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The coming of RNA-based pest controls

The coming of RNA-based pest controls



全 文 :植物保护学报 Journal of Plant Protectionꎬ 2015ꎬ 42(5): 673 - 690 DOI: 10􀆰 13802 / j. cnki. zwbhxb. 2015􀆰 05􀆰 001
Funding: National Institute of Food and Agricultureꎬ U. S. Department of Agricultureꎬ Biotechnology Risk Assessment Grant Program
Competitive Grant (No. 2011 ̄33522 ̄30749)
∗Authors for correspondenceꎬ E ̄mail: xuguozhou@ uky. eduꎬ yphuang@ sibs. ac. cn
Received date: 2015 - 09 - 24
The coming of RNA ̄based pest controls
Xu Linghua1   Zeng Baosheng2   Noland Jeffery E. 1   Huang Yongping2∗   Zhou Xuguo1∗
(1. Department of Entomologyꎬ University of Kentuckyꎬ Lexington 40546 ̄0091ꎬ Kentuckyꎬ USAꎻ
2. Shanghai Institute of Plant Physiology and Ecologyꎬ Chinese Academy of Sciencesꎬ Shanghai 200032ꎬ China)
Abstract: RNA interference (RNAi) is a gene silencing tool that targets messenger RNA (mRNA)
transcripts in a sequence specific manner and down regulates gene expression by interacting with small
interfering RNAs (siRNAs). mRNAs can be silenced either through endogenous degradation via nuclease
activity (e. g. ꎬ RNAi pathway)ꎬ or by inhibiting translation (e. g. ꎬ miRNA). Over the past decadeꎬ
RNAi has been used broadly in entomological research to decipher the gene functions in insects. With the
success of RNAi in functional genomics researchꎬ much attention has shifted to the potential applications
of RNAi in agricultureꎬ especially for the control of insect pests. In addition to RNAi ̄based gene
silencingꎬ genome editingꎬ an exciting new biotechnologyꎬ offers yet another option for pest controls. The
modification of plant genomes to knock ̄in genes that are heritable to increase the tolerance of plants to
insect infestationꎬ or knock ̄out genes in pest insects through genetically modified (GM) ̄insect releases
are on the forefront of the genetic ̄based pest managements. In this reviewꎬ we summarize the current
knowledge regarding RNAi ̄based gene silencing and CRISPR / Cas9 ̄based genome editing. Technical
challenges and regulatory concerns for this new wave of RNA ̄based pest controls are discussed in great
detail. We also share the perspective of modifying current environmental risk assessment frameworks to
better fit the RNA ̄based pest management strategies. Given the current discussions / attentions over the
safety of Genetically Modified Organisms (GMO)ꎬ weꎬ respectivelyꎬ compared pros and cons of RNAi ̄
based gene silencing and CRISPR / Gas9 ̄based genome editingꎬ and later we identified the regulatory
issues that should be addressed before these emerging biotechnologies can move from the bench top to the
table top.
Key words: RNAiꎻ genome editingꎻ CRISPR / Cas9ꎻ gene silencingꎻ pest controlꎻ technical challengesꎻ
regulatory hurdlesꎻ emerging biotechnologyꎻ ecological risk assessment
1 Introduction
1􀆰 1 RNAi ̄based gene silencing
The discovery of gene silencing dates back to
plant ̄virus interaction studies (Wingardꎬ1928). Win ̄
gard (1928) reported that the growth of new leaves in
numerous plants had become resistant to ring ̄spot virus
following inoculation of older leaves. This virus ̄in ̄
duced resistance to subsequent infection was later
shown to be associated with RNA silencing of viral
RNAsꎬ known as virus ̄induced gene silencing (VIGS)
(Waterhouse et al. ꎬ2001). Napoli et al. (1990) in ̄
troduced the chalcone synthase ( CHS) transgene in
petunia to express CHS to increase flavonoid biosynthe ̄
sis. Surprisinglyꎬ it down regulated the expression of
another gene responsible for anthocyanin production.
The phenomenonꎬ termed co ̄suppressionꎬ reduced the
expression of a homologous gene and the transgeneꎬ
which was determined to be post transcriptional gene
silencing (PTGS) (Napoli et al. ꎬ1990). With the pi ̄
oneering work of Andrew Fire and Craig Melloꎬ we now
have a much better understanding of RNA interference
(RNAi) at the mechanistic level as well as the major
machinery involved in the gene silencing process (Fire
et al. ꎬ1998ꎻDykxhoorn et al. ꎬ2003ꎻAgrawal et al. ꎬ
2003). RNAi is a highly conserved mechanism for
post ̄transcriptional regulation triggered by small inter ̄
fering RNAs ( siRNAs) and results in the knockdown
of genes at the mRNA level. As an evolutionarily con ̄
served mechanismꎬ gene silencing has been documen ̄
ted in plants ( PTGS)ꎬ fungi ( quelling)ꎬ metazoans
(RNAi) virus ̄induced gene silencing ( VIGS)ꎬ as
well as transcriptional gene silencing ( TGS )ꎬ and
plays important roles in several biological processesꎬ
such as defense against transposons and viruses (Catal ̄
anotto et al. ꎬ2002ꎻAgrawal et al. ꎬ2003ꎻReardon et
al. ꎬ2010).
