From Regulatory Networks to Precision Breeding: Integrating miRNA and Gene Editing for Trait Improvement in Forest Trees
DOI:
https://doi.org/10.62051/ebpdes72Keywords:
Gene editing; miRNA; target gene regulation; abiotic stress regulation.Abstract
In recent years, with the development of high-throughput sequencing and molecular biology techniques, researchers have identified a large number of miRNA sequences in plants, which play crucial roles in developmental regulation, signal transduction, stress response, and maintenance of nutrient homeostasis. Compared with crops, research on miRNA function in forest trees started later due to their long life cycle and complex genome. However, they have unique regulatory patterns in adaptive evolution, morphological differentiation and stress resistance formation. This article systematically summarizes the functions of plant miRNAs in developmental and hormonal signaling pathways, and in abiotic and biotic stresses, focusing on their mechanisms of action within the forest tree gene regulatory network. Meanwhile, combining the latest advancements in gene editing and viral vector technologies, this study analyzes the application prospects of miRNA-mediated gene silencing in molecular design breeding, and proposes a strategic framework for the precise improvement of complex traits in forest trees by integrating miRNA regulatory modules with CRISPR/Cas technology, providing new theoretical and technical support for molecular breeding of forest trees.
Downloads
References
[1] Yu Y, Wang H, You C, et al. Plant microRNA maturation and function [J]. Nature Reviews Molecular Cell Biology, 2025: 1-16.
[2] Saiyed A N, Vasavada A R, Johar S R K. Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases [J]. Future Journal of Pharmaceutical Sciences, 2022, 8 (1): 24.
[3] Bajczyk M, Jarmolowski A, Jozwiak M, et al. Recent insights into plant miRNA biogenesis: multiple layers of miRNA level regulation [J]. Plants, 2023, 12 (2): 342.
[4] Guo Z, Kuang Z, Zhao Y, et al. PmiREN2. 0: from data annotation to functional exploration of plant microRNAs [J]. Nucleic acids research, 2022, 50 (D1): D1475-D1482.
[5] Li M, Yu B. Recent advances in the regulation of plant miRNA biogenesis [J]. RNA biology, 2021, 18 (12): 2087-2096.
[6] Liu J, Liu X, Zhang S, et al. TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs [J]. BMC genomics, 2021, 22 (1): 348.
[7] Dong Q, Hu B, Zhang C. microRNAs and their roles in plant development [J]. Frontiers in plant science, 2022, 13: 824240.
[8] Dong Q, Hu B, Zhang C. microRNAs and their roles in plant development [J]. Frontiers in plant science, 2022, 13: 824240.
[9] Lauressergues D, Ormancey M, Guillotin B, et al. Characterization of plant microRNA-encoded peptides (miPEPs) reveals molecular mechanisms from the translation to activity and specificity [J]. Cell Reports, 2022, 38 (6).
[10] Zhang F, Yang J, Zhang N, et al. Roles of microRNAs in abiotic stress response and characteristics regulation of plant [J]. Frontiers in Plant Science, 2022, 13: 919243.
[11] Li Y, Deng Y, Qin D, et al. Study of the SPL gene family and miR156-SPL module in Populus tomentosa: Potential roles in juvenile-to-adult phase transition and reproductive phase [J]. International Journal of Biological Macromolecules, 2025, 296: 139547.
[12] Ma Y, Xue H, Zhang F, et al. The miR156/SPL module regulates apple salt stress tolerance by activating MdWRKY100 expression [J]. Plant Biotechnology Journal, 2021, 19 (2): 311-323.
[13] Feyissa B A, Amyot L, Nasrollahi V, et al. Involvement of the miR156/SPL module in flooding response in Medicago sativa [J]. Scientific reports, 2021, 11 (1): 3243.
[14] Nowak K, Wójcik A M, Konopka K, et al. miR156-SPL and miR169-NF-YA modules regulate the induction of somatic embryogenesis in Arabidopsis via LEC-and auxin-related pathways [J]. International Journal of Molecular Sciences, 2024, 25 (17): 9217.
[15] Wei H, Xiao X, Deng J, et al. A miR156-SPL module controls shade-induced inhibition of vascular cambium activity through cytokinin pathway in poplar [J]. Cell reports, 2025, 44 (7).
