gmo-free rnai: exogenous application of rna molecules in plants. · 4 40 rnai in plants 41. in...

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Short title: Exogenous application of RNAi 1

GMO-free RNAi: exogenous application of RNA molecules in 2

plants 3

Athanasios Dalakouras1,2,#

, Michael Wassenegger3, Elena Dadami

1, Ioannis 4

Ganopoulos2, Maria L. Pappas

4 and Kalliope Papadopoulou

1 5

6

1University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece 7

2Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, Thessaloniki, 8

Greece 9

3RLP AgroScience GmbH, AlPlanta Institute for Plant Research, Neustadt, Germany 10

4Democritus University of Thrace, Department of Agricultural Development, Orestiada, 11

Greece 12

# Corresponding author 13

14

Correspondence: 15

Athanasios Dalakouras ([email protected]) 16

University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece, 17

Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, Thessaloniki, 18

Greece 19

One-sentence summary: The latest advances in the field exogenous application of 20

RNA molecules in plants help to protect and modify them through RNA interference 21

(RNAi). 22

Author Contributions: All authors contributed to the writing of this article. 23

Plant Physiology Preview. Published on July 8, 2019, as DOI:10.1104/pp.19.00570

Copyright 2019 by the American Society of Plant Biologists

www.plantphysiol.orgon March 23, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

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Keywords: RNA interference, small RNAs, post-transcriptional gene silencing, RNA-24

directed DNA methylation, high-pressure spraying, trunk injection, petiole absorption. 25



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Summary 26

Since its discovery more than 20 years ago, RNA interference (RNAi) has been 27

extensively used in crop protection platforms. So far, RNAi approaches have been 28

conventionally based on the use of transgenic plants expressing double stranded RNAs 29

(dsRNAs) against selected targets. However, the use of transgenes and genetically 30

modified organisms (GMOs) has raised considerable scientific and public concerns. 31

Hence emerged the need for alternative approaches that avoid the use of transgenes and 32

resort instead to direct exogenous application of RNA molecules that have the potential 33

to trigger RNAi. Here, we highlight the most important advances in this field, 34

discussing the various methods of RNA delivery in plants against diverse targets, such 35

as plant genes, viruses, viroids, fungi, insects, mites, and nematodes. In addition, we 36

examine the possible shortcomings of these methods, underline the critical parameters 37

that have to be met for a desired outcome, and explore feasible possibilities to increase 38

their efficiency and applicability, even against bacterial pathogens. 39



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RNAi in plants 40

In plants, RNA interference (RNAi) is triggered by double stranded RNA (dsRNA) 41

having variable sources of origin, ranging from viral replication intermediates, 42

transcription of inverted repeats, stress-induced overlapping antisense transcripts and 43

RNA-DIRECTED RNA POLYMERASE (RDR) transcription of aberrant transcripts 44

(Hamilton and Baulcombe, 1999; Mette et al., 1999; Borsani et al., 2005; Luo and 45

Chen, 2007). Once present in the plant cell, dsRNAs are processed by DICER-LIKE 46

(DCL) endonucleases into 21-24-nt short interfering RNAs (siRNAs) (Figure 1) (Liu et 47

al., 2009). The model plant Arabidopsis (Arabidopsis thaliana) contains four DCL 48

paralogs. DCL2, DCL3 and DCL4 generate the 22-, 24- and 21-nt siRNAs, 49

respectively, whereas DCL1 recognizes genome-encoded imperfect hairpin RNAs 50

resulting in the biogenesis of 21/22-nt micro RNAs (miRNAs) (Bologna and Voinnet, 51

2014; Borges and Martienssen, 2015). Plant siRNAs and miRNAs, collectively termed 52

small RNAs (sRNAs) (Ruiz-Ferrer and Voinnet, 2009), exhibit 3' 2-nt overhangs and 53

become stabilized though 3’ end methylation by HUE ENHANCER1 (HEN1) (Yu et 54

al., 2005; Yang et al., 2006). After this modification, and depending on its 5´ terminal 55

nucleotide, one of the two sRNA strands will be loaded onto an ARGONAUTE (AGO) 56

protein (Kim, 2008). In general, 21-nt sRNAs with 5’-U are loaded on AGO1 and scan 57

the cytoplasm for complementary transcripts for cleavage and degradation in a process 58

termed post-transcriptional gene silencing (PTGS) (Hamilton and Baulcombe, 1999; Mi 59

et al., 2008) (Figure 1). Twenty-two-nt sRNAs are also loaded on AGO1 but seemingly 60

change AGO1 conformation and recruit RDR6 to the 3’ of the target, transcribing the 61

target transcript into dsRNA and thus generating additional (secondary) siRNAs in a 62

mechanism coined transitive silencing (Dalmay et al., 2000; Chen et al., 2010) (Figure 63



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1). Finally, 24-nt sRNAs with 5’-A are incorporated on AGO4, recognize cognate DNA 64

or its nascent transcript and recruit DNA methyltransferases to methylate the cytosine 65

residues of both DNA strands in a process termed RNA-directed DNA methylation 66

(RdDM) (Wassenegger et al., 1994; Chan et al., 2004) (Figure 1). Importantly, RNAi is 67

not cell-autonomous in plants. Thus, once generated in a single cell, siRNAs are able to 68

move through plasmodesmata to 10-15 neighbouring cells while RNA molecules of a 69

yet unknown nature move through the vasculature system to distant parts of the plant, a 70

phenomenon called systemic silencing (Voinnet and Baulcombe, 1997; Palauqui and 71

Vaucheret, 1998). 72

73

Genetically modified organism (GMO)-free RNAi in plants 74

In addition to mediating a broad range of developmental events, RNAi has great 75

potential against invading pests and pathogens (Eamens et al., 2008; Martinez de Alba 76

et al., 2013). So far, conventional RNAi applications have been largely based on the use 77

of recombinant viruses (virus-induced gene silencing, VIGS), Agrobacterium 78

tumefaciens-mediated transiently expressed transgenes and stably transformed 79

transgenic plants that enable the production of dsRNA molecules against selected 80

targets (host-induced gene silencing, HIGS) (Baulcombe, 2004; Baulcombe, 2015). In 81

2017, the transgenic maize (Zea mays) SmartStax Pro, engineered to expressed dsRNA 82

against corn rootworm (Diabrotica virgivera virgifera), was approved by the United 83

States Environmental Protection Agency, United States Food and Drug Administration 84

and United States Department of Agriculture (https://www.epa.gov/newsreleases/epa-85

registers-innovative-tool-control-corn-rootworm). However, in spite of their 86

demonstrated success, RNAi-based transgenic crops have not been commercialized as 87



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much as one might have expected. Transgenic plants and GMOs in general have met 88

such severe criticism that their chances for widespread approval are gloomy, at least. 89

According to some estimates, it costs approximately 140 million USD to bring a 90

transgenic crop to commercialization (Rosa et al., 2018), and even when that happens, 91

several anti-GMO responses follow. Taking these into consideration, and to tackle this 92

issue, new GMO-free RNAi approaches need to be developed that will enable the 93

activation of RNAi not through the use of recombinant viruses or transgenes but 94

through the direct exogenous delivery of RNA molecules (dsRNAs and/or sRNAs) in 95

plants. In this article, only GMO-free RNAi strategies involving exogenous application 96

of RNA molecules directly in plants will be discussed; transgene-based HIGS and VIGS 97

approaches have been extensively reviewed elsewhere and will not be discussed here 98

(Eamens et al., 2008; Prins et al., 2008; Nowara et al., 2010; Koch and Kogel, 2014; 99

