{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T13:22:32Z","timestamp":1787923352616,"version":"build-2784847793"},"reference-count":64,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Central Finance Forestry Science and Technology Promotion Demonstration Fund Project","award":["E [2025] TG27"],"award-info":[{"award-number":["E [2025] TG27"]}]},{"name":"Central Finance Forestry Science and Technology Promotion Demonstration Fund Project","award":["E [2025] TG22"],"award-info":[{"award-number":["E [2025] TG22"]}]},{"name":"Hubei Province Key Research and Development Program","award":["2024BBB013"],"award-info":[{"award-number":["2024BBB013"]}]},{"name":"Hubei Province Key Research and Development Program","award":["2025BBB001"],"award-info":[{"award-number":["2025BBB001"]}]},{"name":"China Agriculture Research System of MOF and MARA","award":["CARS-17"],"award-info":[{"award-number":["CARS-17"]}]},{"award":["CARS-17"],"award-info":[{"award-number":["CARS-17"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Grafting profoundly influences fruit tree performance, yet the molecular mechanisms underlying rootstock\u2013scion interactions in mulberry (Morus multicaulis) remain poorly understood. To investigate the regulatory networks linking grafting to scion physiology, we performed an integrated analysis combining small RNA sequencing, transcriptome-based KEGG pathway assessment, and qRT-PCR validation of key target genes across five rootstock\u2013scion combinations. High-throughput miRNA profiling of phloem tissues identified 71 conserved and 156 novel miRNAs, which exhibited distinct, genotype-dependent expression patterns. Recurrent activation of nutrient- and stress-responsive families (e.g., miR399, miR397, and miR395) was observed. Target prediction and functional enrichment analyses revealed that these miRNAs likely regulate pathways related to metabolic processes, hormone signaling, cell wall modification, and stress responses. The expression trends of their predicted target genes\u2014including TCP4, Laccase-3, and ATP sulfurylase 1\u2014were subsequently confirmed by qRT-PCR, revealing significant rootstock-specific regulation. Collectively, this study establishes a reference framework for elucidating the molecular mechanisms underlying scion biological processes in Morus species, which is of great significance for improving fruit quality, enhancing abiotic and biotic stress resistance, and boosting long-term planting productivity.<\/jats:p>","DOI":"10.3390\/genes17091024","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T12:27:46Z","timestamp":1787920066000},"page":"1024","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification and Analysis of Graft-Responsive miRNAs in Mulberry Rootstock\u2013Scion Interactions"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5758-7197","authenticated-orcid":false,"given":"Jin","family":"Huang","sequence":"first","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cui","family":"Yu","sequence":"additional","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Den","sequence":"additional","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Wu","sequence":"additional","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangyuan","family":"Song","sequence":"additional","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Mao","sequence":"additional","affiliation":[{"name":"School of Ecology and Environment, Hubei Ecology Polytechnic College, Wuhan 430200, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongcheng","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Ecology and Environment, Hubei Ecology Polytechnic College, Wuhan 430200, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Li","sequence":"additional","affiliation":[{"name":"Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3909","DOI":"10.1016\/j.sjbs.2021.03.056","article-title":"Nutritional Constituents of Mulberry and Their Potential Applications in Food and Pharmaceuticals: A Review","volume":"28","author":"Jan","year":"2021","journal-title":"Saudi J. 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