These silencing mechanisms all share common
triggersꎬ non ̄coding RNAs and a sequence ̄specific
target. With these triggersꎬ the RNAi mechanism un ̄
dergoes two key steps to reduce gene expression in
cells. Degradation of dsRNAs by Dicer endonucleases
is the initial step that process longer dsRNA segments
into siRNAs ranging from 21 to 25 nucleotides (nt) in
length ( Hamilton & Baulcombeꎬ 1999ꎻ Li et al. ꎬ
2013). These processed siRNAs then serve as guides
for the RNA ̄induced silencing complex (RISC)ꎬ an
RNase complex that binds siRNAs and targets cognate
mRNAs to degrade mRNAꎬ or inhibit translation (Fig.
1).
Fig. 1 RNAi ̄based gene silencing
The schematic drawing depicts dsRNA ̄based RNAi: 1: Exogenous dsRNA is taken into the cell either through receptor mediated
endocytosis or SID ̄channel transfer across the membrane to the cytoplasm. Upon uptake into the cell: 2: the dsRNA is processed into
short 21 - 25 nt double ̄stranded fragments with 3′ ̄and 5′ ̄overhanges (siRNAs). The processed siRNAs: 3: are transferred either to
neighboring cells (systemic RNAi) or are bound in the cytoplasm by the RNA ̄induced silencing complex (RISC ̄argonuateꎬ a major
component in the RISC multiprotein complex)ꎻ 4: the RISC ̄bound siRNAs are then processed further leaving the anti ̄sense strand ex ̄
posedꎬ which is used to: 5: target homologous sequences on the mRNA targetꎻ 6: targeted mRNA sequences are degraded and the tar ̄
get gene is silenced.
 
    RNAi ̄based gene silencing has been documented
in eight insect ordersꎬ including Diptera ( Galiana ̄
Arnoux et al. ꎬ2006ꎻWang et al. ꎬ2006ꎻCoy et al. ꎬ
2012)ꎬ Coleoptera ( Baum et al. ꎬ2007)ꎬ Hemiptera
(Zha et al. ꎬ2011ꎻBansal & Michelꎬ2013ꎻXue et al. ꎬ
2015)ꎬ Hymenoptera ( Yoshiyama et al. ꎬ 2013 )ꎬ
Isoptera (Zhou et al. ꎬ2006ꎻ2008)ꎬ Lepidoptera (Cao
et al. ꎬ2012ꎻShi et al. ꎬ2012ꎻKotwica ̄Rolinska et al. ꎬ
2013)ꎬ Orthoptera (Miyawaki et al. ꎬ2004ꎻSmagghe
& Sweversꎬ 2014 )ꎬ and Blattodea ( Martín et al. ꎬ
2006). The efficacy of RNAiꎬ howeverꎬ varies sub ̄
stantially among different insect orders. Typicallyꎬ
RNAi is highly effective in dipterans and coleopteransꎬ
but works rather poorly in the lepidopterans (Toprak et
476 植  物  保  护  学  报 42 卷
al. ꎬ2013). Howeverꎬ we do have successful RNAi at ̄
tempts in few lepidopterans. To elucidate the function
of a clock gene period (per) in the African cotton leaf ̄
wormꎬ Spodoptera littoralisꎬ Kotwica ̄Rolinska et al.
(2013) treated the upper vas deferens (UVD) com ̄
plex of the testes with per dsRNAꎬ and demonstrated
that the UVD oscillator involving per gene is a critical
master regulator modulating V ̄ATPase expression and
pH dynamics in lumen. Efficient knockdown was also
demonstrated in the cotton bollwormꎬ Helicoverpa ar ̄
migeraꎬ through RNAi transgenic cottons constitutively
expressing a P450 monooxygenase (CYP6AE14) dsR ̄
NA. Suppression of this critical detoxification enzyme
restored the larval susceptibility to gossypolꎬ a plant
secondary metabolite (Mao et al. ꎬ2007). Toprak et
al. (2013) was able to silence the peritrophic mem ̄
brane proteins (insect intestinal mucin 1ꎬ insect intes ̄
tinal mucin 4ꎬ and PM protein 1) in the bertha army ̄
wormꎬ Mamestra configurata larvae. Other insect or ̄
ders and the hexapod outgroupsꎬ which are recalcitrant
to dsRNA ̄based RNAiꎬ include dragonflies and dam ̄
selflies (Odonata)ꎬ mayflies (Ephemeroptera)ꎬ jump ̄
ing bristletails (Archaeognatha)ꎬ silverfish (Zygento ̄
ma) Dipluraꎬ springtails ( Collembola) and Protura
(Cullenꎬ2012).
