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Table 2 Function of various lncRNAs regulating various abiotic stress in plants

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

Stress Crop Genotype LncRNA Target gene Regulatory mechanism Reference
Drought Populus Nisqually 1 lincRNA20 and lincRNA2752 Control drought stress by regulating [56]
  trichocarpa   lincRNA2962 and lincRNA1039   ptc-miR476 and ptc-miR169 through eTM
    LincRNA3241    
Drought Rice Oryza sativa cv. Ilmi NAT Os02g0250700–01 Os02g0250600–01 Regulate drought by NAT lncRNAs [57]
    NAT Os02g0180800–01 (late embryogenesis   
     abundant protein)   
     Os02g0180700–01   
     (cinnamoyl-CoA   
     reductase)   
Drought Rice DXWR Up-regulated lncRNAs MSTRG69391 Transcription factor, calmodulin Regulate biological processes in [63]
    MSTRG41712 and MSTRG68635 and HSP genes, mitochondrial carrier response to drought stress  
    down regulated lncRNAs MSTRG65848 protein gene etc   
    MSTRG27834 and MSTRG46301    
Drought Cassava TMS60444 lincRNA340 NUCLEAR FACTOR Y (NF-Y) By targeting miR169 based on target mimicry [60]
Drought Wheat Kiziltan and TR39477 c70772_g2_i1 and c90557_g1_i1 c69036_g1_i1 and Drought stress is regulated by [73]
   TTD-22   c9653_g1_i2 lncRNA-miRNA-mRNA networks  
Drought Panicum Alamo XLOC_053020 Pavir.Ia01153 Regulation of genes related [52]
  virgatum L   XLOC_014465 Pavir.Bb00347 to ethylene synthesis  
    XLOC_033252 Pavir.Eb01847 and signaling, ABA synthesis and signaling,
    XLOC_090250, XLOC_016922, Pavir.J23169 and starch and sucrose biosynthesis gene  
    and XLOC_067866 Pavir.Ca01179   
    XLOC_074836 Pavir.J04626   
    XLOC_008122 Pavir.J10665   
    XLOC_081155 Pavir.Ba00729   
    XLOC_005809 Pavir.Ab03141   
Drought Cassava Ku50 TCONS_00060863, TCONS_00068353 CYP707A1 Genes involved in ABA catabolism, [53]
    TCONS_00097416, TCONS_00069665, CSLD5, ERL1, SPCH, ethylene signaling.  
     LAX2, HDG11,SCR Also regulates gene by targeting miR156,
    TCONS_00040721 GRF1 and HB51,DOX1 miR164, miR169, and miR172  
Drought Cleistogenes   MSTRG.43964.1 Genes related to By regulating miRNA166, miRNA164, miRNA393, and miRNA397a/b and acting as endogenous target mimics [62]
  songorica   MSTRG.4400.2 abscisic acid (ABA)   
     signalling pathway,   
    MSTRG.42613.1 Genes related to starch   
    MSTRG.25585.13 and sucrose metabolism   
Drought Maize B73 lncRNA MSTRG6838.1 V-ATPase encoding gene, lncRNA regulating transcriptional [54]
     vpp4 regulation by cis- and trans-acting modes
Drought Cassava   TCONS_00129136, TCONS_00122745    [71]
    TCONS_00088201,TCONS_00067612   
Drought Cassava   TCONS_00003360, TCONS_00015102   Calcium signaling, ABA and [74]
    TCONS_00149293   ethylene metabolism  
Drought Brassica napus Q2 and Qinyou8 XLOC_042431, XLOC_071559, BnaC06g05090D IAA, Cytokinin and ABA signalling [100]
    XLOC_ 095305, XLOC_100682, BnaA01g17750D alpha-trehalose-phosphate synthase  
    XLOC_019521 and XLOC_ 042894 BnaC07g44670D   
    XLOC_075476 and XLOC_074677, BnaC02g25020D, BnaC02g25150D,  
    XLOC_074677, XLOC_ 093758 BnaC02g25200D   
    XLOC_044363 and XLOC_076449    
    XLOC_052298    
Heat Wheat TAM107 TahlnRNA27, TalnRNA5, Histone acetylation of TalnRNA5 [75]
   Chinease spring TahlnRNA12, TalnRNA21   
    TahlnRNA23 and TahlnRNA29    
Heat Chinese cabbage GHA and XK TCONS_00048391 NAC1 (Bra030820) By targeting bra-miR164a based on [64]
    TCONS_00010856 Bra021232 target mimicry mechanism  
    TCONS_00004594    
Heat Cucumis sativus Improved Jinchun 2 TCONS_00031790, TCONS_00014332, Interact with miR9748 plant hormone signal [101]
    TCONS_00014717,TCONS_00005674   transduction pathways  
Heat and Brassica   TCONS_00051908 By acting as targets and eTMs for the miRNAs [76]
drought juncea   TCONS_00088973    
Cold Cassava TMS60444 lincRNA159 NAM, ATAF1/2, Regulate cold tolerance targeting miRNA164 [60]
     CUC2 based on target mimicry mechanism  
Cold Arabidopsis Col-0 SVALKA CBF1 SVK represses CBF1 and [80]