Baulcombe, 2015; Zotti and Smagghe, 2015; Joga et al., 2016; Cai et al., 2018; Rosa et 100

al., 2018; Zotti et al., 2018; Qi et al., 2019). 101

102

Applying RNA molecules in plants to target endogenes and transgenes 103

The first report wherein exogenous RNA application into plants triggered RNAi of a 104

plant gene was described in a 2011 Monsanto patent; Nicotiana benthamiana plants pre-105

treated with Silwet L-77 surfactant and sprayed (2.5 bar) with in vitro transcribed 685 106

bp dsRNA and/or chemically synthesized 21-nt sRNAs targeting the endogenous 107

phytoene desaturase (PDS) mRNA displayed extensive PDS RNAi (Sammons et al., 108

2011). (Note that since chemically synthesized small RNA oligonucleotide duplexes are 109

not the biological outcome of DCL endonucleolytic processing and/or HEN1 110

methylation, they cannot be considered bona fide siRNAs, and thus will be collectively 111



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called hereafter as sRNAs). After this initial observation, several others followed using 112

diverse methods of RNA application, succinctly mentioned below in chronological 113

order. Hence, when Arabidopsis leaves were infiltrated with 21-nt sRNAs fused to a 114

positively charged carrier peptide that combined a copolymer of histidine and lysine, 115

(KH)9 (18 a.a.), RNAi of the yellow fluorescent protein (YFP) transgene and the 116

chalcone synthase (CHS) endogene was recorded (Numata et al., 2014). Subsequent 117

studies demonstrated that RNA molecules can be absorbed by the roots and display 118

biological activity throughout the plant. SHOOT MERISTEMLESS (STM) is a class I 119

knotted-like homeodomain protein expressed in the shoot apical meristem (SAM) and 120

required for SAM formation, while WEREWOLF (WER) is an R2R3-type MyB-related 121

transcription factor expressed in the root epidermal cells. When STM or WER dsRNA 122

conjugated to cationic fluorescent nanoparticle was applied to Arabidopsis seedling 123

roots for five consecutive days, expression of STM and WER was suppressed and 124

resulted in phenotypic defects (Jiang et al., 2014). Moreover, when dsRNA targeting 125

MOB1A and actin was applied to Arabidopsis and rice (Oryza sativa) roots, 126

respectively, RNAi of the corresponding genes took place and normal root growth was 127

perturbed (Li et al., 2015). These results suggest that irrigation-mediated RNA 128

application is a possibility that needs to be further elaborated. In a subsequent study, 129

instead of using in vitro transcribed dsRNA, crude extracts of Escherichia coli HT115 130

(DE3) (see below) expressing a 430 bp dsRNA targeting MYB1 were mechanically 131

inoculated into the Dendrobium hybrida (hybrid orchid) flower buds (Lau et al., 2015). 132

MYB1 is expressed throughout flower bud development and is involved in the 133

development of the conical cell shape of the epidermal cells of the flower labellum. 134

Scanning electron microscopy of the adaxial epidermal cells revealed that application of 135



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MYB1 dsRNA changed the phenotype of floral cells, an outcome of great interest for 136

floriculture biotechnology. 137

Plant cells contain a very tough cellulose-rich cell wall ranging from 0.1 to 138

several µm in thickness, which poses a physical barrier to biomolecule delivery. To 139

facilitate RNA delivery inside the plant cell, RNA molecules are usually conjugated to 140

carrier compounds, as mentioned above (Jiang et al., 2014; Numata et al., 2014). 141

Recently, DNA nanostructures, such as 3D tetrahedron, 1D hairpin tile and 1D 142

nanostring, were used to facilitate the delivery and biological action of 21-nt GFP 143

sRNAs in infiltrated N. benthamiana leaves (Zhang et al., 2019). Instead of remaining 144

in the mesophyllic apoplast, the nanostructure-conjugated sRNAs entered the symplast 145

and silenced GFP expression. Interestingly, sRNAs tethered to 3D nanostructures 146

exhibited both mRNA degradation and translational arrest of the GFP, whereas sRNAs 147

attached to 1D nanostructures led mainly to translational arrest, although the reasons 148

underlying this observation were not elucidated. It should be noted here that, although 149

carrier compounds greatly facilitate RNA delivery, they are also quite expensive and/or 150

difficult to synthesize. The use of carrier compounds seems to be dispensable when 151

plant cell walls are mechanically damaged. Indeed, RNAi of a GFP transgene was 152

efficiently initiated when 22-nt sRNAs or 720 bp dsRNAs (pure nucleic acids) were 153

applied by high-pressure spraying (8 bar) or brush-mediated application on the leaf 154

surface of N. benthamiana and Arabidopsis, respectively (Dalakouras et al., 2016; 155

Dubrovina et al., 2019). 156

157

Transitivity and systemic silencing. 158



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Although 21-nt sRNAs (miRNAs and siRNAs) mediate RNA cleavage in plants, 22-nt 159

sRNAs seemingly recruit RDR6 to the RNA target and are responsible for the 160

amplification, transitive and, likely, systemic spread of RNAi (Chen et al., 2010; 161

Cuperus et al., 2010; McHale et al., 2013). Yet, it had been also suggested that 162

recruitment of RDR6 to their target transcript is mediated not necessarily by 22-nt 163

sRNAs, but by any-sized sRNA that contains an asymmetric bulge in its duplex 164

structure (Manavella et al., 2012). To investigate how the sRNA size/structure affects 165

the onset of local, transitive and systemic RNAi in GFP-expressing N. benthamiana 166

(Nb-GFP) plants, we applied, by high pressure spraying, chemically synthesized 21-, 167

22- and 24-nt GFP sRNAs either as perfect duplexes or as siRNAs containing an 168

asymmetric bulge (Dalakouras et al., 2016). Ultraviolet light examination of sprayed 169

plants revealed that although all tested sRNAs triggered local RNAi to variable degrees, 170

only 22-nt sRNAs (either as perfect bulges or containing an asymmetric bulge) also 171

triggered systemic silencing (Figure 2, left panel). DCL2, responsible for the biogenesis 172

of 22-nt siRNAs, is required for transitivity (Mlotshwa et al., 2008; Parent et al., 2015). 173

Moreover, 22-nt miRNAs recruit RDR6 and trigger transitivity (Chen et al., 2010; 174

Cuperus et al., 2010; McHale et al., 2013). Thus, it is reasonable to assume that any 175

sRNA (siRNA or miRNA or chemically synthesized oligonucleotide) having a size of 176

22 nt can recruit RDR6 to its target and lead to the biogenesis of secondary siRNAs. 177

Upon transitivity, the siRNA population surpasses a certain threshold required for the 178

onset of systemic silencing (Kalantidis et al., 2006; Kalantidis et al., 2008). Thus, 179

transitivity is seemingly connected to generation of systemic silencing signals in the 180

source tissues. Yet, reception of systemic silencing in the sink tissues requires RDR6 181

processing of the target (Schwach et al., 2005). A growing body of recent evidence has 182



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suggested that in contrast to intron-containing genes, intronless genes are much more 183

susceptible to RDR6 processivity and thus transitivity and systemic silencing (Christie 184

and Carroll, 2011; Christie et al., 2011; Dadami et al., 2013; Dadami et al., 2014). 185

Taking these observations into consideration, the chances of systemic RNAi upon 186

exogenous RNA application may significantly increase when then the trigger is 22-nt 187

sRNA and the target gene is intronless (see Outstanding Questions Box). 188

189

Symplastic and apoplastic delivery of RNA 190

It needs to be noted here that depending on the method of RNA application, the 191

efficiency of RNAi fluctuates. When chemically synthesized 22-nt sRNAs were applied 192

in Nb-GFP upon high pressure spraying, they triggered local and systemic RNAi; yet, 193

when they were applied by petiole absorption, they failed to do so (Dalakouras et al., 194

2018). Confocal microscopy revealed that the petiole-absorbed sRNA was transported 195

through the xylem and was restricted to the apoplast (Figure 2, middle panel) 196

(Dalakouras et al., 2018). Similarly, a 499-nt GFP hairpin RNA (hpRNA) applied 197

through petiole absorption and/or trunk injection in grapevine (Vitis vinifera) and apple 198

(Malus domestica) trees was also confined to the xylem and apoplast, and no RNAi was 199

observed (Figure 2, middle and right panel). In summary, when the target of 200

exogenously applied RNA is an intracellular transcript (e.g. plant mRNA or viral/viroid 201

