Regulatory noncoding RNAs (rncRNAs) have emerged as important modulators of gene expression, influencing plant development and adaptation to diverse stresses. This chapter presents a comprehensive overview of current knowledge on the biogenesis, structural features, and modes of action of major rncRNA classes, including RNA-directed DNA methylation, chromatin remodeling, translational repression, and mRNA cleavage. We discuss how rncRNAs orchestrate developmental transitions from germination to senescence and mediate plant responses to biotic and abiotic stresses. Advances in high-throughput sequencing, transcriptomic profiling, and machine-learning-based target prediction have greatly accelerated the discovery of trait-associated rncRNAs, while modern genome-editing tools such as CRISPR/Cas enable their precise manipulation with minimal off-target effects. Despite these rapid advances, critical knowledge gaps remain, particularly regarding rncRNA cross talk, long-distance mobility, and organelle-specific functions. Future research should focus on expanding and functionally validating ncRNA repertoires linked to yield, stress resilience, and immunity; unraveling mechanisms governing ncRNA movement across cells and tissues; and integrating ncRNA-based regulatory modules into crop improvement pipelines to develop smart and climate-resilient cultivars. Harnessing the full potential of the plant ncRNome will be pivotal for advancing sustainable agriculture and ensuring global food security.

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Transcriptomics and Related Omics: The Role of Regulatory Noncoding RNAs in Plant Development and Stress Responses

  • Shashidhar B. Reddappa,
  • Pavan K. Naik,
  • Gyan P. Mishra,
  • Nandakumar Shekharappa,
  • Muralidhar S. Aski,
  • Manju Kohli,
  • Bidwan Rath,
  • Pream Kumar,
  • Rohit Sarkar,
  • Mallikarjun Biradar,
  • K. N. Kiran,
  • Harsh K. Dikshit

摘要

Regulatory noncoding RNAs (rncRNAs) have emerged as important modulators of gene expression, influencing plant development and adaptation to diverse stresses. This chapter presents a comprehensive overview of current knowledge on the biogenesis, structural features, and modes of action of major rncRNA classes, including RNA-directed DNA methylation, chromatin remodeling, translational repression, and mRNA cleavage. We discuss how rncRNAs orchestrate developmental transitions from germination to senescence and mediate plant responses to biotic and abiotic stresses. Advances in high-throughput sequencing, transcriptomic profiling, and machine-learning-based target prediction have greatly accelerated the discovery of trait-associated rncRNAs, while modern genome-editing tools such as CRISPR/Cas enable their precise manipulation with minimal off-target effects. Despite these rapid advances, critical knowledge gaps remain, particularly regarding rncRNA cross talk, long-distance mobility, and organelle-specific functions. Future research should focus on expanding and functionally validating ncRNA repertoires linked to yield, stress resilience, and immunity; unraveling mechanisms governing ncRNA movement across cells and tissues; and integrating ncRNA-based regulatory modules into crop improvement pipelines to develop smart and climate-resilient cultivars. Harnessing the full potential of the plant ncRNome will be pivotal for advancing sustainable agriculture and ensuring global food security.