Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

Jha, Uday Chand; Nayyar, Harsh; Jha, Rintu; Khurshid, Muhammad; Zhou, Meiliang; Mantri, Nitin; Siddique, Kadambot H. M.

doi:10.1186/s12870-020-02595-x

BMC Plant Biology

Table 1 Various types of lncRNAs that control abiotic stress responses in plants

From: Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

Name of stress	Crop	No. of lncRNAs identified	Number of lncRNAs expressed under stress	Platform and technique used for lncRNAs identification and their function	Function	Reference
Drought	Foxtail millet	19 lncRNAs	19	IlluminaHiSeq 2000,qRT-PCR	Control drought stress response	[59]
Drought	Populus trichocarpa	2542 lincRNAs	504	HiSeq™ 2000, RT-qPCR	Drought- stress response	[56]
Drought	Rice	98 lncRNAs	98	Illumina HiSeq 2500, qRT-PCR	Regulatory role in drought response	[57]
Drought	Arabidopsis	DROUGHT INDUCED lncRNA (DRIR)	DROUGHT INDUCED lncRNA (DRIR)	HiSeq 2000, RT-qPCR	Participate in regulating set of drought responsive genes	[37]
Drought	Rice	3714	21	RT-qPCR, PLncPRO	Differentially expressed under drought stress	[72]
Drought	Wheat	–	59,110	Illumina HiSeq. 2000, qRT-PCR	Differential expression under drought stress response	[73]
Drought and cold	Cassava	682 lncRNAs	318	HiSeq 2500,qRT-PCR, CNCI, CPC,	Hormone signal transduction, sucrose metabolism pathway etc.	[60]
Drought	Pyrus betulifolia	14,478	251	Illumina HiSeq 4000, CNCI, CPC, qRT-PCR	Various metabolic processes	[70]
Drought	Panicum virgatum L	16,551 novel lncRNAs	1597	HiSeq2500, qRT-PCR	Regulating drought-stress response	[52]
Drought	Maize	3488	1535	Illumina HiSeq 2500, qRT-PCR	Oxidoreductase activity, water binding, and electron carrier activity	[54]
Drought	Cleistogenes songorica	3397 lncRNAs	468	HiSeq2500, CPC, CNCI, CPATqRT-PCR	Regulating drought-stress response	[62]
Drought	Cassava	833	124	Hiseq 4000, qRT-PCR, CNCI, CPC,	Cell-related metabolism, Calvin cycle, hormone metabolism etc.	[53]
Drought	Cassava	1405	185	qRT-PCR	Melatonin responsive controlling drought-stress response	[74]
Drought	Cassava	1379	194	qRT-PCR	ABA signaling regulation	[71]
Heat stress	Wheat	125 putative	77	Solexa sequencing technology wheat Affymetrix GeneChip, qRT-PCR	Heat responsive	[75]
Heat stress	Brassica rapa ssp. chinensis	4594 putative lncRNAs	1686	Illumina Hiseq. 2500, qRT-PCR CPC,CNCI	Differential expression of these RNA suggested involvement of various phytohormones in heat stress tolerance.	[64]
Heat stress and drought	Brassica juncea	7613 putative lncRNAs	1614	qRT-PCR	Associated with enzymatic and non-enzymatic antioxidants under drought and heat stress	[76]
Cold and heat	Chinease cabbage	10,001	2236	Illumina HiSeq™ 2000 qRT-PCR, CPC	Total of 67 and 192 target genes for cold and heat were regulated	[77]
Cold stress	Banana	12,462 lncRNAs	20	Illumina HiSeqTM 4000, qPCR, CPC	Cold stress response	[78]
Cold stress	Arabidopsis	379	135	Illumina HiSeq 2500, RT-qPCR	Cold or freezing acclimation	[79]
Cold stress	Arabidopsis	SVALKA	SVALKA		Repress CBF1 expression and freezing tolerance	[80]
Cold stress	Grapevine	2088	466	HiSeq 2500, qRT-PCR, CNCI, CPC,	Related to cold stress response	[81]
Cold stress	Chinese cabbage	2088	549	Illumina HiSeqTM 2000, qPCR	Controlling vernalization	[82]