1􀆰 2 RNA ̄guided genome editing
The recent explosion of RNA ̄guided genome edi ̄
ting technology benefits from the development of artifi ̄
cially engineered nucleases. The discovery of zinc fin ̄
ger nucleases (ZFNs) in 1990s opened a new area of
genome engineeringꎬ which is based on the introduc ̄
tion of a double strand break (DSB) at specific regions
of a chromosome. The construction of zinc finger array
with FokIꎬ a bacterial (Flavobacterium okeanokoites)
type IIS restriction endonuclease consisting of an N ̄ter ̄
minal DNA ̄binding domain and a C ̄terminal non ̄spe ̄
cific DNA cleavage domain (Wah et al. ꎬ1997ꎻDurai
et al. ꎬ2005)ꎬ is time consuming and labor intensiveꎬ
limiting the system to be broadly applied. The other
type of nucleases called transcription activator ̄like ef ̄
fector nucleases ( TALENs )ꎬ modified from phyto ̄
pathogenic bacteriaꎬ was gradually replaced the ZFNs
with higher efficiency. Transcription activator ̄like ef ̄
fectors (TALEs) are programmable DNA binding pro ̄
teinsꎬ which can be used to facilitate accurate genome
editing and control transcription of endogenous genes.
Moscou & Bogdanove (2009 ) revealed the code of
DNA recognition by TALEs and found four optimal
TALE monomers targeting all four nucleotidesꎬ ade ̄
nineꎬ thymineꎬ guanine and cytosine. The specificity
of TALEs depends on several 34 amino acid repeats.
The amino acid positions 12 and 13 are called repeat ̄
variable di ̄residues (RVD)ꎬ corresponding to the rec ̄
ognition of target sites. Each TALE monomer targets
one nucleotide and has no significant interference when
random combinations of multiple TALE monomers oc ̄
cur ( Boch et al. ꎬ 2009 ). TALEN substantially im ̄
prove the construction of gene drive system and has
since been applied to many model organisms. Where ̄
asꎬ TALE arrays need to be customized when targeting
new DNA sequencesꎬ which areꎬ againꎬ time consu ̄
ming and labor intensive.
Ishino et al. (1987) found an unusual structure
in the 3′ ̄UTR of iap geneꎬ which is responsible for al ̄
kaline phosphatase isozyme conversion in E. coli. Lat ̄
erꎬ similar sequences were identified in many other
prokaryotic genomes and were defined as the clustered
regularly interspaced short palindromic repeats
(CRISPR). A total of 45 CRISPR ̄associated (Cas)
proteins were identified and systematically analyzed
and the critical role of CRISPR / Cas in the immune
system of bacteria and archaea was elucidated (Haft et
al. ꎬ 2005ꎻ Horvath & Barrangouꎬ 2010 ). CRISPR /
Cas9 can cleave DNA and limits the spread of antibiot ̄
ic resistance ( Marraffini & Sontheimerꎬ 2008 ). By
2013ꎬ researchers suggested the possibility of using the
CRISPR / Cas9 system in modifying human genome
(Cong et al. ꎬ2013ꎻMali et al. ꎬ2013). Since thenꎬ
the CRISPR / Cas9 system has been applied to many
model organismsꎬ such as D. melanogasterꎬ Danio re ̄
rioꎬ and Arabidopsis thaliana (Feng et al. ꎬ2013ꎻGratz
et al. ꎬ2013ꎻHwang et al. ꎬ2013) and non ̄model or ̄
ganismsꎬ including Bombyx moriꎬ and Oryza sativa
(Wang et al. ꎬ2013ꎻXie & Yangꎬ2013). The newly
engineered CRISPR / Cas9 system was derived from nat ̄
ural bacteria immune systems. It fuses the original
CRISPR RNA ( crRNA) and trans ̄activating crRNA
(tracrRNA) into a single guide RNA (sgRNA)ꎬ then
5765 期 Xu Linghuaꎬ et al. : The coming of RNA ̄based pest controls
combines with the Cas9 protein to target specific ge ̄
nomic regions (Sander & Joungꎬ2014). Recognition of
certain targets with a 20 bp sgRNA is based on the
Watson ̄Crick base ̄pairing. The Cas9 protein from
bacteriaꎬ Streptococcus pyogenesꎬ contains two impor ̄
tant cleavage domainsꎬ RuvC and HNH. Mutation of
these two domains causes a loss of the DNA cleavage
capability (Ran et al. ꎬ2013). CRISPR / Cas9 system
has gradually replaced ZFNs and TALENs and devel ̄
oped into a powerful genome editing tool (Hsu et al. ꎬ
2014).