RNA), then the high pressure method ensures efficient RNA delivery into plant cells 202

leading to the onset of, at least, local RNAi. In contrast, RNA applied through petiole 203

absorption and trunk injection is retained in the xylem and apoplast and does not trigger 204

RNAi. However, this is not necessarily a drawback. When dsRNAs are applied to plants 205

with the aim of targeting some insects or fungi (see below), it may be of advantage to 206



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deliver non-processed (by plant DCLs) dsRNAs. Should the plant-applied dsRNAs 207

avoid plant DCL processing, they will be taken up intact by the insects or fungi and be 208

processed therein by the pathogen/pest DICER proteins; the resulting siRNAs will 209

conceivably exhibit greater biological activity against insect or fungal genes. To achieve 210

this, recent approaches rely on the expression of dsRNA transgenes in chloroplasts 211

(Bally et al., 2016; Bally et al., 2018). Chloroplasts lack DCLs and thus the chloroplast-212

expressed dsRNAs remain intact for pathogen/pest uptake. Our own observations 213

suggest that dsRNA application through petiole uptake and/or trunk injection could 214

serve as a GMO-alternative to such transplastomic plants since they both maintain 215

dsRNA intact. 216

217

The issue of epigenetic changes 218

So far, all reports on exogenous applications of dsRNAs in plants aimed to trigger 219

degradation of a given mRNA. However, once present in the plant cell, the applied 220

dsRNAs may be processed not only by DCL4/DCL2 into 21/22-nt siRNAs but also by 221

DCL3 into 24-nt siRNAs, given the DCL co-localization (Pontes et al., 2013; Pumplin 222

et al., 2016). Thus, besides mRNA degradation in the cytoplasm, the applied dsRNAs 223

may also trigger RdDM of the cognate coding region in the nucleus (Dubrovina et al., 224

2019; Dubrovina and Kiselev, 2019). Thus, dsRNA-treated plants considered on the 225

one hand GMO-free, could, on the other hand, be epigenetically modified. Moreover, 226

exogenous application of dsRNA targeting a promoter sequence may trigger not only 227

RdDM but also histone modifications that will eventually result in transcriptional gene 228

silencing (TGS) (Wassenegger, 2005). If RdDM takes place in the dsRNA-treated 229

plants, DOMAINS REARRANGED METHYLTRANSFERASE (DRM2) will mediate 230



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the de novo methylation of the cognate DNA sequence (promoter or coding region) at 231

any sequence context: CG, CHG and CHH (Pelissier et al., 1999; Cao and Jacobsen, 232

2002; Aufsatz et al., 2004). In the progeny of treated plants, CG and, to a lesser extent, 233

CHG methylation can be maintained by METHYLTRANSFERASE 1 (MET1) and 234

CHROMOMETHYLASE 3 (CMT3), respectively (Lindroth et al., 2001; Aufsatz et al., 235

2004). While CG/CHG methylation of a coding region does not seem to negatively 236

affect transcription in plants, CG/CHG methylation of promoter sequences reinforces 237

the heterochromatic state, and thus, TGS can be trans-generationally maintained (Wang 238

et al., 2015; Wakasa et al., 2018). Whether such scenario holds remains to be validated 239

(see Outstanding Questions Box). 240

241

Applying RNA molecules in plants against viruses 242

It has been suggested that RNAi in plants evolved as an antiviral defence mechanism. 243

Indeed, most plant viruses contain single stranded RNA genomes that replicate through 244

dsRNA intermediates. The dsRNA is processed into virus-derived siRNAs resulting in 245

degradation of any homologous RNA, including the single stranded virus RNA 246

genomes. To counter host’s defence, viruses encode RNA silencing suppressors (RSSs), 247

most of which sequester and/or inhibit the function of the siRNAs (Silhavy and 248

Burgyan, 2004; Szittya and Burgyan, 2013). However, the cellular pre-existence of 249

dsRNAs/siRNAs designed to target the virus already before it manages to replicate and 250

generate RSSs is a well-established antiviral crop protection strategy. The GMO 251

approach wherein transgenic plants express dsRNAs against viral proteins has been well 252

documented with very satisfactory results (Prins et al., 2008; Khalid et al., 2017; 253

Pooggin, 2017). Focusing here only on the non-transgenic approaches, Tenllado and 254



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co-workers were the first to demonstrate that exogenous application of dsRNA 255

molecules in plants renders them resistant to viral infections. When pepper mild mottle 256

virus (PMMoV), tobacco etch virus (TEV) and alfalfa mosaic virus (AMV) were 257

mechanically co-inoculated in N. benthamiana leaves with in vitro transcribed 997 bp, 258

1483 bp and 1124 bp dsRNAs targeting the PMMoV replicase, TEV helper component 259

and AMV RNA3, respectively, viral infections were attenuated (Tenllado and Diaz-260

Ruiz, 2001). The authors applied crude extract from E. coli HT115 (DE3) expressing 261

the corresponding dsRNA fragments by lysing cell pellets with a French press and 262

documented similar resistance phenotypes (Tenllado et al., 2003). Using bacterial 263

expression systems, dsRNA expression can easily be scaled-up and still remain cost-264

effective. With an average dsRNA yield of 4 μg per ml of bacterial culture, large 265

fermenters would most possibly meet the huge agricultural demands (Tenllado et al., 266

2004). Besides HT115 (DE3), alternative strains such as M-JM109lacY have been used 267

with equally satisfactory results. Mechanical inoculation of RNA extract from E. coli 268

M-JM109lacY expressing 480 bp dsRNA that target the tobacco mosaic virus (TMV) 269

coat protein (CP) and RNA extract from E. coli HT115 (DE3) expressing 480 bp 270

dsRNA targeting the TMV movement protein (MP) both resulted in viral resistance in 271

tobacco (Nicotiana tabacum) (Yin et al., 2009; Yin et al., 2010). Recently, an 272

alternative system for high quality long dsRNA production was developed, based on 273

Pseudomonas syringae harbouring components of the bacteriophage phi6, wherein 274

dsRNA generation is based not on DNA transcription but on RNA transcription by an 275

RNA-dependent RNA polymerase (RdRP) (Niehl et al., 2018). Compared to E. coli-276

expressed dsRNA, which may result in relatively low yields of fully duplexed dsRNA, 277

the P. syringae system seems advantageous since the RdRP of phage phi6 converts 278



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ssRNA templates into dsRNA with high processivity using a de novo, primer-279

independent initiation mechanism. 280

Using the aforementioned methods, viral resistance has been achieved in a 281

plethora of other cases as listed below: in maize, upon spraying of crude extract from E. 282

coli HT115 (DE3) expressing dsRNA targeting the sugarcane mosaic virus (SCMV) CP 283

(Gan et al., 2010); in papaya (Carica papaya), upon mechanical inoculation of crude 284

extract from E. coli M-JM109lacY expressing 279 bp dsRNA targeting the papaya 285

ringspot virus (PRSV) CP (Shen et al., 2014); in pea (Pisum sativum), upon biolistic 286

delivery of in vitro-transcribed 500 bp dsRNA targeting the pea seed-borne mosaic 287

virus (PSbMV) CP (Safarova et al., 2014); in orchid (Brassolaeliocattleya hybrida), 288

upon mechanical inoculation of crude extract from E. coli HT115 (DE3) expressing 289

dsRNA targeting the cymbidium mosaic virus (CymMV) CP (Lau et al., 2014); in 290

tobacco (N. tabacum), upon mechanical inoculation of in vitro transcribed 237 bp 291

dsRNA targeting the TMV p126 (Konakalla et al., 2016); in cucurbits, upon mechanical 292

inoculation of in vitro transcribed 588 bp dsRNA targeting the zucchini yellow mosaic 293

virus (ZYMV) helper component proteinase (HcPro) (Kaldis et al., 2018); and in N. 294

benthamiana, upon spraying of RNA extracts from P. syringae LM2691 expressing 295

dsRNAs targeting a 2611 bp region of TMV replicase and MP (Niehl et al., 2018). 296