      increase cold acclimation  
Cold Arabidopsis Col-0 COLDWRAP FLC COLDWRAP reinforc estable [102]
      repression of FLC under cold stress  
Cold Arabidopsis Col-0 TAS1a By alternative spicing of lncRNA [79]
Cold Arabidopsis Col-0 MAS MAF4 gene Histone modification and role of [103]
      NAT-lncRNAs regulating gene expression
Cold Brachypodium BdCOOLAIR1,BdCOOLAIR2 BdODDSOC1, BdCOOLAIR transcript represses [104]
  distachyon    BdODDSOC2 function of BdODDSOC gene [104]
Cold Grapevine Cabernet Sauvignon VIT_203s0017n00360 Upregulation of the following target up and down regulation of the target genes [81]
    VIT_207s0031n00070 genes VIT_216s0100g00380   
    VIT_201s0011n00530. VIT_208s0058g00960   
    IT_209s0002n00340 VIT_215s0046g02110   
    VIT_213s0158n00020 VIT_202s0025g01280   
    VIT_213s0067n00110 VIT_200s0246g00150   
    VIT_200s0225n00020 VIT_202s0154g00610   
Cold stress Chinease cabbage RJKB-T24 MSTRG.4795, MSTRG.18513, BrFLC and BrMAF genes Epigenetic modification at BrFLC2as locus, [82]
    MSTRG21908, related to vernalization epigenetic modification at Bra024350 and
    MSTRG.259, MSTRG.491   Bra031888, Bra024351 and Bra031884 loci
    MSTRG.17153    
Cold stress Medicago truncatula Jemalong A17 lncRNA MtCIR1 MtCBF genes Targeting MtCBF genes [84]
Salinity Medicago truncatula Jemalong A17 lncRNA TCONS_00097188, Medtr6g006990, By regulating various genes [68]
Salinity    TCONS_00046739, cytochrome P450 related to ROS activity,  
Salinity    TCONS_00100258 Transmembrane proteins gene secondary messenger molecules,  
    and TCONS_00118328    
salinity    TCONS_00047650 Medtr3g069280, carbonic anhydrase gene etc.  
Salinity    lncRNA TCONS_00020253 Medtr1g081900 and   
Salinity    TCONS_00116877 Medtr7g094600   
Salinity Arabidosis DRIR ANNAT7,NAC3 and Affecting fucosyltransferase or [37]
     WRKY8 NAC3 transcription factor  
Salinity Cotton SN91–11 lnc_388,lnc_883, Gh_A09G1182, Targeting Gh_A09G1182, [86]
      Gh_D03G0339 genes  
    lnc_973 and lnc_253 and Gh_D03G0339 genes Regulating ghr-miR399 and ghr-156e by eTM
Salinity Poplar P. euphratica Peu_00167161, Pal_00184400 HKT1  
   P.alba var. pyramidalis Pal_00132209 fucosyltransferase or NAC3   
Salinity Cotton SN91–11 lncRNA973 SOD, CAT, POD and P5CS, lncRNA973 regulate the [105]
     RBOHB, RBOHD, NHX7 ghr-miR399 and its target gene GhPHO2  
     MYB5, WRKY46, ERF62, NAC29   
Salinity Pistacia vera L. Ghazvini and Sarakhs 5 NAT-lncRNAs CERK1, LEA, Laccase genes NAT-lncRNA regulate ATPase, [106]
     TF genes, genes related to cation transporter, kinase  
     hormone signaling pathways and UDP-glycosyltransferases genes  
Water Maize B73 TCONS_00177501 Zm00001d029280 Assist in water logging tolerance [92]
logging    TCONS_00124833 Zm00001d012263   
    TCONS_00105920 Zm00001d015618   
logging    TCONS_00092298 Zm00001d018819   
Cadmium Rice DX142 XLOC_086307 OS03G0196600 Genes regulating cysteine and [88]
     cysteine-rich peptide methionine metabolism and  
    XLOC_086119 and XLOC_066284 metabolism-related gene carotenoid biosynthesis  
     carotenoid biosynthesis   
Phosphate Arabidopsis   XLOC_020833, XLOC_001691 PHR1 Regulating phosphate homeostasis [93]
starvation    and XLOC_013661   by targeting miR399  
Phosphate Medicago Jemalong A17 PDIL1,PDIL2 and PDIL3 MtPHO2   [61]
starvation truncatula    Medtr1g074930   
Nitrogen Rice Nipponbare cis-NATAMT1.1,cis-NATAMT1.2 AMT1.1and AMT1.2 Regulate nitrogen use efficiency [14]
starvation       
Nitrogen Arabidopsis   trans-acting siRNA3 (TAS3) Nitrate transporter 2, NRT2.4 Maintains cellular N homeostasis by multiple [99]
starvation     SEC14p-like protein/Patellin-4 tasiRNAs targeting ARF2, 3, and 4  
     Regulatory component   
     of ABA receptor 3   
     PPC3   
Nitrogen Barley Liuzhutouzidamai lnc00090 and lnc000248 lnc00090 and lnc000248 target mimics for [97]
starvation      for hvu-miR399  
Boron Poncirus trifoliata XLOC_002224 Ciclev10008338m Targetting Ciclev10008338m gene [98]
deficiecy