2 Application Potentials
2􀆰 1 RNAi ̄based gene silencing technology
The last decade has seen a drastic increase in
RNAiꎬ both in functional genomics and translational
research in medical and agricultural sciences. RNAi
has revolutionized the field of functional genomicsꎬ and
has been an indispensable component of the genomics
tool box to decode the functions of genes. On the other
handꎬ enormous efforts and resources have been inves ̄
ted into diagnosticsꎬ therapeutics and agriculture. Re ̄
sults from the clinical trials showed that siRNAs targe ̄
ting vascular endothelial growth factor (VEGF) was an
effective cure for the ocular disease (Fattal & Bochotꎬ
2006ꎻGuzman ̄Aranguez et al. ꎬ2013). Alongside its
potential in developing a new class of pharmaceutical
drugs to silence genes associated with human diseaseꎬ
RNAi has also shown great promise in agriculture to
improve desired traits of cropsꎬ boost resistance to vari ̄
ous environmental and biological stressesꎬ and develop
RNA ̄based pest control strategies ( Whyard et al. ꎬ
2009ꎻZhuꎬ2013ꎻZotti & Smaggheꎬ2015).
Currentlyꎬ there are three potential applications of
RNAi ̄based gene silencing technology in pest manage ̄
mentsꎬ i) transgenic plants expressing insect active
genesꎬ i. e. ꎬ in planta RNAi (Mao et al. ꎬ2007ꎻWh ̄
yardꎬ2015ꎻZhang et al. ꎬ2015)ꎬ ii) baiting control
(Zhou et al. ꎬ2006ꎻ2008)ꎬ and iii) formulation (Zhu
et al. ꎬ 2010ꎻ Miguel & Scottꎬ 2015 ). Baum et al.
(2007) developed a high ̄throughput dietary RNAi sys ̄
tem in D. virgifera to screen for target genes to develop
transgenic RNAi maize. A total of 14 genes from an in ̄
itial gene pool of 290 exhibited larval control potential.
The most effective active ingredientꎬ a dsRNA targeted
at a gene encoding V ̄type ATPase subunit ̄Aꎬ resulted
in a rapid suppression of corresponding endogenous
mRNA within 24 ̄h of ingestion and triggered a specific
RNAi response with low concentrations of dsRNA. In
additionꎬ dsRNAs directed against two other house ̄
keeping genes including β ̄tubulin and V ̄ATPase sub ̄
unit ̄E showed an effective RNAi response that resulted
in high larval mortality. Mao et al. (2007) strategized
that potential of transgenic RNAi crops for pest control
could be achieved by compromising the target pest’s a ̄
bility to tolerate exposure to a host plant’ s defensive
allelochemicals. Mao and colleagues demonstrated that
suppression of CYP6AE14ꎬ a cytochrome P450 gene
which is presumably involved in the detoxification of
gossypolꎬ a defensive allelochemical in cottonꎬ signifi ̄
cantly increased the sensitivity of the cotton bollwormꎬ
H. armigera (Hübner)ꎬ larvae to gossypol. Zhou et
al. (2008) silenced the expression of two vital termite
genes using a similar dietary RNAi approach. These
two genes targeted an endogenous digestive cellulase
enzyme and a caste ̄regulatory hexamerin storage pro ̄
teinꎬ respectively. Knocking out either of these genes
reduced colony fitness and caused significant mortality.
The delivery mechanism of the dietary RNAi approach
fits well with the existing baiting strategies against
structural and urban pestsꎬ and represents a truly u ̄
nique opportunity to integrate RNAi into pest control
practices. Zhu et al. (2010) demonstrated that bacte ̄
ria expressed dsRNAs can induce gene silencing in
Colorado potato beetles ( CPB). In additionꎬ RNAi
has been integrated into the sterile male release pro ̄
grams and has shown great success in a model systemꎬ
D. melanogaster (Lin & Wangꎬ2015).
Insect pests cost agricultural industry billions of
dollars in crop losses and pest management expendi ̄
tures. This cost is directly proportional to the develop ̄
ment of resistance to current pest control practicesꎬ in ̄
cluding synthetic insecticides and Bacillus thuringiensis
(Bt) toxins (Huvenne & Smaggheꎬ2010). The ulti ̄
mate goal in pest management is to find an environmen ̄
tally sustainableꎬ efficient and target specific approach
to manage pest populations under the economical
threshold. One of the reasons to choose RNAi ̄base
676 植  物  保  护  学  报 42 卷
pest control is the target specificity. Bachman et al.
(2013) examined the activity spectrum of DvSnf7 dsR ̄
NA by exposing surrogate species to lethal and sub ̄le ̄
thal doses. These representative insect species were se ̄
lected from four orders and ten families based on their
phylogenetic relatedness to the target insect pestꎬ D.
virgifera virgifera. DvSnf7 is a housekeeping gene de ̄
rived from D. virgifera virgiferaꎬ and it encodes a key
ESCRT (endosomal sorting complex required for trans ̄
port) ̄Ⅲ protein required for unconventional secretions
(e. g. ꎬ endocytic trafficking) in eukaryotes (Weiss et
al. ꎬ2009). Given the narrow range of activity as de ̄
termined by the sequence ̄specific manner of the en ̄
dogenous RNAi pathwayꎬ a shared sequence length
of ≥21 nt was required for efficacy against WCR.