A major issue concerning the aforementioned approaches is that dsRNA 297

application offers a short antiviral protection window (usually 5-10 days), since dsRNA 298

eventually is degraded. Thus, dsRNA would need to be supplied afresh in frequent 299

intervals for lifelong crop protection. To increase the dsRNA stability and thus prolong 300

antiviral protection, Mitter and co-workers bound dsRNA to layered double hydroxide 301

clay nanosheets having an average particle size of 80 to 300 nm (BioClay) (Mitter et al., 302



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2017). The dsRNA bound to BioClay was significantly protected from nucleases, while 303

the dsRNA/BioClay complex did not wash off, even after rigorous rinsing. On the leaf 304

surface, atmospheric CO2 and moisture resulted in a gradual breakdown of BioClay into 305

a biocompatible residue, releasing the dsRNA in the plant cell either by passive 306

diffusion or active transport. A 330 bp dsRNA targeting the CMV CP and bound to 307

BioClay could be detected even 30 days post application (dpa) and upon single 308

application in tobacco resulted in CMV protection for at least 20 days (Mitter et al., 309

2017). Similar results were recently obtained, when spraying of 461 bp dsRNA bound 310

to BioClay and targeting the bean common mosaic virus (BCMV) CP protected N. 311

benthamiana and cowpea (Vigna unguiculata) plants against BCMV infection (Worrall 312

et al., 2019). 313

314

Applying RNA molecules in plants against viroids 315

Viroids are infectious single stranded RNA pathogens that, unlike viruses, are non-316

encapsidated and non-coding but, similar to viruses, trigger the host RNAi mechanism 317

(Tabler and Tsagris, 2004; Tsagris et al., 2008; Flores et al., 2014; Flores et al., 2017). 318

Single-stranded circular RNA viroids exhibit significant intramolecular folding and 319

resemble dsRNA molecules and as such are processed by plant DCLs into siRNAs. 320

Initial reports suggested that viroids are resistant to siRNA-mediated degradation due to 321

their extensive secondary structure (Itaya et al., 2007). Yet, subsequent studies 322

demonstrated that transgenic plants expressing viroid dsRNAs were viroid-resistant 323

(Schwind et al., 2009). Hence, despite their secondary structure, and similar to viruses, 324

viroids can most likely be targeted for sRNA-mediated degradation (Dalakouras et al., 325

2015; Flores et al., 2017). Returning to the non-transgenic approaches, and to the best 326



16

of our knowledge, there is only one study where exogenous RNA was applied in plants 327

for anti-viroid resistance, wherein Carbonell and co-workers applied dsRNA in plants 328

against both nuclear-replicating Pospiviroidae and chloroplast-replicating 329

Avsunviroidae members. In tomato (Solanum lycopersicum), gynura (Gynura 330

aurantiaca) and chrysanthemum (Dendranthema grandiflora), mechanical inoculation 331

of in vitro transcribed 353 bp, 364 bp and 399 bp dsRNA targeting regions of Potato 332

spindle tuber viroid (PSTVd), Citrus exocortis viroid (CEVd) and Chrysanthemum 333

chlorotic mottle viroid (CChMVd), respectively, resulted in significant inhibition of 334

infection, at least for up to 30 days dpa (Carbonell et al., 2008). Interestingly, the effect 335

was temperature-dependent, reminiscent of previous reports on the temperature-336

dependency of the general RNAi mechanism in plants (Kalantidis et al., 2002; Szittya et 337

al., 2003). Taking these observations into consideration, exogenous application of RNA 338

in plants for any applications should be performed in a temperature regime of 20-30ο C, 339

since the efficiency of the RNAi machinery is compromised outside this temperature 340

window. 341

342

Applying RNAi molecules in plants against fungi 343

With the exception of Saccharomyces cerevisiae, all fungi, like the rest of eukaryotes, 344

contain several Dicer and Argonaute genes and thus display active RNAi mechanisms. 345

Transgenic plants expressing dsRNAs against fungal genes is a very promising 346

antifungal approach (Koch and Kogel, 2014; Baulcombe, 2015) but will not be 347

addressed here. Koch and co-workers demonstrated that spraying of barley (Hordeum 348

vulgare) with in vitro transcribed 791 bp dsRNA simultaneously targeting three 349

Fusarium graminearum ergosterol biosynthesis genes (CYP51A, CYP51B and 350



17

CYP51C) strongly inhibited fungal growth (Koch et al., 2016). Interestingly, the 351

sprayed dsRNA was poorly processed in barley into siRNAs, and the effect on fungal 352

growth was due to the uptaken dsRNA rather than the barley-produced siRNAs, since 353

upon dsRNA spraying no RNAi was observed in a dcl1 F. graminearum mutant. 354

Spraying of in vitro-produced siRNAs also inhibited fungal growth but to lesser extent 355

than dsRNA did. Surprisingly, dsRNA seemed to be more mobile throughout the barley 356

than the smaller siRNAs, but the reasons underlying this phenomenon are unclear. It is 357

also unclear how the dsRNA that first reached the apoplast was transported to the 358

symplast (Koch et al., 2016). In another study, foliar application in Brassica napus of in 359

vitro transcribed dsRNA targeting various fungal genes conferred plant protection 360

against Sclerotinia sclerotium and Botrytis cinerea (McLoughlin et al., 2018). More 361

recently, spraying of in vitro transcribed dsRNA targeting the myosine 5 of Fusarium 362

asiaticum in wounded wheat (Triticum aestivum)oleoptiles resulted in reduced fungal 363

virulence (Song et al., 2018). Yet, the RNAi effect lasted for only 9 hours, unless the 364

dsRNA was continuously supplied. Interestingly, despite the presence of RDR genes in 365

F. asiaticum, small RNA deep sequencing revealed that no secondary siRNAs were 366

generated, suggesting that fungal myosine 5 mRNA could not processed by RDR6. 367

Thus, in contrast to plants where RNAi is maintained through an RDR-mediated self-368

amplification loop, this is likely not happening in fungi. 369

Recent advances from the Hailing Jin laboratory have broadened our knowledge 370

of the mechanistic details of RNA transport phenomena between plants and fungi. 371

Hence, it was discovered that the aggressive fungal pathogen B. cinerea is able not only 372

to deliver siRNAs into host plant cells to suppress host immunity genes, but also uptake 373

exogenously applied dsRNAs and siRNAs that inhibit its growth, providing a typical 374



18

case of bi-directional trans-kingdom RNAi (Weiberg et al., 2013; Wang et al., 2016). 375

More specifically, when in vitro-transcribed dsRNA or siRNAs targeting the Bc-DCL1 376

and Bc-DCL2 genes were applied on the surface of fruits (tomato, S. lycopersicum 377

‘Roma’; strawberry, Fragaria × ananassa; and grape, V. labrusca ‘Concord’)), 378

vegetables (iceberg lettuce, Lactuca sativa; and onion, Allium cepa)and flowers (rose, 379

Rosa hybrida) they significantly inhibited grey mould disease (Wang et al., 2016). 380

These findings illustrated that exogenous RNA application can be used to control 381

diseases in post-harvest fruits and vegetables. Whereas the movement of siRNAs 382

through plasmodesmata to neighbouring cells and through the vasculature system to 383

distant parts of the plant is well established, it was unknown until recently how 384

siRNAs/dsRNAs travel across the boundaries between organisms of different 385

taxonomic kingdom, e.g. from plants to fungi and/or vice versa. To investigate how 386

