Progress of long non-coding RNA regulating growth, development and response to stress in plants

doi:10.3969/j.issn.1004-1524.2022.09.25

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (9): 2066-2076.DOI: 10.3969/j.issn.1004-1524.2022.09.25

• Review • Previous Articles

Progress of long non-coding RNA regulating growth, development and response to stress in plants

LI Chunmei(), WAN Xiaorong, GUAN Ziying, LAI Xiaofeng, LUO Kaiqing, LIU Kai()

Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China

Received:2021-12-16 Online:2022-09-25 Published:2022-09-30
Contact: LIU Kai

Abstract

Abstract:

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA, whose transcript length are longer than 200 nt. LncRNAs have been reported involved in various biological processes in animals and plants, in spite of its lower expression and conservation than protein-coding mRNA. Plant lncRNAs did not attract phytologists attention widely until recent years. Here, we reviewed the functionally verified lncRNAs engaged in growth, development, reproduction, response to abiotic stress, disease and insect resistance regulation in plants. Additionally, the mechanisms of plant lncRNAs were discussed according to their origins from the genome. This review will guide for further discovering, and functionally identifying and characterizing new lncRNAs in plants.

Key words: plant, lncRNAs, development, stress, molecular mechanism

CLC Number:

Q943.2

LI Chunmei, WAN Xiaorong, GUAN Ziying, LAI Xiaofeng, LUO Kaiqing, LIU Kai. Progress of long non-coding RNA regulating growth, development and response to stress in plants[J]. Acta Agriculturae Zhejiangensis, 2022, 34(9): 2066-2076.

Figures/Tables 2

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物种 Species	基因 Gene name	来源 Origin	功能 Function	作用机制 Mechanism
拟南芥	COOLAIR^{[19⇓⇓-22]}	NAT	开花Flowering	染色质重塑Chromatin remodeling
Arabidopsis	COLDAIR^[19,23]	incRNA	开花Flowering	染色质重塑Chromatin remodeling
thaliana	COLDWRAP^[19,23]	sense lncRNA	开花Flowering	染色质重塑Chromatin remodeling
	MAS^[24]	NAT	开花Flowering	染色质重塑Chromatin remodeling
	FLORE^[38]	NAT	开花 Flowering	抑制关联结构基因CDFs转录 Repressing transcription of the associated structural gene CDFs
	npc48^[39]	lincRNA	叶片发育、开花 Leaf development and flowering	—
	asHSFB2a^[40]	NAT	配子体发育Fertility	—
	LINC-AP2^[41]	lincRNA	花发育Flower development	—
	AG-incRNA4^[16]	incRNA	叶片发育Leaf development	染色质重塑Chromatin remodeling
	1GOD/asDOG1^[32-33]	NAT	种子休眠Seed dormancy	—
	HID1(nc3020)^[42-43]	lincRNA	光形态建成 Photomorphogenesis	抑制非邻近基因PIF3转录 Repressing transcription of the non-neighboring structural gene PIF3
	ASCO-lncRNA(npc351)^[39,44]	lincRNA	根发育 Root development	靶基因的可变剪接 Alternative splicing on the target gene
	APOLO (npc34)^[39,44]	lincRNA	根发育Root development	染色质重塑Chromatin remodeling
	npc536^[39]	lincRNA	应对盐胁迫Salt stress	—
	DRIR^[45]	lincRNA	应对干旱和盐胁迫 Drought and salt stress	—
	SVALKA^[46]	lincNAT	应对低温胁迫 Cold stress	抑制邻近基因CBF1转录 Repressing transcription of the neighboring structural gene CBF1
