园艺作物果实发育的miRNA调控网络：从分子机制到种质创新

doi:10.13560/j.cnki.biotech.bull.1985.2025-1434

摘要/Abstract

摘要：

园艺作物果实是人类膳食营养的重要来源，其发育过程和品质形成受到复杂遗传网络的精准调控。近年来，随着分子生物学与功能基因组学的发展，以微小RNA（microRNA, miRNA）为代表的非编码RNA作为一类重要的转录后调控因子，在果实发育与品质调控中的作用日益凸显。本文系统综述了miRNA在果实发育中的多重调控功能：首先概述了植物miRNA的保守生物合成途径及其在果实中的表达特征和现有资源；随后依据发育进程详细阐述了miRNA在坐果与早期果实形成、果实膨大、成熟转色与软化，以及品质形成中的核心调控模块与作用机制，特别是miR156/157-SPL、miR172-AP2、miR396-GRF、miR397-LAC、miR828/858-MYB、miR159-GAMYB2与miR164-NAC等模块在果实大小与形态塑造、成熟时序调控、色泽与风味形成、细胞壁改造及货架期维持等方面所发挥的关键作用；进而探讨了miRNA在不同胁迫条件下通过离子稳态、激素及活性氧信号等途径的耦合作用，调控果实发育与品质形成的特征；分析了基于miRNA的基因编辑、STTM和组织特异性表达等策略在分子育种中的应用潜力，并指出了目前该领域在功能验证、调控网络解析和育种实践等方面所面临的挑战。最后，展望了整合多组学、单细胞测序与人工智能等前沿技术，系统解析miRNA调控网络、推动果实性状分子设计育种的研究趋势，以期为深入理解miRNA调控果实发育的分子机理、推动其在园艺作物遗传改良中的应用提供系统的理论参考。

关键词: 园艺作物, 果实发育, microRNA, 靶标基因, 调控机制, 分子育种, 品质形成, 环境胁迫

Abstract:

As an important source of human dietary nutrition, the development and quality formation of fruits from horticultural crops are fine-tuned by sophisticated genetic networks. In the past several years, along with the rapid development of molecular biology and functional genetics, microRNAs (miRNAs), a representative class of non-coding RNAs, have emerged as key post-transcriptional regulators, playing an increasingly prominent role in fruit development and quality control. In this review, the multiple regulatory functions of miRNAs are systematically elucidated during fruit development. Firstly, a brief introduction about the conserved biosynthetic pathways of plant miRNAs and their expression profiles in fruits are provided. Subsequently, the core regulatory modules and functional programs of miRNAs are well described by following the developmental stages, mainly including fruit setting and early initiation, fruit enlargement, ripening-associated coloration and softening, and quality formation. In particular, the key modules such as miR156/157-SPL, miR172-AP2, miR396-GRF, miR397-LAC, miR828/858-MYB, miR159-GAMYB2 and miR164-NAC are highlighted to regulate fruit size and morphological shaping, the timing of ripening, the formation of color and flavor, cell-wall remodeling, the maintenance of shelf life, and so on. Moreover, the action features of miRNAs, mainly via cooperating mineral homeostasis, hormone signaling, reactive oxygen species pathways, are discussed in modulating fruit development and quality under different stressful conditions. The potential application of miRNA-involved strategies, including gene editing, short tandem target mimics (STTM) and tissue-specific expression, is also evaluated in molecular breeding, while simultaneously challenges are highlighted in current miRNA research about functional validation, regulatory network dissection and breeding adoption. Cutting-edge technologies in this field are finally proposed, emphasizing the integration of multi-omics, single-cell sequencing, and artificial intelligence to systematically decipher miRNA regulatory networks and advance the molecular design breeding of fruit traits. Altogether, this review provides a comprehensive theoretical reference for mechanistic understanding of miRNA-mediated regulation in fruit development and its future utilization in genetic enhancement of horticultural crops.