RNA molecules move from plants into interacting fungal cells, Hailing Jin and co-387

workers demonstrated that Arabidopsis secretes exosome-like extracellular vesicles to 388

deliver RNA molecules into B. cinerea (Cai et al., 2018). It is reasonable to assume that 389

such observations reflect a more generalized mechanism of exosome involvement in 390

trans-kingdom RNA transport, and if so, exosomes are likely to be employed in the 391

future in the development of antifungal RNA delivery methods. 392

393

Applying RNAi molecules in plants against insects 394

Triggering RNAi in insects upon exogenous application of dsRNA in plants is a 395

challenging task. Subsequent to the uptake by chewing/sucking insects, the dsRNA 396

must survive the salivary nucleases in the midgut and/or haemolymph, which threaten to 397

quickly degrade it. Next, the dsRNA must be taken up from the epithelial cells through 398



19

either the endocytic pathway or the transmembrane Sid-1 channel protein-mediated 399

pathway and processed by Dicer-2 into siRNAs, which will be loaded onto Ago-2 and 400

trigger local RNAi. To be efficiently established throughout the insect, the RNAi 401

molecules (dsRNAs or siRNAs) need to systemically spread to neighbouring and to 402

distant cells. In plants and the nematode Caenorhabditis elegans, systemic spread of 403

RNAi is associated with RNAi amplification by RDRs, proteins that are not present in 404

insects. Yet, despite all these barriers, a proof-of-concept paper demonstrated that 405

western corn rootworm ingestion of vacuolar ATPase dsRNA through artificial diet or 406

upon feeding on dsRNA-expressing transgenic maize plants resulted in significant 407

larval mortality, suggesting that widespread RNAi in insects can be established. Indeed, 408

coleopterans seem to exhibit systemic RNAi spread, although the enzymes involved 409

have not been identified yet (Velez and Fishilevich, 2018). 410

Induction of RNAi in insects through the use of methods such as dsRNA 411

injection, dsRNA-expressing transgenic plants, dsRNA-containing artificial diet or 412

dsRNA-coating of leaf discs has been thoroughly reviewed elsewhere (Zotti and 413

Smagghe, 2015; Joga et al., 2016; San Miguel and Scott, 2016; Bally et al., 2018; Velez 414

and Fishilevich, 2018; Zotti et al., 2018). Exogenous application of dsRNA directly in 415

plants against insects was first demonstrated by Hunter and co-workers, who injected 416

the trunk and/or drenched the roots of citrus and grapevine trees with dsRNA targeting 417

the arginine kinase of two psyllids (Diaphorina citri and Bactericera cockerelli) and the 418

sharpshooter Homalodisca vitripennis. Interestingly, the introduced dsRNA was 419

detected in 2.5 m tall 6-year-old Mexican limes (Citrus aurantifolia) even after 7 weeks 420

post single application (2 g dsRNA diluted in 15 l of water). After this proof-of-concept 421

report, several others followed, exhibiting significant degrees of pest management upon 422



20

exogenous application of in vitro transcribed/synthesized RNAs in plants: in Brassica 423

oleracea, upon spraying of 5’-PEG 21-nt siRNAs targeting the diamondback moth 424

Plutella xylostella acetylcholine esterase genes AChE1 and AChE2; in tomato, upon 425

application of dsRNA targeting the Diabrotica virgifera vacuolar ATPase (Ivashuta et 426

al., 2015); in rice, upon root absorption of dsRNA targeting the brown planthopper 427

Nilaparyata lugens P450 (Li et al., 2015); in maize, upon root absorption of dsRNA 428

targeting the Ostrinia furnacalis KTI (Li et al., 2015); in potato (Solanum tuberosum), 429

upon spraying of dsRNA targeting the Colorado potato beetle Leptinosa decemlineata 430

actin; in tomato, upon petiole uptake of dsRNA targeting the tomato leafminer Tuta 431

absoluta vacuolar ATPase (Camargo et al., 2016) and upon root absorption of dsRNA 432

targeting Tuta absoluta ryanodine, acetylcholinesterase and nicotinic acetylcholine 433

alpha 6 (Majidiani et al., 2019). In general, the orders Coleoptera, Lepidoptera and 434

Hemiptera include key pests of crops. Coleopterans are the most susceptible to RNAi, 435

while lepidopterans and hemipterans seem recalcitrant to RNAi, most likely because 436

lepidopterans restrict the up-taken dsRNA to endocytic compartments, and hemipterans 437

inject nucleases into the plant tissue prior to feeding (Lomate and Bonning, 2016; 438

Shukla et al., 2016). Of note, and to improve dsRNA stability, uptake and overall RNAi 439

response, various insecticidal dsRNA formulations have been explored, such as 440

liposomes, chitosan nanoparticles, cationic core-shell nanoparticles and guanylated 441

polymers (Joga et al., 2016; Velez and Fishilevich, 2018). 442

443

Applying RNA molecules in plants against mites 444

Mites belong to the subphylum Chelicerata, a subgroup in the phylum Arthropoda to 445

which insects also belong. Mite genomes encode for most known RNAi enzymes, 446



21

including two DICERs, seven AGOs and, importantly, five RDRs (Grbic et al., 2011), 447

suggesting that amplification of RNAi and systemic RNAi spread in mites may occur. 448

Indeed, in the citrus red mite Panonychus citri, RNAi spread from the gut to more 449

distant tissues such as cuticle, hemolymph and prothoracic glands (Li et al., 2017). 450

Similar to insects, mites have been targeted for RNAi by various methods, such as 451

feeding on leaves floating on dsRNA solution, dsRNA-expressing transgenic plants and 452

dsRNA-containing artificial diet, as discussed elsewhere (Suzuki et al., 2017; Niu et al., 453

2018). To the best of our knowledge, the only study wherein mites took up dsRNA that 454

was exogenously applied in plants involved mechanical inoculation of tomato leaves 455

with in vitro transcribed dsRNA (targeting the otherwise irrelevant ZYMV HcPro) and 456

the concomitant detection by stem loop RT-PCR of the corresponding siRNAs in the 457

two-spotted spider mite Tetranychus urticae 3 and 10 dpa (Gogoi et al., 2017). 458

However, in that case it was not possible to determine whether the mite absorbed the 459

applied dsRNA or rather the plant-produced siRNAs. In addition, no conclusions could 460

be drawn concerning the RNAi action of the detected siRNAs, since the applied dsRNA 461

had no mite target. In another study where T. urticae was fed on Arabidopsis leaves 462

coated with in vitro transcribed dsRNA targeting the vacuolar ATPase, the mite 463

exhibited visible dark body phenotype but lethality was not observed (Suzuki et al., 464

2017). Interestingly, to identify the most suitable RNAi target genes for mite mortality, 465

two independent studies suggested that coatamer I (COPI) genes and genes involved in 466

the biosynthesis and action of juvenile hormone and action of ecdysteroids were the best 467

candidates (Kwon et al., 2016; Yoon et al., 2018) and should be thus taken into 468

consideration for future RNA applications. 469

470



22

Applying RNA molecules in plants against nematodes 471

RNAi was discovered in the model nematode Caenorhabditis elegans (Fire et al., 472

1998). In agriculture, root-knot nematodes cause significant crop losses in several plant 473

species worldwide. Transgenic Arabidopsis expressing 16D10 dsRNA against 474

Meloidogyne incognita, M. javanica, M. arenaria and M. hapla exhibited significant 475

reductions in the number of nematode eggs per gram of root (Huang et al., 2006). So 476

far, no reports on exogenous RNA application in plants against nematodes are available. 477

Arguably, the challenge here would be to deliver RNA molecules to the root tissues. 478

Trunk injection would deliver RNA mainly to the xylem (Dalakouras et al., 2018) and 479

thus only to the upper/aerial part of the plant. Alternatively, RNA molecules can be 480

directly absorbed by the roots (Jiang et al., 2014; Li et al., 2015). It is thus reasonable to 481

assume that RNA molecules conjugated to compounds that would protect them against 482

degradation in the aggressive soil environment could be delivered through irrigation as 483

a nematode protection strategy. 484

485

Perspectives for bacterial management 486

Plant pathogenic bacteria may cause devastating diseases and huge crop losses. 487