	IPS1^[47]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	At4^[48]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	TARs (TAR191/212/224/66)^[49]	lincRNA	尖孢镰刀菌抗性 Fusarium oxysporum resistance	—
	ELENA1^[50]	lincRNA	细菌性叶斑病抗性 Bacterial leaf spot resistance	激活邻近基因PR1表达 Activating expression of the neighboring structural gene PR1
水稻	LAIR^[51]	lincNAT	产量Yield	染色质重塑Chromatin remodeling
Oryza sativa	Ef-cd^[25]	NAT	开花Flowering	染色质重塑Chromatin remodeling
	LDMAR^[27,52-53]	lincRNA	育性Fertility	siRNA前体siRNA precursor
	XLOC_057324 (MISSEN)^[29-30]	lincRNA	育性 Fertility	结合非邻近基因靶蛋白质HeFP Binding HeFP encoded by the non-neighboring gene
	PMS1T^[28]	lincRNA	育性Fertility	siRNA前体siRNA precursor
	TL^[17]	NAT	叶片发育Leaf development	染色质重塑Chromatin remodeling
	ALEX1/XLOC_437338^[54]	NAT	白叶枯病抗性 Bacterial blight resistance	—
小麦 Triticum	Iw1^[55]	lincRNA	蜡质合成 β-diketone waxes biosynthesis	miRNA前体 miRNA precursor
aestivum	VAS^[26]	sense lncRNA	开花 Flowering	激活关联结构基因TaVRN1转录 Activating transcription of the associated structural gene TaVRN1
番茄	lncRNA1459^[36-37]	lincRNA	果实成熟Fruit ripening	—
Solanum lycopersicum	lncRNA16397^[56]	NAT	晚疫病抗性 Phytophthora infestans resistance	诱导关联结构基因SIGRX21表达 Inducing expression of the associated structural gene SIGRX21
	lncRNA33732^[57]	lincRNA	晚疫病抗性 Phytophthora infestans resistance	诱导邻近基因RBOH表达 Inducing expression of the neighboring structural gene RBOH
	slylnc0195^[58]	lincRNA	黄化曲叶病毒抗性 TYLCV resistance	—
	slylnc1077^[58]	lincRNA	黄化曲叶病毒抗性 TYLCV resistance	—
蒺藜苜蓿 Medicago	ENOD40^[59]	lincRNA	结瘤 Root nodule formation	蛋白质重定位 Cytoplasmic relocalization of nuclear proteins
truncatula	PDIL1^[60]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	PDIL2^[60]	NAT	P代谢 Phosphate metabolism	抑制关联结构基因表达 Repressing expression of the associated structural gene
	PDIL3^[60]	NAT	P代谢 Phosphate metabolism	抑制关联结构基因表达 Repressing expression of the associated structural gene
	Mt4/TPSI1^[61]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
棉花	lncRNA973^[62]	lincRNA	应对盐胁迫Salt stress	—
Gossypium hirsutum	GhlncNAT-ANX2^[63]	NAT	黄萎病、灰霉病抗性 Verticillium dahlia and Botrytis cinerea resistance	—
	GhlncNAT-RLP7^[63]	NAT	黄萎病、灰霉病抗性 Verticillium dahlia and Botrytis cinerea resistance	—
芜菁 Brassica rapa	bra-eTM160-1^[31]	NA	育性 Fertility	与靶基因竞争结合miRNA Competing for miRNA against target gene
	bra-eTM160-2^[31]	NA	育性 Fertility	与靶基因竞争结合miRNA Competing for miRNA against target gene
野生烟草 Nicotiana	JAL1^[10]	lincRNA	JA介导的植物防御植食昆虫 JA-mediated herbivore resistance	—
attenuata	JAL3^[10]	lincRNA	JA介导的植物防御植食昆虫 JA-mediated herbivore resistance	—
甘蓝 Brassica oleracea	BoNR8^[35]	lincRNA	种子萌发 Seed germination	—
大白菜 Brassica rapa L. ssp. pekinensis	MSTRG.19915^[64]	NAT	霜霉病 Downy mildew resistance	—
小白菜 Brassica campestris	BcMF11^[65-66]	lincRNA	育性 Fertility	—
苹果 Malus domestica	MdLNC499^[67]	lincRNA	花青素合成 Anthocyanin biosynthesis	激活邻近基因MdERF109表达 Activating expression of the neighboring structural gene MdERF109

