{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T16:52:08Z","timestamp":1790009528022,"version":"4.0.1"},"reference-count":283,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Fungal diseases continue to limit global crop production and drive major economic losses. Conventional diagnostic and control approaches depend on time-consuming culture-based methods and broad-spectrum chemicals, which offer limited precision. Advances in molecular identification have changed this landscape. PCR, qPCR, LAMP, sequencing and portable platforms enable rapid and species-level detection directly from plant tissue. These tools feed into RNA-based control strategies, where knowledge of pathogen genomes and sRNA exchange enables targeted suppression of essential fungal genes. Host-induced and spray-induced gene silencing provide selective control without the long-term environmental costs associated with chemical use. CRISPR\/Cas9 based tools now refine both diagnostics and resistance development, and bioinformatics improves target gene selection. Rising integration of artificial intelligence indicates a future in which disease detection, prediction and management connect in near real time. The major challenge lies in limited field validation and the narrow range of fungal species with complete molecular datasets, yet coordinated multi-site trials and expansion of annotated genomic resources can enable wider implementation. The combined use of molecular diagnostics and RNA-based strategies marks a shift from disease reaction to disease prevention and moves crop protection towards a precise, sustainable and responsive management system. This review synthesizes the information related to current molecular identification tools and RNA-based management strategies, and evaluates how their integration supports precise and sustainable approaches for fungal disease control under diverse environmental settings.<\/jats:p>","DOI":"10.3390\/ijms27021073","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T13:59:54Z","timestamp":1769003994000},"page":"1073","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR\/Cas9"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1632-4627","authenticated-orcid":false,"given":"Rizwan Ali","family":"Ansari","sequence":"first","affiliation":[{"name":"Department of Ecology and Life Safety, Faculty of Geography and Ecology, Samarkand State University Named After Sharof Rashidov, Samarkand 140104, Uzbekistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1060-0264","authenticated-orcid":false,"given":"Younes","family":"Rezaee Danesh","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Faculty of Agriculture, Van Yuzuncu Yil University, Van 65090, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivana","family":"Castello","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 100, 95123 Catania, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7339-4034","authenticated-orcid":false,"given":"Alessandro","family":"Vitale","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 100, 95123 Catania, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cheng, Y., Tang, X., Gao, C., Li, Z., Chen, J., Guo, L., Wang, T., and Xu, J. (2020). Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops. Pathogens, 9.","DOI":"10.3390\/pathogens9030223"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Wang, T., Gao, C., Cheng, Y., Li, Z., Chen, J., Guo, L., and Xu, J. (2020). Molecular Diagnostics and Detection of Oomycetes on Fiber Crops. 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