[16] Tripathi R K, Bekele W A, Tinker N A, et al. Differential expression and global analysis of miR156/SQUAMOSA promoter binding-like proteins (SPL) module in oat [J]. Scientific Reports, 2024, 14 (1): 9928.
[17] Imran M, Liu T, Wang Z, et al. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana [J]. Frontiers in Plant Science, 2022, 13: 948751.Garighan J, Dvorak E, Estevan J, et al. The identification of small RNAs differentially expressed in apple buds reveals a potential role of the Mir159-MYB regulatory module during dormancy [J]. Plants, 2021, 10 (12): 2665.
[18] Gull S, Uddin S, Hussain H A, et al. Genome-wide analysis reveals the TCP-miR159-miR319 module is crucial for rice (Oryza sativa L.) growth and response to drought and salinity [J]. Plant Stress, 2023, 10: 100215.
[19] Kumar R, Saini R, Singh D, et al. miR159b, an epigenetic target of RSI1/FLD, negatively regulates systemic acquired resistance [J]. The Plant Journal, 2025, 124 (1): e70519.
[20] Anand S, Lal M, Bhardwaj E, et al. MIR159 regulates multiple aspects of stamen and carpel development and requires dissection and delimitation of differential downstream regulatory network for manipulating fertility traits [J]. Physiology and Molecular Biology of Plants, 2023, 29 (10): 1437-1456.
[21] Gao J, Chen L, Yuan N, et al. Multifaceted Regulation and Functional Versatility of miR164 in Plant: From Molecular Mechanisms to Crop Improvement [J]. Physiologia Plantarum, 2025, 177 (5): e70548.
[22] Wang M, Li A M, Liao F, et al. Sugarcane microRNA shy-miR164 regulates sugar metabolism through direct cleavage of the transcription factor ScNAC mRNA [J]. Plant Physiology, 2025, 198 (4): kiaf354.
[23] Tsai W A, Sung P H, Kuo Y W, et al. Involvement of microRNA164 in responses to heat stress in Arabidopsis [J]. Plant Science, 2023, 329: 111598.
[24] Segura M, García A, Gamarra G, et al. An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development [J]. Journal of Experimental Botany, 2024, 75 (7): 1948-1966.
[25] Pawłasek N, Sokołowska A, Koter M, et al. The interaction between miR165/166 and miR160 regulates Arabidopsis thaliana seed size, weight, and number in a ROS-dependent manner [J]. Planta, 2024, 260 (3): 72.
[26] Hendrix S. In the heat of the moment: The miR165/166-PHB module mediates thermotolerance in Arabidopsis [J]. 2023.
[27] Fedorin D N, Eprintsev A T, Chuykova V O, et al. Participation of miR165a in the phytochrome signal transduction in maize (Zea mays L.) leaves under changing light conditions [J]. International Journal of Molecular Sciences, 2024, 25 (11): 5733.
[28] Gautam V, Singh A, Yadav S, et al. Conserved LBL1-ta-siRNA and miR165/166-RLD1/2 modules regulate root development in maize [J]. Development, 2021, 148 (1): dev190033.
[29] Diener C, Keller A, Meese E. Emerging concepts of miRNA therapeutics: from cells to clinic [J]. Trends in Genetics, 2022, 38 (6): 613-626.
[30] Diener C, Keller A, Meese E. The miRNA–target interactions: an underestimated intricacy [J]. Nucleic Acids Research, 2024, 52 (4): 1544-1557.
[31] Menon A, Abd-Aziz N, Khalid K, et al. miRNA: a promising therapeutic target in cancer [J]. International journal of molecular sciences, 2022, 23 (19): 11502.
[32] Vishnoi A, Rani S. miRNA biogenesis and regulation of diseases: an updated overview [J]. MicroRNA profiling: methods and protocols, 2022: 1-12.
[33] Cui Y, Qi Y, Ding L, et al. miRNA dosage control in development and human disease [J]. Trends in Cell Biology, 2024, 34 (1): 31-47.
[34] Pagoni M, Cava C, Sideris D C, et al. miRNA-based technologies in cancer therapy [J]. Journal of personalized medicine, 2023, 13 (11): 1586.