物种 Species	基因 Gene name	来源 Origin	功能 Function	作用机制 Mechanism
拟南芥	COOLAIR^{[19⇓⇓-22]}	NAT	开花Flowering	染色质重塑Chromatin remodeling
Arabidopsis	COLDAIR^[19,23]	incRNA	开花Flowering	染色质重塑Chromatin remodeling
thaliana	COLDWRAP^[19,23]	sense lncRNA	开花Flowering	染色质重塑Chromatin remodeling
	MAS^[24]	NAT	开花Flowering	染色质重塑Chromatin remodeling
	FLORE^[38]	NAT	开花 Flowering	抑制关联结构基因CDFs转录 Repressing transcription of the associated structural gene CDFs
	npc48^[39]	lincRNA	叶片发育、开花 Leaf development and flowering	—
	asHSFB2a^[40]	NAT	配子体发育Fertility	—
	LINC-AP2^[41]	lincRNA	花发育Flower development	—
	AG-incRNA4^[16]	incRNA	叶片发育Leaf development	染色质重塑Chromatin remodeling
	1GOD/asDOG1^[32-33]	NAT	种子休眠Seed dormancy	—
	HID1(nc3020)^[42-43]	lincRNA	光形态建成 Photomorphogenesis	抑制非邻近基因PIF3转录 Repressing transcription of the non-neighboring structural gene PIF3
	ASCO-lncRNA(npc351)^[39,44]	lincRNA	根发育 Root development	靶基因的可变剪接 Alternative splicing on the target gene
	APOLO (npc34)^[39,44]	lincRNA	根发育Root development	染色质重塑Chromatin remodeling
	npc536^[39]	lincRNA	应对盐胁迫Salt stress	—
	DRIR^[45]	lincRNA	应对干旱和盐胁迫 Drought and salt stress	—
	SVALKA^[46]	lincNAT	应对低温胁迫 Cold stress	抑制邻近基因CBF1转录 Repressing transcription of the neighboring structural gene CBF1
	IPS1^[47]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	At4^[48]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	TARs (TAR191/212/224/66)^[49]	lincRNA	尖孢镰刀菌抗性 Fusarium oxysporum resistance	—
	ELENA1^[50]	lincRNA	细菌性叶斑病抗性 Bacterial leaf spot resistance	激活邻近基因PR1表达 Activating expression of the neighboring structural gene PR1
水稻	LAIR^[51]	lincNAT	产量Yield	染色质重塑Chromatin remodeling
Oryza sativa	Ef-cd^[25]	NAT	开花Flowering	染色质重塑Chromatin remodeling
	LDMAR^[27,52-53]	lincRNA	育性Fertility	siRNA前体siRNA precursor
	XLOC_057324 (MISSEN)^[29-30]	lincRNA	育性 Fertility	结合非邻近基因靶蛋白质HeFP Binding HeFP encoded by the non-neighboring gene
	PMS1T^[28]	lincRNA	育性Fertility	siRNA前体siRNA precursor
	TL^[17]	NAT	叶片发育Leaf development	染色质重塑Chromatin remodeling
	ALEX1/XLOC_437338^[54]	NAT	白叶枯病抗性 Bacterial blight resistance	—
小麦 Triticum	Iw1^[55]	lincRNA	蜡质合成 β-diketone waxes biosynthesis	miRNA前体 miRNA precursor
aestivum	VAS^[26]	sense lncRNA	开花 Flowering	激活关联结构基因TaVRN1转录 Activating transcription of the associated structural gene TaVRN1
番茄	lncRNA1459^[36-37]	lincRNA	果实成熟Fruit ripening	—
Solanum lycopersicum	lncRNA16397^[56]	NAT	晚疫病抗性 Phytophthora infestans resistance	诱导关联结构基因SIGRX21表达 Inducing expression of the associated structural gene SIGRX21
	lncRNA33732^[57]	lincRNA	晚疫病抗性 Phytophthora infestans resistance	诱导邻近基因RBOH表达 Inducing expression of the neighboring structural gene RBOH
	slylnc0195^[58]	lincRNA	黄化曲叶病毒抗性 TYLCV resistance	—
	slylnc1077^[58]	lincRNA	黄化曲叶病毒抗性 TYLCV resistance	—
蒺藜苜蓿 Medicago	ENOD40^[59]	lincRNA	结瘤 Root nodule formation	蛋白质重定位 Cytoplasmic relocalization of nuclear proteins
truncatula	PDIL1^[60]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
	PDIL2^[60]	NAT	P代谢 Phosphate metabolism	抑制关联结构基因表达 Repressing expression of the associated structural gene
	PDIL3^[60]	NAT	P代谢 Phosphate metabolism	抑制关联结构基因表达 Repressing expression of the associated structural gene
	Mt4/TPSI1^[61]	lincRNA	P代谢 Phosphate metabolism	与靶基因竞争结合miRNA Competing for miRNA against target gene
棉花	lncRNA973^[62]	lincRNA	应对盐胁迫Salt stress	—
Gossypium hirsutum	GhlncNAT-ANX2^[63]	NAT	黄萎病、灰霉病抗性 Verticillium dahlia and Botrytis cinerea resistance	—
	GhlncNAT-RLP7^[63]	NAT	黄萎病、灰霉病抗性 Verticillium dahlia and Botrytis cinerea resistance	—
芜菁 Brassica rapa	bra-eTM160-1^[31]	NA	育性 Fertility	与靶基因竞争结合miRNA Competing for miRNA against target gene
	bra-eTM160-2^[31]	NA	育性 Fertility	与靶基因竞争结合miRNA Competing for miRNA against target gene
野生烟草 Nicotiana	JAL1^[10]	lincRNA	JA介导的植物防御植食昆虫 JA-mediated herbivore resistance	—
attenuata	JAL3^[10]	lincRNA	JA介导的植物防御植食昆虫 JA-mediated herbivore resistance	—
甘蓝 Brassica oleracea	BoNR8^[35]	lincRNA	种子萌发 Seed germination	—
大白菜 Brassica rapa L. ssp. pekinensis	MSTRG.19915^[64]	NAT	霜霉病 Downy mildew resistance	—
小白菜 Brassica campestris	BcMF11^[65-66]	lincRNA	育性 Fertility	—
苹果 Malus domestica	MdLNC499^[67]	lincRNA	花青素合成 Anthocyanin biosynthesis	激活邻近基因MdERF109表达 Activating expression of the neighboring structural gene MdERF109

Progress of long non-coding RNA regulating growth, development and response to stress in plants

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