microRNA-based Regulatory Network for Fruit Development of Horticultural Crops： From Molecular Mechanism to Germplasm Innovation

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

Abstract

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

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.

Figures/Tables 4

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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］

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］