Key words: horticultural crops, fruit development, microRNA, target gene, regulatory mechanism, molecular breeding, quality formation, environmental stress

李成泉, 史庆华, 杨晓玉. 园艺作物果实发育的miRNA调控网络：从分子机制到种质创新[J]. 生物技术通报, 2026, 42(3): 19-36.

LI Cheng-quan, SHI Qing-hua, YANG Xiao-yu. microRNA-based Regulatory Network for Fruit Development of Horticultural Crops： From Molecular Mechanism to Germplasm Innovation[J]. Biotechnology Bulletin, 2026, 42(3): 19-36.

图/表 4

图1 植物microRNA的合成途径与作用机制植物miRNA在细胞核内完成转录与加工，输出至细胞质后装载形成miRISC，最终通过切割或翻译抑制调控靶基因的表达。从上至下依次表示：MIR为miRNA基因位点，Pol II为RNA聚合酶II，可驱动MIR转录生成miRNA初级转录本（pri-miRNA）；m⁷G为5'端帽结构，AAAn为3'端poly（A）尾；pri-miRNA在细胞核内被DCL1（Dicer-like 1）、HYL1（HYPONASTIC LEAVES 1）和SE（SERRATE）组成的加工复合体识别并切割生成miRNA前体（pre-miRNA），并进一步产生miRNA/miRNA*双链。HEN1（HUA ENHANCER 1）介导双链3'端发生2'-O-Me（2'-O-甲基化）修饰以增强稳定性；HST（HASTY）为核输出因子，促进成熟miRNA/双链由细胞核转运至细胞质。AGO1（ARGONAUTE1）为核心效应蛋白，装载miRNA后形成miRISC（miRNA-induced silencing complex，miRNA诱导的沉默复合体）。虚线箭头暗示除经典“核输出后装载”外，miRISC亦可能在细胞核内初步组装后再转运至细胞质的途径；实线箭头指示分子加工、转运、装载的方向；底部两分支分别代表靶基因切割和翻译抑制2种miRNA作用模式

Fig. 1 Synthetic pathways and action modes of microRNAs in plantsPlant miRNAs are transcribed and processed in the nucleus, exported to the cytoplasm, and loaded into miRISC to regulate target gene expression through cleavage or translational inhibition. The schematic flow from top to bottom illustrates this process: MIR denotes the miRNA gene locus, which is transcribed by RNA polymerase II (Pol II) to generate primary miRNAs (pri-miRNAs) featuring a 5' m⁷G cap and a 3' poly(A) tail. Within the nucleus, pri-miRNAs are recognized and cleaved by a processing complex comprising DCL1 (Dicer-like 1), HYL1 (HYPONASTIC LEAVES 1), and SE (SERRATE), yielding precursor miRNAs (pre-miRNAs) and subsequently miRNA/miRNA* duplexes. HEN1 (HUA ENHANCER 1) mediates 2'-O-methylation (2'-O-Me) at the 3' ends of the duplex to enhance stability. The nuclear export factor HASTY (HST) facilitates the translocation of mature miRNA duplexes from the nucleus to the cytoplasm. AGO1 (ARGONAUTE 1) serves as the core effector protein, loading the mature miRNA to form the miRNA-induced silencing complex (miRISC). Dashed arrows indicate an alternative pathway in which miRISC may undergo preliminary assembly within the nucleus prior to nuclear export; solid arrows denote the directionality of molecular processing, transport, and loading. The two branches at the bottom indicate the primary modes of miRNA-mediated regulation, namely transcript cleavage and translational inhibition