Although RNAi is absent in bacteria, similar RNA-based regulation mechanisms do 488

exist in which ~100-nt cis and trans antisense transcripts repress translation and lead to 489

transcript decay (Good and Stach, 2011). Typically, antisense RNAs (asRNAs) that are 490

cis-encoded display high degrees of complementarity with the target mRNA, whereas 491

asRNAs that are trans-encoded exhibit limited complementarity with the target mRNA 492

and require Hfq chaperones to facilitate binding to the target mRNA. So far, exogenous 493

application in plants of synthetic asRNAs designed to combat bacterial pathogens has 494



23

not been tested. In contrast to dsRNAs applied in RNAi approaches, asRNAs are single 495

stranded and thus more susceptible to plant nucleases. To tackle this problem, 496

exogenously applied asRNAs based on peptide nucleic acids (PNAs) and/or 497

phosphorothioate morpholino oligomers (PMOs) could be used (Good and Stach, 2011). 498

Yet, the biggest challenge upon exogenous application of synthetic asRNAs would be 499

the intracellular delivery across the stringent bacterial cell barriers, since nucleobase 500

oligomers are too large for uptake by simple diffusion. To this end, conjugating the 501

PNA or PMO oligomers to cell cationic entry peptides would greatly facilitate their 502

intracellular delivery (Mellbye et al., 2009). These being said, exogenously applied 503

antibacterial asRNAs could be used with considerable chances of success, particularly 504

in the case of xylem-restricted bacteria such as Xylella fastidiosa, Clavibacter xyli and 505

Pseudomonas syzygii, especially when taking into account that delivery of RNA with 506

robust methods, such as trunk injection or petiole absorption, restricts the presence of 507

the applied RNA to the xylem (Dalakouras et al., 2018) . Besides the aforementioned 508

direct management of bacterial pathogens through exogenous application of synthetic 509

asRNAs, indirect RNAi-based strategies could be applied. For example, although RNAi 510

cannot be used directly against X. fastidiosa, it can nevertheless be employed against its 511

xylem sap-feeding vectors, mainly sharpshooters and spittlebugs (Rosa et al., 2010; 512

Overall and Rebek, 2015). Trunk injected-dsRNAs designed to target essential insect 513

mRNAs will remain unprocessed in the xylem of the woody plant, and provided that 514

they are taken up by the xylem-feeding insect, they will be processed into siRNAs that 515

that will lead to RNAi-mediated insect lethality, ideally minimizing the spread of the 516

devastating pathogen (see Outstanding Questions Box). 517

518



24

Concluding Remarks 519

For field-scale management of pests and pathogens, metric ton levels of dsRNAs would 520

be required. A rough estimation suggests 10 g dsRNA per hectare, although this amount 521

may vary depending on the target sensitivity to RNAi and its capacity for systemic 522

RNAi (Zotti et al., 2018). Conceivably, such huge needs could not be merely met by in 523

vitro dsRNA transcription systems, which exhibit a minimum cost of 100 UDS per 1 g 524

of dsRNA. To this end, several industrial companies enable low-cost (almost 2 USD per 525

1 g of dsRNA), large-scale manufacturing of dsRNA (Zotti et al., 2018). According to 526

‘RNAagri’ proprietary technology (https://www.rnagri.com/), bacteria and yeast are 527

engineered to produce the desired dsRNA and a capsid protein which offers protection 528

against nucleases. As the bacteria multiply in the fermentators, the dsRNA:protein 529

complex is self-assembled and accumulates in huge quantities that can be isolated with 530

conventional low-cost methods. The final product is environmentally stable and ready-531

to-use. Field-scale trunk injection of such huge amounts of dsRNAs could be 532

performed by commercially available trunk drilling equipment as the one developed by 533

‘Arborjet’ (https://arborjet.com/arborjet-advantage/). Such advances have facilitated the 534

development of commercial products that are soon to emerge in the market, such as 535

‘BioDirect’, which is designed for insect, virus and weed control and which has already 536

passed the phase I or II of research and development process (Zotti et al., 2018). 537

In summary, exogenous application of RNA molecules with the potential to 538

trigger RNAi is a very powerful tool in modern crop protection and improvement 539

platforms, considering the political and public pressure for sustainable solutions to 540

current agricultural problems. Compared to conventional disease management 541

strategies, exogenous RNAi promises significantly lower off-target effects, since its 542


https://arborjet.com/arborjet-advantage/


25

activity can be narrowed down to a window of few nucleotide complementarity with its 543

target. With the rapidly accumulating sequence datasets, non-conserved regions can be 544

selected as targets to exclude as much as possible off-target effects. To the same end, 545

applying unique sRNAs, rather than long dsRNAs which are processed in a diverse 546

population of siRNAs, would also greatly decrease off-targets. Arguably, the lack of 547

genome data for any existing organisms near the site of exogenous RNA application 548

undermines the proper ecological risk of RNAi technology in the agroecosystem. 549

Nevertheless, the chance to silence non-intended targets is very low and far beyond any 550

other available crop protection strategy has yet to offer. It cannot be excluded that 551

certain pathogens may display gene mutations rendering them resistant to RNAi sprays. 552

In cases of monogenic resistance, alternating ~200 bp regions of the target sequence 553

could tackle this issue, while for polygenic resistance cases, using chimeric RNAs or a 554

mixture of different RNAs could offer a solution, underpinning the overall flexibility of 555

the RNA-based approaches. In the near future, it is reasonable to assume that 556

optimization of RNA production, delivery and stability methods may pave the way for 557

the exogenous application of diverse RNA molecules not necessarily triggering RNAi. 558

Indicatively, such molecules could include: capped and polyadenylated mRNAs when 559

accumulation of a protein is desired; miRNA decoys/sponges for sequestering of a 560

given miRNA and thus upregulating its endogenous target; and even clustered regularly 561

interspaced short palindromic repeats (CRISPR) components (Cas9 mRNA, sgRNAs) 562

for the induction of editing events in a GMO-free manner (see Outstanding Questions 563

Box). 564



26

565



27

FOOTNOTES 566

AD and KP acknowledge funding from the European Union’s Horizon 2020 research 567

and innovation programme under the Marie Skłodowska-Curie grant agreement N. 568

793186 (RNASTIP). 569

570



28

571



29

FIGURE LEGENDS 572

573

Figure 1. DCL processing of exogenously applied dsRNA in plants. DCL4 generates 574

21-nt siRNAs that are loaded onto AGO1 and target complementary transcripts for 575

cleavage. DCL2 generates 22-nt siRNAs that are also loaded onto AGO1 and recruit 576

RDR6 to the target transcripts’ 3’ ends for the generation of secondary siRNAs. Finally, 577

DCL3 generates 24-nt siRNAs that are loaded onto AGO4 and trigger de novo DNA 578

methylation by hybridizing with nascent Pol V or Pol II transcripts. Whether DCL1, 579

which is mainly involved in the miRNA pathway, also processes exogenously applied 580

dsRNA is not clear. 581

582

Figure 2. Methods for RNA delivery to plants. Left panel: High-pressure spraying of 583

chemically synthesized GFP sRNAs in GFP-expressing N. benthamiana allows the 584

delivery of sRNAs into the symplast and initiation of RNAi. Only the 22-nt GFP 585

siRNAs, with or without an asymmetric bulge, are able to trigger efficient local (2 dpa) 586

and systemic (20 dpa) RNAi (ultraviolet examination). Notably, targeting the bud 587

instead of the leaf results in more pronounced and widespread RNAi. Middle panel: 588

Petiole absorption of chemically synthesized sRNAs and in vitro transcribed GFP 589

hpRNAs results in the localization of applied RNAs in the apoplast and xylem (confocal 590

microscopy of CY3-labelled RNAs). Thus, the applied 22-nt GFP sRNAs fails to induce 591

RNAi in GFP-expressing N. benthamiana (ultraviolet examination) while the applied 592

GFP hpRNA is not processed by DCLs into GFP siRNAs (Northern blot analysis). 593

Right panel: Trunk injection of in vitro transcribed GFP hpRNA into apple and 594

grapevine results in its localization in the apoplast and xylem. Thus, similar to petiole 595



