from shoot, root and stolon tissues of potato varietie Kufri Gaurav, under high and low regimes of nitrogen stress conditions and their roles in regulating genes associated with nitrogen use efficiency (NUE), growth-development and yield. A total of 269 DE-lncRNAs, 26 DE-circRNAs and 20,625 AS genes were identified from in silico studies. A few DE-lncRNAs were found targeting the nitrogen related genes such as L-asparaginase, ubiquitin fold modifier, while rest were involved in metabolic pathways and biosynthesis of secondary metabolites. A total of 12 DE-lncRNAs were validated by real-time qPCR and found to be involved in metabolic processes such as tuber formation, growth & development, lipid homoeostasis, nitrogen-relocation. The competing endogenous RNAs (ceRNAs) acting as sponges for miRNAs were studied from interaction point of view. It was observed that 42 and 31 miRNA response elements (MREs) were present on DE-circRNAs and DE-lncRNAs respectively. Interestingly, five miRNAs involved in protein transport, iron homeostasis, adaptive growth etc. were predicted as absorbed by DE-lncRNA and DE-circRNAs simultaneously. The internal ribosomal entry sites (IRES) and AS genes regulating the nitrogen like mandelonitrile lyase, nitrate transporter, and carbon–nitrogen hydrolase were identified as likely contributors to crop nitrogen use efficiency (NUE) and yield. A user-friendly information system based on the findings was developed and made available at https://potatotransdb.rf.gd/ for potato breeders and geneticists. Our findings may help to understand the role of regulatory elements under nitrogen stress in potato and achieve the targets of improving agronomic traits through marker assisted breeding.