图2 miRNA介导果实性状调控机制的研究路径该图概述了果实miRNA研究中从“组学鉴定‒靶基因鉴定与验证‒功能转化与验证”到“miRNA‒转录因子‒结构基因‒代谢物‒表型”整合解析的整体技术路线。上方依次为三大研究环节：组学鉴定（以不同发育阶段/性状的果实为材料，采用small RNA-seq解析miRNA表达谱，筛选候选关键miRNA）、靶基因鉴定与验证（生物信息学预测靶标，并结合PARE-seq与5'-RACE验证，完成靶基因确认）、功能转化与验证（材料创制获得稳定或瞬时功能体系：过表达、STTM/eTM沉默、CRISPR/Cas9以及VIGS沉默，并通过表型观测、靶基因验证与代谢物测定建立因果证据）。下方为“miRNA‒转录因子‒结构基因‒代谢物‒表型”机制网络构建示意：转录因子（ARF、SPL、AP2、MYB、NAC、GRF、LAC）、激素信号（IAA、GA、ABA、Eth）、代谢与品质（糖、有机酸、色素、香气/风味）及表观遗传与RNA调控（DNA甲基化、组蛋白修饰、染色质重塑、非编码RNA调控等）

Fig. 2 Research routine of miRNA-mediated fruit trait regulation mechanismThis diagram presents the comprehensive technical outline for fruit miRNA research, progressing from “omics-based identification-target gene validation-functional characterization and translational verification” to the integrated dissection of the “miRNA-transcription factor-structural gene-metabolite-phenotype” regulatory network. The upper panel shows three major stages: Omics-based identification (Small RNA-seq is performed on fruit samples representing distinct developmental stages or phenotypic traits to profile miRNA expression and prioritize candidate miRNAs), target gene identification and validation (Putative targets are predicted via bioinformatics and empirically validated using PARE-seq and 5'-RACE, thereby confirming miRNA-target interactions), and functional characterization and translational validation (Stable or transient functional systems are established through genetic materials, including overexpression, STTM/eTM-mediated silencing, CRISPR/Cas9, and VIGS silencing, and causal relationships are subsequently built by integrating phenotypic observation, target gene validation, and metabolite profiling). The lower panel illustrates the architecture of the “miRNA-transcription factor-structural gene-metabolite-phenotype” regulatory network, incorporating key regulatory layers of transcription factors (e.g., ARF, SPL, AP2, MYB, NAC, GRF, and LAC), hormone signaling (IAA, GA, ABA, and ethylene), metabolic and quality traits (sugars, organic acids, pigments, and aroma/flavor compounds), as well as epigenetic/RNA-based regulatory mechanisms (DNA methylation, histone modification, chromatin remodeling, and non-coding RNA regulation)

图3 园艺作物果实发育关键性状的miRNA核心调控网络示意图以microRNAs为核心，该图整合不同园艺作物在果实发育与逆境应答过程中的关键miRNA-靶基因模块及其关联性状。图中外圈为代表性作物，每个作物旁列出已报道的miRNA-靶基因（或通路）调控模块，并按果实发育阶段/性状分类汇总：坐果、果实膨大、果实成熟、果实软化、品质形成与胁迫响应。灰色引线表示对应作物与其总结模块的关联

Fig. 3 Schematic diagram of the core miRNA regulatory network underlying key traits during fruit development in horticultural cropsCentered on microRNAs, this integrative diagram illustrates key miRNA-target gene modules and their associated traits across various horticultural crops during fruit development and stress responses. The outer ring features representative crop species, each accompanied by experimentally validated miRNA-target gene (or pathway) regulatory modules. These modules are systematically categorized according to fruit developmental stages and trait categories: fruit setting, fruit expansion, fruit ripening, fruit softening, quality formation, and stress response. Gray connecting lines indicate associations between each crop and its corresponding regulatory modules

表1 果实发育调控相关miRNA及其靶基因

Table 1 Summary of miRNAs and their target genes involved in fruit developmental regulation