30

absorption, no DCL processing takes place (Northern blots). Image adapted from 596

Dalakouras et al., 2016; Dalakouras et al., 2018. 597

598

Figure 3. Exogenous application of RNA molecules into plants against various targets, 599

such as endogenous plant genes, viruses, insects and fungi. In the first two cases, RNAi 600

should take place inside the plant cell. Thus the most suitable application method is 601

high-pressure spraying, which allows symplastic RNA delivery. In contrast, in the cases 602

of insects and fungi, RNAi takes place inside the insect and fungal cells, which thus 603

need to uptake intact dsRNA (unprocessed by the plant DCLs) to achieve efficient 604

RNAi. Hence, in these cases, trunk injection, petiole absorption and/or low-pressure 605

spraying (wherein RNA stays on the leaf surface) are the most suitable methods, since 606

these methods do not result in symplastic RNA delivery. Importantly, while trunk 607

injection and/or petiole absorption is the ideal method for xylem-feeding and/or 608

chewing insects, the spraying method would be more suitable for phloem-feeding 609

insects (e.g. aphids). 610



31

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958



ADVANCES

• Exogenous application of RNA molecules (dsRNAs, siRNAs) in plants can trigger RNAi in a GMO-free manner.

• So far, exogenous application of RNA in plants has efficiently triggered RNAi of plant genes, viruses, viroids, fungi, insects and mites.

• Conjugating RNA molecules to nanoparticles and carrier peptides greatly enhances their resistance to nucleases and efficiency of delivery.

• Exogenously applied 22-nt siRNAs are the most potent inducers of local and systemic RNAi in plants.

• High pressure spraying allows the symplastic delivery of exogenous RNA whereas petiole absorption and/or trunk injection results in apoplastic delivery of the exogenous RNA.



OUTSTANDING QUESTIONS

• Besides RNA degradation, do exogenously applied RNA molecules also trigger epigenetic modifications in plants?

• In contrast to intron-containing genes, are intronless genes more susceptible to systemic RNAi upon exogenous application of RNAs in plants?

• Is the efficiency of RNAi inside insects and fungi higher when they take up dsRNAs that did not undergo processing by plant DCLs?

• Are bacteria susceptible to exogenously applied synthetic asRNAs?

• Besides dsRNAs and siRNAs, could other RNA molecules, such as mRNAs, miRNA sponges and CRISPR components, be efficiently applied in plants?



DCL4

AGO1 AGO4

DCL2 DCL3

AGO1

AGO1 RDR6

Pol V

CH3

CH3 CH3 CH3

21-nt 22-nt 24-nt Primary siRNAs

dsRNA

RNA RNA DNA

RNA degradation Transitivity DNA methylation

Secondary siRNAs

Figure 1

RDR6

AGO1

CH3 CH3



2 dpa 20 dpa 30 dpa

sRNA Local RNAi Systemic RNAi

21-nt + -

21-nt asym. + -

22-nt +++ +++

22-nt asym. +++ +++

24-nt - -

24-nt asym. + +

Leaf spraying Bud spraying

HIGH PRESSURE SPRAYING

Applied sRNAs in symplast local and systemic RNAi

PETIOLE ABSORPTION

1 dpa, leaf 1 dpa, petiole 30 dpa

hpRNA siRNAs U6

TRUNK INJECTION

1 3 10 dpa

1 3 10 dpa

hpRNA siRNAs U6

hpRNA siRNAs U6

1 3 10 dpa

Petiole absorption of CY3-labelled 22-nt GFP sRNAs from GFP-expressing N. benthamiana

GFP GFP GFP

GFP GFP GFP

CY3 CY3 GFP

CY3 CY3

Spraying of 22-nt GFP sRNAs in GFP-expressing N. benthamiana

Petiole absorption of CY3-labelled 499-nt GFP hpRNA from N. benthamiana and Northern blots in leaves

Trunk injection of 499-nt GFP hpRNA and Northern blots in leaves

V. vinifera

M. domestica

Applied sRNAs in apoplast/xylem no RNAi

Applied hpRNA in apoplast/xylem no DCL processing no RNAi

Applied hpRNA in apoplast/xylem no DCL processing no RNAi

1 dpa, petiole 1 dpa, stem



PLANT CELL

Healthy

Insect attack

Viral attack

Fungal attack

dsRNA against plant gene

dsRNA against virus

dsRNA against insect

dsRNA against fungus

INSECT CELL

AAA Plant mRNA

RNAi

PLANT CELL

AAA

RNAi

CAP

VPg Viral RNA

AAA

RNAi

CAP

CAP AAA

nucleus

nucleus

nucleus

nucleus

virus

FUNGAL CELL

Insect mRNA

dsRNA siRNAs

dsRNA siRNAs

dsRNA siRNAs

AAA Fungal mRNA

RNAi

CAP

dsRNA siRNAs

AAA CAP AAA VPg

AAA CAP



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https://www.ncbi.nlm.nih.gov/pubmed?term=Christie M%2C Carroll BJ %282011%29 SERRATE is required for intron suppression of RNA silencing in Arabidopsis%2E Plant Signal Behav&dopt=abstract

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https://scholar.google.com/scholar?as_q=SERRATE is required for intron suppression of RNA silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Christie&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Christie M%2C Croft LJ%2C Carroll BJ %282011%29 Intron splicing suppresses RNA silencing in Arabidopsis%2E Plant J&dopt=abstract

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https://scholar.google.com/scholar?as_q=Intron splicing suppresses RNA silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Christie&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Cuperus JT%2C Carbonell A%2C Fahlgren N%2C Garcia%2DRuiz H%2C Burke RT%2C Takeda A%2C Sullivan CM%2C Gilbert SD%2C Montgomery TA%2C Carrington JC %282010%29 Unique functionality of 22%2Dnt miRNAs in triggering RDR6%2Ddependent siRNA biogenesis from target transcripts in Arabidopsis%2E Nat Struct Mol Biol&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Dadami E%2C Moser M%2C Zwiebel M%2C Krczal G%2C Wassenegger M%2C Dalakouras A %282013%29 An endogene%2Dresembling transgene delays the onset of silencing and limits siRNA accumulation%2E FEBS Lett&dopt=abstract

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Huang G, Allen R, Davis EL, Baum TJ, Hussey RS (2006) Engineering broad root-knot resistance in transgenic plants by RNAi silencingof a conserved and essential root-knot nematode parasitism gene. Proc Natl Acad Sci U S A 103: 14302-14306


Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B (2007) A structured viroid RNA servesas a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J Virol 81: 2980-2994


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Jiang L, Ding L, He B, Shen J, Xu Z, Yin M, Zhang X (2014) Systemic gene silencing in plants triggered by fluorescent nanoparticle-delivered double-stranded RNA. Nanoscale 6: 9965-9969


Joga MR, Zotti MJ, Smagghe G, Christiaens O (2016) RNAi Efficiency, Systemic Properties, and Novel Delivery Methods for Pest InsectControl: What We Know So Far. Front Physiol 7: 553


Kalantidis K, Psaradakis S, Tabler M, Tsagris M (2002) The occurrence of CMV-specific short Rnas in transgenic tobacco expressingvirus-derived double-stranded RNA is indicative of resistance to the virus. Mol Plant Microbe Interact 15: 826-833


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Kalantidis K, Tsagris M, Tabler M (2006) Spontaneous short-range silencing of a GFP transgene in Nicotiana benthamiana is possiblymediated by small quantities of siRNA that do not trigger systemic silencing. Plant J 45: 1006-1016


Kaldis A, Berbati M, Melita O, Reppa C, Holeva M, Otten P, Voloudakis A (2018) Exogenously applied dsRNA molecules deriving fromthe Zucchini yellow mosaic virus (ZYMV) genome move systemically and protect cucurbits against ZYMV. Mol Plant Pathol 19: 883-895