Cold stress	Rice	1485 lncRNAs	566	Illumina HiSeq 2500 platform, qRT-PCR	Controlling cold stress response	[83]
Cold stress	Medicago
	truncatula	24,368 unique lncRNAs	983 and 1288	Illumina HiSeq 4000,Q-PCR	Controlling cold stress response	[84]
Salinity	Arabidopsis	DROUGHT INDUCED lncRNA (DRIR)	DROUGHT INDUCED lncRNA (DRIR)	HiSeq 2000, RT-qPCR	Participate in regulating set of salinity responsive genes	[37]
Salinity and drought	Chickpea	3457	13	RT-qPCR, PLncPRO	Differentially expressed under drought and salinity stress	[72]
Salinity	Barley	CNT0018772 and CNT0031477	2	qPCR	Both up- and down- regulatory role in salinity stress	[85]
Salinity	Cotton	1117 unique lncRNAs	44	Illumina HiSeq 4000, RT-qPCR	Controls salinity stress genes	[86]
Salinity and boron	Maize	48,345	1710	Illumina MiSeq, RT-qPCR, AgriGO	Nicotianamine biosynthetic and metabolic processes, gene regulation	[87]
Salinity	Poplar	10,646 and 10,531 lncRNAs	8592 and 3425	HiSeq 2500	Regulating osmotin 34, NHX7, RARE-COLD-INDUCIBLE 2B, and WRKY 33 genes
Cadmium stress	Rice	3558	69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated	Illumina HiSeq 2000,CPC, RT-qPCR	Genes related to phtosynthetic pathways are involved in response to Cd stress	[88]
and salinity	Wheat	44,698	2064 and 2278		Regulatory roles in numerous biological processes	[89]
Ca²⁺-channel blocker	Wheat	6309	177	HiSeqTM2000, qRT-PCR	Affects various biological processes	[90]
Oxidative stress	Rice	7000 lncRNAs		Hiseq2000, DEGSeq	Down-regulated poly adenylation lncRNAs participate in abiotic stress tolerance	[91]
Waterlogging	Maize	6099	3190	Illumina HisSeq 4000, qRT-PCR	Metabolic pathways, such as glycolysis and methionine metabolism in response to water logging	[92]
Phosphate starvation	Arabidopsis	1212 novel lncRNAs	309	Illumina Hiseq 2000/2500,	Phosphate starvation signaling and regulation	[93]
				qRT-PCR	Cell wall organization and photosynthesis
Phosphate deficiency	Medicago truncatula	10, 785	358 and 224	Illumina Hiseq2000, qRT-PCRCPC,CNCI	Involved in various signal transduction, chemical detoxification	[61]
Phosphorus use efficiency	barley	188 and 209	–	Illumina sequencing, qRT-PCR	Related to phosphate starvation	[94]
Nitrogen deficiency	Poplar	388	126		Low nutrition adaptation	[95]
Nitrogen deficiency	Maize	7245	637	Illumina HiSeq™2500,CPC,qPCR	Nitrogen metabolism, oxidative phosphorylation	[96]
Nitrogen deficiency	Rice	2588 novel putative lncRNA	2588	Illumina HiSeq 2500, qRT-PCR	Regulatory role in N-starvation- response	[14]
Nitrogen deficiency	Barley	498 lncRNAs	56	Illumina Hiseq Xten platform	Regulatory role in N-starvation- response	[97]
				qPCR		[98]
Boron deficiency	Poncirus	2101 unique lncRNAs		Illumina HiSeq X Ten platform	Regulatory role in B-starvation response
	trifoliata			qRT-PCR
Low nutrient deficiency	Arabidopsis	60 differentially expressed lincRNAs	60 differentially expressed lincRNAs	HiSeq2000TM, qRT-PCR	Controlling various nutrient response	[99]
CPC=Coding Potential Calculator
CNCI=Coding-Non-Coding Index
CPAT = Coding Potential Assessment Tool

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ISSN: 1471-2229

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