[35] Hill M, Tran N. miRNA interplay: mechanisms and consequences in cancer [J]. Disease models & mechanisms, 2021, 14 (4): dmm047662.
[36] Saiyed A N, Vasavada A R, Johar S R K. Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases [J]. Future Journal of Pharmaceutical Sciences, 2022, 8 (1): 24.
[37] Xu Q, Qin X, Zhang Y, et al. Plant miRNA bol-miR159 regulates gut microbiota composition in mice: In vivo evidence of the crosstalk between plant miRNAs and intestinal microbes [J]. Journal of agricultural and food chemistry, 2023, 71 (43): 16160-16173.
[38] Li B, Tao P, Xu F, et al. Function of soybean miR159 family members in plant responses to low phosphorus, high salinity, and abscisic acid treatment [J]. Agronomy, 2023, 13 (7): 1798.
[39] Imran M, Liu T, Wang Z, et al. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana [J]. Frontiers in Plant Science, 2022, 13: 948751.
[40] Lei P, Qi N, Zhou Y, et al. Soybean miR159-GmMYB33 regulatory network involved in gibberellin-modulated resistance to Heterodera glycines [J]. International Journal of Molecular Sciences, 2021, 22 (23): 13172.
[41] Chieb M, Gachomo E W. The role of plant growth promoting rhizobacteria in plant drought stress responses [J]. BMC plant biology, 2023, 23 (1): 407.
[42] Wang M, Wang R, Mur L A J, et al. Functions of silicon in plant drought stress responses [J]. Horticulture Research, 2021, 8.
[43] Bashir S S, Hussain A, Hussain S J, et al. Plant drought stress tolerance: Understanding its physiological, biochemical and molecular mechanisms [J]. Biotechnology & Biotechnological Equipment, 2021, 35 (1): 1912-1925.
[44] Ahmad H M, Fiaz S, Hafeez S, et al. Plant growth-promoting rhizobacteria eliminate the effect of drought stress in plants: a review [J]. Frontiers in Plant Science, 2022, 13: 875774.
[45] Chen P W, Gasilina A, Yadav M P, et al. Control of cell signaling by Arf GTPases and their regulators: Focus on links to cancer and other GTPase families [J]. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 2022, 1869 (2): 119171.
[46] Fanelli M J, Welsh C M, Lui D S, et al. Immunity-linked genes are stimulated by a membrane stress pathway linked to Golgi function and the ARF-1 GTPase [J]. Science Advances, 2023, 9 (49): eadi5545.
[47] Yang Z, Hui S, Lv Y, et al. miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice [J]. Molecular Plant, 2022, 15 (4): 671-688.
[48] Székely A, Gulyás Z, Balogh E, et al. Identification of ascorbate‐and salicylate‐responsive miRNAs and verification of the spectral control of miR395 in Arabidopsis [J]. Physiologia Plantarum, 2023, 175 (6): e14070.
[49] Han X, Tang S, Ma X, et al. Blocking miR528 function promotes tillering and regrowth in switchgrass [J]. Plant Biotechnology Journal, 2024, 22 (3): 712-721.
[50] LEI Z, WANG T, Ji X, et al. Overexpression of miR528 Enhances K+ Homeostasis in Rice Seedling under Salt Stress [J]. Journal of Henan Agricultural Sciences, 2022, 51 (4): 30.
[51] Hussen B M, Rasul M F, Abdullah S R, et al. Targeting miRNA by CRISPR/Cas in cancer: advantages and challenges [J]. Military Medical Research, 2023, 10 (1): 32.
[52] Molla K A, Sretenovic S, Bansal K C, et al. Precise plant genome editing using base editors and prime editors [J]. Nature Plants, 2021, 7 (9): 1166-1187.
[53] Rajput M, Choudhary K, Kumar M, et al. RNA interference and CRISPR/Cas gene editing for crop improvement: paradigm shift towards sustainable agriculture [J]. Plants, 2021, 10 (9): 1914.
[54] Cardi T, Murovec J, Bakhsh A, et al. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation [J]. Trends in Plant Science, 2023, 28 (10): 1144-1165.
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Transactions on Environment, Energy and Earth Sciences
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