2􀆰 2 CRISPR/ Gas 9 ̄based genome editing technology
Fig. 2 CRISPR / Cas9 ̄based genome editing
This representation of CRISPR / Cas9 genome editing depicts: 1: the incorporation of genomic DNA (gDNA) into the Cas9 pro ̄
tein. 2: the two functional domainsꎬ RuvC and HNHꎬ are responsible for inducing a double ̄stranded break (DSB) in the target se ̄
quence that allows for 3: the incorporation of a donor DNA sequence in this example of homologous recombination of the nicked gD ̄
NA target.
 
Genome editing technologyꎬ i. e. ꎬ RNA ̄guided
gene drive systemꎬ has revolutionized reverse genetic
research. Similar to RNAi ̄based gene silencing toolsꎬ
genome editing techniques initially flourished in func ̄
tional genomic research though single or multi ̄gene
knock out and gene specific disruption. Currentlyꎬ
CRISPR / Cas9 is the most widely used genome editing
tool and showed enormous potential in gene therapy.
Mice with mutations in the Crygc gene or dystrophin
gene (Dmd) that causes cataracts or Duchenne muscu ̄
lar dystrophy ( Bulfield et al. ꎬ 1984ꎻ Zhao et al. ꎬ
2010) were corrected by CRISPR / Cas9 ̄based genome
editingꎬ suggesting the potential application of this
gene ̄drive system in combating genetic diseases caused
by the mutations (Wu et al. ꎬ2013ꎻLong et al. ꎬ2014ꎻ
Wu et al. ꎬ2015). Alsoꎬ a defect associated with cyst ̄
ic fibrosis was repaired by CRISPR / Cas9 in adult hu ̄
man stem cells (Schwank et al. ꎬ2013). In addition to
gene therapyꎬ genome editing technology can also be
used to treat virusesꎬ including the Human immunode ̄
ficiency virus (HIV)ꎬ Hepatitis B virus (HBV)ꎬ and
Epstein ̄Barr virus (EBV) (Seeger & Sohnꎬ2014ꎻLiao
et al. ꎬ2015ꎻYuen et al. ꎬ2015) and other infectious
diseasesꎬ such as malaria and dengue (Ghorbal et al. ꎬ
2014).
Structural analyses suggest that RuvC and HNH
domains in the Cas9 protein are essential for the cleav ̄
age of dsRNAs to create a double ̄stranded break
(DSB) in the target sequence (Nishimasu et al. ꎬ2014ꎻ
Jiang & Doudnaꎬ2015) (Fig. 2). Mutation at these do ̄
7765 期 Xu Linghuaꎬ et al. : The coming of RNA ̄based pest controls
mains makes Cas9 “non ̄functional”ꎬ i. e. ꎬ catalytically
inactive or dead (dCas9). The dCas9 can ligate with
certain effectors for CRISPR interference or activationꎬ
which makes it similar to RNAi (Qi et al. ꎬ2013). For
exampleꎬ the Krüppel associated box (KRAB) domain
and the VP64 transcriptional activation domain can be
fused to dCas9 to repress or activate transcription of the
target gene in eukaryotesꎬ making the CRISPR / Gas9
system a modular and flexible DNA ̄targeting system
(Gilbert et al. ꎬ2013). CRISPR / Gas9 system was used
in dynamic imaging of genomic loci in living human
cells by an enhanced green fluorescent protein (EGFP) ̄
tagged dCas9 and structurally optimized sgRNA (Chen
et al. ꎬ2013). Shalem et al. (2014) and Wang et al.
(2014a) described a pooledꎬ loss of function type of
high ̄through put screening to identify genes involved in
resistance to the nucleotide analog 6 ̄thioguanine and
vemurafenibꎬ suggesting the great potential of using ge ̄
nome ̄scale CRISPR / Cas9 knockout screening in drug
discovery process.
Although much of the initial research efforts have
been invested in therapeuticsꎬ the exploration of these
genome editing tools in agricultural applications has
picked up the pace in recent years. Gene functions
from model plantsꎬ such as A. thaliana and O. sativaꎬ
have been elucidated using the CRISPR / Gas9 system
(Xie & Yangꎬ2013). To combat a destructive fungal
pathogenꎬ powdery mildewꎬ researchers created a re ̄
sistant wheat strain by knocking out genes encoding
mildew ̄resistance locus (MLO) proteins that repress
defenses against the mildew (Wang et al. ꎬ2014b).
Advanced genome editing toolsꎬ including both TALEN
and CRISPR / Cas9ꎬ allow researchers to produce herit ̄
able traits and generate stable transgenic plantsꎬ which
can not only resist environmental stressꎬ including in ̄
sects and diseasesꎬ but can also function as a factory to
produce specific / desirable metabolites and / or proteins
(Xiong et al. ꎬ2015). The advent and recent develop ̄
ment of CRISPR / Cas9 system allows RNA ̄guided gene
drives to edit nearly any gene in sexually reproducing
populations (Esvelt et al. ꎬ2014). By engineering the
genomes of target organismsꎬ this revolutionary ap ̄
proach gives us a toolset to manipulate the entire popu ̄
lation of wild organisms to address some outstanding
ecologicalꎬ environmentalꎬ and health ̄related prob ̄
lemsꎬ such as the control of malaria and other insect ̄
borne diseases (Oye et al. ꎬ2014).
