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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