发育阶段Developmental stage	miRNA	靶基因 Target gene	物种 Species	靶向表型/通路 Target phenotype/pathway	参考文献Reference
坐果与早期果实形成 Fruit setting and early formation	miR156a	AGL80	葡萄 Vitis vinifera	调控开花、坐果等发育过程	［65］
	miR156h	SPL13B	苹果 Malus domestica	调控赤霉素（GA）代谢/信号、促进单性结实/坐果	［66］
	miR159	GAMYB2	番茄 Solanum lycopersicum和拟南芥 Arabidopsis thaliana	GA信号与坐果启动，以及幼果早期形态建成/果形调控	［61-63］
	miR159c	GAMYB	葡萄 Vitis vinifera	调控GA-DELLA相关通路、及单性结实/坐果等发育过程	［64］
	miR160	ARF10A/10B/17	番茄 Solanum lycopersicum	调控生长素（IAA）信号、坐果与幼果早期膨大	［54］
	miR166	SlHB15A	番茄 Solanum lycopersicum	平衡生长素-乙烯信号、调控温度胁迫下的坐果/单性结实	［60］
	miR167	ARF6/8	番茄 Solanum lycopersicum	花器官发育与坐果/单性结实；影响子房壁细胞伸长	［55-56］
	miR390	ARF2/3/4	拟南芥 Arabidopsis thaliana	调控TAS3-tasiARF通路及早期果实形成与器官生长	［59］
	miR393	TIR1， AFB2/3	拟南芥 Arabidopsis thaliana和黄瓜 Cucumis sativus	调控生长素通路、及坐果和结实等过程	［57-58］
果实膨大 Fruit expansion	miR156	SPL	苹果 Malus domestica和梨 Pyrus spp.	调控细胞分裂和膨大及果实大小	［19，71］
	miR172	AP2	苹果 Malus domestica、番茄 Solanum lycopersicum 拟南芥 Arabidopsis thaliana	调控组织分化与膨大及果实大小/形态	［72-75］
	miR396	GRF	番茄 Solanum lycopersicum	调控细胞增殖与器官大小，及果实大小和形状	［19，23，67-70］
果实成熟 Fruit ripening	miR156/157	SPL	蓝莓 Vaccinium corymbosum、梨 Pyrus spp.、荔枝 Litchi chinensis、番茄 Solanum lycopersicum和苹果 Malus domestica	调控果实成熟和转色，及花青素/叶绿素代谢	［76，79-80］
	miR396	FtsZs	蓝莓 Vaccinium corymbosum	调控色素体/叶绿体发育，及成熟转色和色素积累	［86］
	miR828/miR858	MYB	番茄 Solanum lycopersicum、葡萄 Vitis vinifera、梨 Pyrus spp.和猕猴桃 Actinidia chinensis	调控花青素/黄酮合成通路，影响着色与抗氧化品质	［26，77-78，81-85］
	miR7125	CCR	苹果 Malus domestica	调控木质素-花青素平衡及光诱导着色	［87］
	NEW41	CHI	荔枝 Litchi chinensis	调控黄酮/花青素合成结构基因，影响着色	［80］
果实软化 Fruit softening	miR393	生长素-乙烯信号通路	桃 Prunus persica	调控激素互作引发的软化进程，影响贮藏期	［53］
	miR397	LAC1/2/18	梨 Pyrus spp.	调控木质素/细胞壁木质化与硬度，影响质地与货架期	［88］
	miR397a	LOX	葡萄 Vitis vinifera	调控脂质代谢/膜脂过氧化、软化及与风味相关过程	［89］
	miR399g	ACO3	葡萄 Vitis vinifera	调控乙烯生物合成、果实成熟和软化	［89］
	miR479	BGA	葡萄 Vitis vinifera	调控β-半乳糖苷酶等细胞壁多糖降解基因，影响软化	［89］
	miR3627-5p	Grip-22/PAL	葡萄 Vitis vinifera	调控苯丙烷代谢/细胞壁相关基因，影响果实软化进程	［89］
	miR2950	CHS	葡萄 Vitis vinifera	调控黄酮合成相关基因及软化伴随的次生代谢途径	［89］
	novel_miR22	PE	葡萄 Vitis vinifera	调控果胶酯酶等促进软化	［89］
	miR164	NAC	番茄 Solanum lycopersicum、葡萄 Vitis vinifera和猕猴桃 Actinidia chinensis	乙烯合成和响应及色泽、质地相关基因表达调控	［96-98］
品质形成 Quality formation	miR156	SPL	桃 Prunus persica和番茄Solanum lycopersicum	糖酸代谢/品质形成相关通路调控及代谢重塑	［100，102］
	miR159	MYB	番茄 Solanum lycopersicum	色素/次生代谢与风味品质相关通路的转录调控	［63］
	miR396	GRF	番茄 Solanum lycopersicum	果实大小-品质耦合调控，影响代谢/可溶性固形物等	［27，43，70］
	miR399	PHO2	草莓 Fragaria × ananassa	磷稳态‒糖积累耦合影响品质形成	［105，124］
	miR828/858	MYB	番茄 Solanum lycopersicum、葡萄 Vitis vinifera、梨 Pyrus spp.、猕猴桃Actinidia chinensis和苹果 Malus domestica	调控花青素/黄酮合成，影响着色与抗氧化品质	［26，77，101］
胁迫响应 Stress response	miR393	TIR1/AFB	香蕉 Musa × paradisiaca	逆境下生长素信号调控与适应性响应	［111］
	miR396a-5p	GRF3/4/8	番茄 Solanum lycopersicum	干旱与高温下生长素信号调控与适应性响应	［112］
	miR396	GRF	番茄 Solanum lycopersicum和火龙果 Hylocereus undatus	调控逆境下的生长/细胞增殖和抗逆响应	［67，113］