3 Technical Challenges
3􀆰 1 RNAi ̄based gene silencing
3􀆰 1􀆰 1 Design of dsRNA
Several factors can affect the efficacy of RNAi
within an insectꎬ such as target gene selectionꎬ con ̄
structionꎬ concentrationꎬ persistence of dsRNAsꎬ and
life stage of the target organism. Detection methodology
and the above mentioned factors can together explain
the variable results of RNAi in insects. Howeverꎬ com ̄
parisons based on existing data are difficult because of
varying susceptibilities of different targets to RNAi in
model species ( Kennedy et al. ꎬ2004ꎻPrice & Gate ̄
houseꎬ2008).
The first step in developing an RNAi ̄based pesti ̄
cide is the design of dsRNAꎬ which includes target
gene selectionꎬ dsRNA region selection and dsRNA
length. Improvements in target gene selection depend
upon the availability of insect genomes and bioinformat ̄
ics supports. Housekeeping genesꎬ such as Vacuolar
ATPase and Snif7ꎬ are essential for maintaining the
fundamental metabolism of living organisms and silen ̄
cing of these genes will impair biological functions of
critical metabolic processes and may lead to eventual
death (Baum et al. ꎬ2007). A key mechanism to de ̄
velop insecticide resistance is through up ̄regulation of
the innate metabolic resistance / detoxification system in
insectsꎬ thus down ̄regulation of key components within
the detoxification cascadeꎬ such as cytochrome P450sꎬ
can reduce the metabolic rates of synthetic insecticides
and / or plant secondary metabolites. Mao et al.
(2007) silenced a cytochrome P450 monooxygenaseꎬ
CYP6AE14ꎬ in the cotton bollwormꎬ H. armigeraꎬ lar ̄
vae by in planta RNAi. As a resultꎬ the resistance to
gossypolꎬ a major anti ̄herbivory alleochemical in cot ̄
tonꎬ was significantly reduced. Although targeting at
housekeeping genes can archive the satisfactory control
under the high dose strategy (Bolognesi et al. ꎬ2012)ꎬ
the highly conserved nature of their sequences across
different taxonomic groups leads us to search for other
molecular targets. The development of stable transgenic
876 植  物  保  护  学  报 42 卷
crops usually targets at virus ̄derived suppressor pro ̄
teins (Rameshꎬ2013). Neuron related genesꎬ which
are crucial in regulating insect behaviorꎬ are targeted
to manipulate the insect mating behaviorꎬ and host
finding behavior. In C. elegansꎬ howeverꎬ most of the
neuronal expressed genes have been shown to be com ̄
pletely refractory to suppression ( Kennedy et al. ꎬ
2004ꎻ Price & Gatehouseꎬ 2008 ). Within the target
genesꎬ the region and length of dsRNA sequences
should be meticulously designed to specifically target at
the target pest speciesꎬ since non ̄target and off ̄target
effects may arise due to the sequence homology of dsR ̄
NAs to an unintended gene sequence. Although syn ̄
thetic siRNAs had been demonstrated to produce simi ̄
lar effects as long dsRNAs in C. elegans and D. mela ̄
nogaster (Yang et al. ꎬ2000ꎻElbashir et al. ꎬ2001)ꎬ
Bolognesi et al. (2012) suggested that a minimal of 60
bp in length are required for dsRNAs to be biologically
active against target insects.
3􀆰 1􀆰 2 dsRNA uptake
Two separateꎬ but interdependent processes of
dsRNA uptake are characterized in insects from the
study of C. elegans (Fire et al. ꎬ1998)ꎬ i. e. ꎬ cell au ̄
tonomous RNAi and non ̄cell autonomous RNAi (Fire
et al. ꎬ1998ꎻCalixto et al. ꎬ2010ꎻZhuang & Hunterꎬ
2012). Cell autonomous RNAi includes all the RNAi
activities within a single cell. Non ̄cell autonomous
RNAi includes environmental RNAi and systemic
RNAi. RNAi strategies have enormous potential for the
use in controlling insect pestsꎬ and for this purposeꎬ
the insect should be autonomously receptive to dsRNA
(Huvenne & Smaggheꎬ 2010 ) and induce a robust
RNAi effect (a systemic long ̄lasting RNAi response)ꎻ
both are requirements to have effective protection
(Price & Gatehouseꎬ2008). Systemic RNAi has been
studied in nematodesꎬ C. elegans ( Hinas et al. ꎬ
2012)ꎬ as well as in insects including flour beetle Tri ̄
bolium castaneum ( Tomoyasu et al. ꎬ2008)ꎬ soybean
aphid Aphis glycines ( Bansal & Michelꎬ2013)ꎬ fruit
flies Drosophila spp. (Karlikow et al. ꎬ2014)ꎬ termite
Reticulitermes flavipes (Zhou et al. ꎬ2006ꎻ2008)ꎬhon ̄
eybee Apis mellifera (Jarosch & Moritzꎬ2011) and Af ̄
rican sweet potato weevil Cylas puncticollis (Prentice et
al. ꎬ2015). The translocation of RNAi silencing signa ̄
ling from the insect gut to other tissues has been dem ̄
onstrated by Zhou et al. (2006ꎻ2008) who observed
the suppressed gene expression in salivary gland
(Cell ̄1) and in fat body ( Hex ̄2 )ꎬ respectivelyꎬ
through dietary RNAi.