Khalid A, Zhang Q, Yasir M, Li F (2017) Small RNA Based Genetic Engineering for Plant Viral Resistance: Application in CropProtection. Front Microbiol 8: 43



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https://scholar.google.com/scholar?as_q=Bacterially expressed dsRNA protects maize against SCMV infection&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Gan&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Gogoi A%2C Sarmah N%2C Kaldis A%2C Perdikis D%2C Voloudakis A %282017%29 Plant insects and mites uptake double%2Dstranded RNA upon its exogenous application on tomato leaves%2E Planta&dopt=abstract

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https://scholar.google.com/scholar?as_q=Plant insects and mites uptake double-stranded RNA upon its exogenous application on tomato leaves&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Plant insects and mites uptake double-stranded RNA upon its exogenous application on tomato leaves&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Gogoi&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Good L%2C Stach JE %282011%29 Synthetic RNA silencing in bacteria %2D antimicrobial discovery and resistance breaking%2E Front Microbiol&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Good&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Synthetic RNA silencing in bacteria - antimicrobial discovery and resistance breaking.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Synthetic RNA silencing in bacteria - antimicrobial discovery and resistance breaking.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Good&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Grbic M%2C Van Leeuwen T%2C Clark RM%2C Rombauts S%2C Rouze P%2C Grbic V%2C Osborne EJ%2C Dermauw W%2C Ngoc PC%2C Ortego F%2C Hernandez%2DCrespo P%2C Diaz I%2C Martinez M%2C Navajas M%2C Sucena E%2C Magalhaes S%2C Nagy L%2C Pace RM%2C Djuranovic S%2C Smagghe G%2C Iga M%2C Christiaens O%2C Veenstra JA%2C Ewer J%2C Villalobos RM%2C Hutter JL%2C Hudson SD%2C Velez M%2C Yi SV%2C Zeng J%2C Pires%2DdaSilva A%2C Roch F%2C Cazaux M%2C Navarro M%2C Zhurov V%2C Acevedo G%2C Bjelica A%2C Fawcett JA%2C Bonnet E%2C Martens C%2C Baele G%2C Wissler L%2C Sanchez%2DRodriguez A%2C Tirry L%2C Blais C%2C Demeestere K%2C Henz SR%2C Gregory TR%2C Mathieu J%2C Verdon L%2C Farinelli L%2C Schmutz J%2C Lindquist E%2C Feyereisen R%2C Van de Peer Y %282011%29 The genome of Tetranychus urticae reveals herbivorous pest adaptations%2E Nature&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Huang G%2C Allen R%2C Davis EL%2C Baum TJ%2C Hussey RS %282006%29 Engineering broad root%2Dknot resistance in transgenic plants by RNAi silencing of a conserved and essential root%2Dknot nematode parasitism gene%2E Proc Natl Acad Sci U S A&dopt=abstract

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https://www.ncbi.nlm.nih.gov/pubmed?term=Itaya A%2C Zhong X%2C Bundschuh R%2C Qi Y%2C Wang Y%2C Takeda R%2C Harris AR%2C Molina C%2C Nelson RS%2C Ding B %282007%29 A structured viroid RNA serves as a substrate for dicer%2Dlike cleavage to produce biologically active small RNAs but is resistant to RNA%2Dinduced silencing complex%2Dmediated degradation%2E J Virol&dopt=abstract

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https://scholar.google.com/scholar?as_q=Sorting out small RNAs&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Sorting out small RNAs&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kim&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Koch A%2C Biedenkopf D%2C Furch A%2C Weber L%2C Rossbach O%2C Abdellatef E%2C Linicus L%2C Johannsmeier J%2C Jelonek L%2C Goesmann A%2C Cardoza V%2C McMillan J%2C Mentzel T%2C Kogel KH %282016%29 An RNAi%2DBased Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery%2E PLoS Pathog 12%3A e&dopt=abstract

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https://scholar.google.com/scholar?as_q=An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Koch&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Koch A%2C Kogel KH %282014%29 New wind in the sails%3A improving the agronomic value of crop plants through RNAi%2Dmediated gene silencing%2E Plant Biotechnol J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Koch&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=New wind in the sails: improving the agronomic value of crop plants through RNAi-mediated gene silencing&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=New wind in the sails: improving the agronomic value of crop plants through RNAi-mediated gene silencing&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Koch&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Konakalla NC%2C Kaldis A%2C Berbati M%2C Masarapu H%2C Voloudakis AE %282016%29 Exogenous application of double%2Dstranded RNA molecules from TMV p126 and CP genes confers resistance against TMV in tobacco%2E Planta&dopt=abstract

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https://scholar.google.com/scholar?as_q=Screening of target genes for RNAi in Tetranychus urticae and RNAi toxicity enhancement by chimeric genes&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

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https://scholar.google.com/scholar?as_q=New insights into an RNAi approach for plant defence against piercing-sucking and stem-borer insect pests&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

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https://www.ncbi.nlm.nih.gov/pubmed?term=Martinez de Alba AE%2C Elvira%2DMatelot E%2C Vaucheret H %282013%29 Gene silencing in plants%3A A diversity of pathways%2E Biochim Biophys Acta&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Martinez&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Gene silencing in plants: A diversity of pathways&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Gene silencing in plants: A diversity of pathways&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Martinez&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=McHale M%2C Eamens AL%2C Finnegan EJ%2C Waterhouse PM %282013%29 A 22%2Dnt artificial microRNA mediates widespread RNA silencing in Arabidopsis%2E Plant J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=McHale&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=McHale&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=McLoughlin AG%2C Wytinck N%2C Walker PL%2C Girard IJ%2C Rashid KY%2C de Kievit T%2C Fernando WGD%2C Whyard S%2C Belmonte MF %282018%29 Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea%2E Sci Rep&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=McLoughlin&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=McLoughlin&as_ylo=2018&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mellbye BL%2C Puckett SE%2C Tilley LD%2C Iversen PL%2C Geller BL %282009%29 Variations in amino acid composition of antisense peptide%2Dphosphorodiamidate morpholino oligomer affect potency against Escherichia coli in vitro and in vivo%2E Antimicrob Agents Chemother&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mellbye&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Variations in amino acid composition of antisense peptide-phosphorodiamidate morpholino oligomer affect potency against Escherichia coli in vitro and in vivo&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Variations in amino acid composition of antisense peptide-phosphorodiamidate morpholino oligomer affect potency against Escherichia coli in vitro and in vivo&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mellbye&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mette MF%2C van der Winden J%2C Matzke MA%2C Matzke AJ %281999%29 Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans%2E EMBO J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mette&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mette&as_ylo=1999&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mi S%2C Cai T%2C Hu Y%2C Chen Y%2C Hodges E%2C Ni F%2C Wu L%2C Li S%2C Zhou H%2C Long C%2C Chen S%2C Hannon GJ%2C Qi Y %282008%29 Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5%27 terminal nucleotide%2E Cell&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mi&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mi&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mitter N%2C Worrall EA%2C Robinson KE%2C Li P%2C Jain RG%2C Taochy C%2C Fletcher SJ%2C Carroll BJ%2C Lu GQ%2C Xu ZP %282017%29 Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses%2E Nat Plants&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mitter&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mitter&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mlotshwa S%2C Pruss GJ%2C Peragine A%2C Endres MW%2C Li J%2C Chen X%2C Poethig RS%2C Bowman LH%2C Vance V %282008%29 DICER%2DLIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis%2E PLoS One 3%3A e&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mlotshwa&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mlotshwa&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Niehl A%2C Soininen M%2C Poranen MM%2C Heinlein M %282018%29 Synthetic biology approach for plant protection using dsRNA%2E Plant Biotechnol J&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Niehl&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Synthetic biology approach for plant protection using dsRNA.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Synthetic biology approach for plant protection using dsRNA.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Niehl&as_ylo=2018&as_allsubj=all&hl=en&c2coff=1

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gmo-free rnai: exogenous application of rna molecules in plants. · 4 40 rnai in plants 41. in...

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