表1 果实发育调控相关miRNA及其靶基因

Table 1 Summary of miRNAs and their target genes involved in fruit developmental regulation

发育阶段Developmental stage	miRNA	靶基因 Target gene	物种 Species	靶向表型/通路 Target phenotype/pathway	参考文献Reference
坐果与早期果实形成 Fruit setting and early formation	miR156a	AGL80	葡萄 Vitis vinifera	调控开花、坐果等发育过程	［65］
	miR156h	SPL13B	苹果 Malus domestica	调控赤霉素（GA）代谢/信号、促进单性结实/坐果	［66］
	miR159	GAMYB2	番茄 Solanum lycopersicum和拟南芥 Arabidopsis thaliana	GA信号与坐果启动，以及幼果早期形态建成/果形调控	［61-63］
	miR159c	GAMYB	葡萄 Vitis vinifera	调控GA-DELLA相关通路、及单性结实/坐果等发育过程	［64］
	miR160	ARF10A/10B/17	番茄 Solanum lycopersicum	调控生长素（IAA）信号、坐果与幼果早期膨大	［54］
	miR166	SlHB15A	番茄 Solanum lycopersicum	平衡生长素-乙烯信号、调控温度胁迫下的坐果/单性结实	［60］
	miR167	ARF6/8	番茄 Solanum lycopersicum	花器官发育与坐果/单性结实；影响子房壁细胞伸长	［55-56］
	miR390	ARF2/3/4	拟南芥 Arabidopsis thaliana	调控TAS3-tasiARF通路及早期果实形成与器官生长	［59］
	miR393	TIR1， AFB2/3	拟南芥 Arabidopsis thaliana和黄瓜 Cucumis sativus	调控生长素通路、及坐果和结实等过程	［57-58］
果实膨大 Fruit expansion	miR156	SPL	苹果 Malus domestica和梨 Pyrus spp.	调控细胞分裂和膨大及果实大小	［19，71］
	miR172	AP2	苹果 Malus domestica、番茄 Solanum lycopersicum 拟南芥 Arabidopsis thaliana	调控组织分化与膨大及果实大小/形态	［72-75］
	miR396	GRF	番茄 Solanum lycopersicum	调控细胞增殖与器官大小，及果实大小和形状	［19，23，67-70］
果实成熟 Fruit ripening	miR156/157	SPL	蓝莓 Vaccinium corymbosum、梨 Pyrus spp.、荔枝 Litchi chinensis、番茄 Solanum lycopersicum和苹果 Malus domestica	调控果实成熟和转色，及花青素/叶绿素代谢	［76，79-80］
	miR396	FtsZs	蓝莓 Vaccinium corymbosum	调控色素体/叶绿体发育，及成熟转色和色素积累	［86］
	miR828/miR858	MYB	番茄 Solanum lycopersicum、葡萄 Vitis vinifera、梨 Pyrus spp.和猕猴桃 Actinidia chinensis	调控花青素/黄酮合成通路，影响着色与抗氧化品质	［26，77-78，81-85］