3􀆰 1􀆰 3 dsRNA stability and delivery
dsRNAs can be produced in vitro using commer ̄
cial kitsꎬ in vivo through bacterial expression systemsꎬ
or in planta by transgenic plants. A major technical
challenge is the lack of an RNAi amplification mecha ̄
nism in insects. A polymerase called RNA ̄dependent
RNA polymerase (RdRp)ꎬ which is used to amplify
insect ̄active siRNAsꎬ has yet been found in the se ̄
quenced insect genomes ( Gordon & Waterhouseꎬ
2007ꎻPrice & Gatehouseꎬ2008). As a resultꎬ it is
challenging to deliver sufficient and continuous dsR ̄
NAs to achieve significant suppression in the target in ̄
sects. The efficacy of RNAi also depends on the stabil ̄
ity of dsRNAs in multiple organisms within a trophic
cascadeꎬ including the producer ̄plants and the primary
consumers ̄insect herbivores. Hunter et al. ( 2012 )
showed that dsRNAs can be still effective 57 days post
treatmentꎬ demonstrating the persistence of dsRNA in
plants. The combined results from dsRNA stability as ̄
say and dietary RNAi bioassay showed that Cell ̄1 dsR ̄
NAsꎬ an endogenous termite cellulaseꎬ was active a
24 ̄day assay periodꎬ suggesting the potential of incor ̄
porating dsRNAs into a termite baiting station (Zhou et
al. ꎬ2008).
Mode of delivery also determines the success of
RNAi efficiency in insects. Some insects respond well
to both ingestion and injection of dsRNAsꎬ howeverꎬ
other insect taxaꎬ like orthopteransꎬ are more receptive
to RNAi when dsRNA was injected into the hemoceol
(Smagghe & Sweversꎬ2014). How we deliver RNAiꎬ
a long dsRNAꎬ or processed formsꎬ siRNAs or miRNAs
(microRNA)ꎬ to the target organism is the other major
technical challenge (Zotti & Smaggheꎬ2015). Current
delivery methods include reagent ̄mediated transfection
or electroporationꎬ soaking / drenching through the cuti ̄
cleꎬ transgenic plantsꎬ injectionꎬ and feedingꎬ either
with “naked” dsRNAs or dsRNAs produced by bacteri ̄
a ( Agrawal et al. ꎬ2003ꎻZhu et al. ꎬ2010ꎻPitino et
al. ꎬ2011). In C. elegansꎬ RNAi can be achieved by
9765 期 Xu Linghuaꎬ et al. : The coming of RNA ̄based pest controls
injection of dsRNA solution into worms ( Fire et al. ꎬ
1998 )ꎬ by soaking nematodes in dsRNA solution
(Tabara et al. ꎬ 1998ꎻ Joseph et al. ꎬ 2012 ) and by
feeding nematodes with bacteria expressing dsRNA
( Timmons & Fireꎬ 1998 ). The preferred delivery
methodology used in insect functional genomics studies
is through injection / microinjection ( Price & Gate ̄
houseꎬ2008)ꎬ which is direct and quantifiable way to
apply RNAi under laboratory conditionsꎬ but injection
is not practical for the field level control of insect
pests.
In field applicationsꎬ dsRNAs should be taken up
autonomously by the pestsꎬ e. g. through feeding and
digestion (Huvenne & Smaggheꎬ2010)ꎬ as oral deliv ̄
ery and transition through the midgut seems to be most
feasible approach (Zha et al. ꎬ2011). Insect cuticles
have a chitin ̄containing exoskeletonꎬ which protect the
insects from direct exposure to the environment factorsꎬ
thus limiting their contacts with externally applied dsR ̄
NAs. Internallyꎬ some insects can readily degrade
dsRNAs before they reach the target genes. The pea a ̄
phidꎬ Acyrthosiphon pisumꎬ was not responsive to dsR ̄
NAs by feeding or injections. The ingested dsRNAs
were degraded when they passed through saliva and he ̄
molymph ( Christiaenset al. ꎬ 2014 ). Alternativelyꎬ
transgenic plants constitutively express dsRNAs targe ̄
ting insect pests is a promising delivering approach
(Baum et al. ꎬ2007ꎻ Price & Gatehouseꎬ2008ꎻLi et
al. ꎬ2015).
