Noncoding RNAs (ncRNAs), once considered the “dark matter” of the genome, have emerged as critical regulators of gene expression in plants. Research initially focused on model organisms has laid the groundwork for harnessing the potential of ncRNAs in agriculture, particularly for crop protection, improvement, and modulation. This review explores the role of long and small ncRNAs in plant biology, highlighting their application as powerful tools in agricultural biotechnology. We examine the latest strategies for ncRNA expression and delivery in crops, including transgenic and nontransgenic approaches, as well as emerging technologies that enable precise and efficient modulation of gene activity in plants and pathogens. Additionally, we provide a comprehensive overview of the current state-of-the-art in the regulation of RNA-based products, addressing the challenges and opportunities for integrating these innovations into sustainable agricultural practices. As the regulatory landscape evolves, understanding the safety, efficacy, and environmental impact of ncRNA-based technologies will be crucial for their successful deployment. By leveraging the advances in plant science research, long and small ncRNAs hold promise for designing highly specific tools to boost crop productivity while preserving genetic diversity, contributing to global food security and sustainable agriculture.

The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.

Huanglongbing (HLB), caused mainly by Candidatus Liberibacter asiaticus (CLas), is a devastating disease threatening citrus production worldwide, leading to leaf mottling, fruit deformation, and significant yield losses. This study generated a comprehensive co-expression network analysis using RNA-seq data from 17 public datasets. Weighted gene co-expression network analysis (WGCNA) was applied to identify gene modules associated with citrus species, tissue types, and days post-infection (DPIs). These modules revealed significant enrichment in biological pathways related to stress responses, metabolic reprograming, ribosomal protein synthesis, chloroplast and plastid function, cellular architecture, and intracellular transport. The results offer a molecular framework for understanding HLB pathogenesis and host response. By elucidating module-specific functions and their correlation with species- and tissue-specific responses, this study provides a robust foundation for identifying key genetic targets. These insights facilitate breeding programs focused on developing HLB-tolerant citrus cultivars, contributing to the long-term sustainability and resilience of global citrus production.

The SNAKIN/GASA family comprises antimicrobial peptides with proven activity against bacteria and fungi, making them promising candidates for improving disease resistance in citrus rootstocks. In sixty-seven new GASA variants from a citrus germplasm collection, the presence of the characteristic 12-cysteine domain was confirmed and were classified into three subfamilies. The absolute expression levels of ten representative genes were analyzed in floral tissues, young leaves, and mature leaves from five citrus accessions with contrasting susceptibility to Xanthomonas citri. Expression profiling revealed tissue-specific patterns, with higher transcript abundance in juvenile and floral tissues of tolerant accessions. Meta-analysis of HLB-related RNA-seq datasets revealed the upregulation of specific GASA genes. Three genes from Poncirus trifoliata—PtGASA6, PtGASA8, and PtGASA10—were then selected for functional validation in Nicotiana benthamiana. Transient overexpression of PtGASA6 and PtGASA10 significantly reduced disease symptoms caused by Pseudomonas syringae and heightened the hypersensitive response to X. citri, whereas PtGASA8 showed no detectable effect. Notably, PtGASA6 enhanced the hypersensitive response by 30% more than PtGASA10, while PtGASA10 delayed necrosis by 40% more than PtGASA6, indicating distinct antimicrobial mechanisms. Together, these results identify PtGASA6 and PtGASA10 as strong candidates for breeding and biotechnological strategies aimed at improving broad-spectrum bacterial disease resistance in citrus.

Huanglongbing (HLB), caused mainly by Candidatus Liberibacter asiaticus (CLas), is a devastating disease which threatens citrus production worldwide, manifesting as leaf greening, fruit deformation and yield losses. This study generated a comprehensive co-expression network analysis using RNA-seq data from 17 public datasets and ap-plied Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene modules associated with citrus species, tissue types and days post infection (DPI). Key modules were identified among different conditions. We found a significant gene enrichment involved in stress responses, metabolic processes, ribosomal protein syn-thesis; chloroplast and plastid functions; cellular structure; intracellular organization, and stress responses. These findings provide a molecular framework for understanding HLB pathogenesis and host tolerance. By elucidating module-specific functions and their correlation with species- and tis-sue-specific responses, this study provides a robust foundation for identifying key ge-netic targets. These insights facilitate breeding programs focused on developing HLB-tolerant citrus cultivars, contributing to the long-term sustainability and resili-ence of global citrus production.

The SNAKIN/GASA family comprises antimicrobial peptides with proven activity against phytopathogens that may play a significant role in citrus rootstock breeding. We identified 67 new curated GASA variants present in a germplasm collection. They were checked for the diagnostic 12-cysteine-domain and classified into three GASA subfamilies. Absolute expression of ten representative GASA genes was analyzed in floral, young leaf and mature leaf tissues from five accessions with contrasting levels of disease tolerance against Xanthomonas citri. Expression profiling revealed tissue-specific patterns, with higher transcript abundance in juvenile and floral tissues of tolerant accessions. Meta‑analysis of HLB‑related RNA‑seq datasets revealed the upregulation of specific GASA genes. Three candidate genes (PtGASA6, PtGASA8, and PtGASA10) derived from Poncirus trifoliata (a rootstock cultivar conferring disease tolerance), were selected and functionally assessed via transient overexpression in Nicotiana benthamiana. Overexpression of PtGASA6 and PtGASA10 significantly reduced disease symptoms caused by Pseudomonas syringae and enhanced hypersensitive response to Xanthomonas citri, whereas PtGASA8 showed no effect. Specific time-course dynamics and structural predictions suggest distinct antimicrobial mechanisms among these 2 genes. These findings provide new genetic targets for breeding and biotechnological strategies aimed at improving broad-spectrum bacterial disease resistance in citrus.