	miR7125	CCR	苹果 Malus domestica	调控木质素-花青素平衡及光诱导着色	［87］
	NEW41	CHI	荔枝 Litchi chinensis	调控黄酮/花青素合成结构基因，影响着色	［80］
果实软化 Fruit softening	miR393	生长素-乙烯信号通路	桃 Prunus persica	调控激素互作引发的软化进程，影响贮藏期	［53］
	miR397	LAC1/2/18	梨 Pyrus spp.	调控木质素/细胞壁木质化与硬度，影响质地与货架期	［88］
	miR397a	LOX	葡萄 Vitis vinifera	调控脂质代谢/膜脂过氧化、软化及与风味相关过程	［89］
	miR399g	ACO3	葡萄 Vitis vinifera	调控乙烯生物合成、果实成熟和软化	［89］
	miR479	BGA	葡萄 Vitis vinifera	调控β-半乳糖苷酶等细胞壁多糖降解基因，影响软化	［89］
	miR3627-5p	Grip-22/PAL	葡萄 Vitis vinifera	调控苯丙烷代谢/细胞壁相关基因，影响果实软化进程	［89］
	miR2950	CHS	葡萄 Vitis vinifera	调控黄酮合成相关基因及软化伴随的次生代谢途径	［89］
	novel_miR22	PE	葡萄 Vitis vinifera	调控果胶酯酶等促进软化	［89］
	miR164	NAC	番茄 Solanum lycopersicum、葡萄 Vitis vinifera和猕猴桃 Actinidia chinensis	乙烯合成和响应及色泽、质地相关基因表达调控	［96-98］
品质形成 Quality formation	miR156	SPL	桃 Prunus persica和番茄Solanum lycopersicum	糖酸代谢/品质形成相关通路调控及代谢重塑	［100，102］
	miR159	MYB	番茄 Solanum lycopersicum	色素/次生代谢与风味品质相关通路的转录调控	［63］
	miR396	GRF	番茄 Solanum lycopersicum	果实大小-品质耦合调控，影响代谢/可溶性固形物等	［27，43，70］
	miR399	PHO2	草莓 Fragaria × ananassa	磷稳态‒糖积累耦合影响品质形成	［105，124］
	miR828/858	MYB	番茄 Solanum lycopersicum、葡萄 Vitis vinifera、梨 Pyrus spp.、猕猴桃Actinidia chinensis和苹果 Malus domestica	调控花青素/黄酮合成，影响着色与抗氧化品质	［26，77，101］
胁迫响应 Stress response	miR393	TIR1/AFB	香蕉 Musa × paradisiaca	逆境下生长素信号调控与适应性响应	［111］
	miR396a-5p	GRF3/4/8	番茄 Solanum lycopersicum	干旱与高温下生长素信号调控与适应性响应	［112］
	miR396	GRF	番茄 Solanum lycopersicum和火龙果 Hylocereus undatus	调控逆境下的生长/细胞增殖和抗逆响应	［67，113］

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