3􀆰 1􀆰 4 in planta RNAi
To produce insect ̄resistant plantsꎬ a dsRNA se ̄
quence is inserted into a recombinant plant virus vec ̄
torꎬ the Tobacco mosaic virus ( TMV)ꎬ which infects
the plantꎬ induces a systemic RNAi response and leads
to the production of dsRNAs / siRNAs. dsRNA targeting
insect genes can be expressed continuously and consti ̄
tutively in planta. When chewing and / or phloem ̄feed ̄
ing insects attack the plantꎬ dsRNAs will be ingested
and induce the RNAi pathway in insects. The in planta
expression technique has been reported previously to
protect the crops against plant parasitic nematodes and
to fend off phytopathogensꎬ such as virusesꎬ bacteria
and fungiꎬ as well as invertebrate pests (Mao et al. ꎬ
2007ꎻPrice & Gatehouseꎬ2008ꎻKurth et al. ꎬ2012).
Transgenic plants expressing dsRNAs targeting insects
have been reported for lepidopteran ( Baum et al. ꎬ
2007)ꎬ coleopteran (Baum et al. ꎬ2007ꎻ Mao et al. ꎬ
2007) and hemipteran insects ( Zha et al. ꎬ2011 ).
Baum et al. (2007) demonstrated that the transgenic
maize expressing western corn rootworm V ̄ATPase dsR ̄
NA can cause nearly 100% larvae mortality and signifi ̄
cantly reduced the root damage.
Kurth et al. (2012) introduced desired traits into
several grapevine varieties by regulating the expression
of endogenous genes via virus ̄induced gene ̄silencing.
Unlike the transgene ̄triggered RNAi via Agrobacterium
tumefaciensꎬ integration of exogenous genes into the
plant genomeꎬ the RNA virus expressing target gene
were self ̄replicated within the plant tissues without in ̄
tegration into the plant genome (Mansoor et al. ꎬ2006ꎻ
Kurth et al. ꎬ2012). Similar to vaccination against hu ̄
man diseasesꎬ modified plant RNA viruses can be used
to protect the host plants against a wide range of phyto ̄
pathogens and insect pests by delivering a single or
multigene cassette to the host plant by the viral vector
(Kurth et al. ꎬ2012).
Another alternative method to induce transient
RNAi is to spray siRNAs produced by bacteria. For ex ̄
ampleꎬ resistance to plant RNA viruses has been a ̄
chieved by spraying bacterially expressedꎬ virus ̄specif ̄
ic siRNA on plants five days before challenge with the
viruses ( Mansoor et al. ꎬ 2006 ). Tenllado et al.
(2003) had demonstrated that crude extracts of bacte ̄
rially expressed dsRNAs were sufficient to effectively
protect plants against virus infections. Bacterial expres ̄
sion system can produce large amount of dsRNAs in a
simple and cost effective mannerꎬ and this approach
provides an alternative to in planta RNAi.
in planta RNAi has shown great potential for in ̄
sect pest controlꎬ especially for pest species without ef ̄
fective control measurementsꎬ such as phloem ̄sucking
hemipteransꎬ including planthoppersꎬ aphids and
whiteflies. Zha et al. (2011) first reported the poten ̄
tial of dsRNA ̄mediated RNAi for field level control of
a brown planthopperꎬ Nilaparvata lugens ( Stål)ꎬ as
three midgut genes were successfully silenced. Hunter
et al. (2012) have demonstrated RNAi effects on two
psyllid species through root drenching and vascular up ̄
086 植  物  保  护  学  报 42 卷
take of exogenous dsRNAs that were capable of knoc ̄
king down gene expression in the glassy ̄winged sharp ̄
shooterꎬ Homalodisca vitripennisꎬ a major pest of gra ̄
pevine and citrus.
Overallꎬ proper dsRNA designꎬ continuously pro ̄
duction of dsRNA in a constitutive mannerꎬ and deter ̄
mining an efficient delivery system are three critical
technical challenges that need to be resolved for appli ̄
cation of RNAi in agriculture. Pest control managers
should take these three factors into account and be a ̄
ware of the developmental stagesꎬ particularly younger
stagesꎬ are more sensitive to RNAi treatments com ̄
pared to adult stages (Araujo et al. ꎬ2006).
3􀆰 2 CRISPR / Gas 9 ̄based genome editing
3􀆰 2􀆰 1 CRISPR / Cas9 system
The type ̄Ⅱ prokaryotic CRISPR / Cas9 technology
was derived from the bacterial immune system that in ̄
hibits exogenous viral invasion ( Jinek et al. ꎬ2012).
The most commonly used CRISPR / Cas9 system origi ̄
nated from Streptococcus pyogenes with a proto ̄spacer
motif sequence (PAM sequence) that consists of three
nucleotidesꎬ NGGꎬ at the 3′ ̄end of the CRISPR sites.
The recognition of targeting sites in the genome is a ̄
chieved by sgRNAꎬ which ligates the Cas9 protein as a
reactionary complex to induce DSBs ( Mali et al. ꎬ
2013). When DSB is occursꎬ the internal DNA repair
cascade will begin with two different mechanismsꎬ non ̄
homologous end joining (NHEJ) and homologous re ̄
combination (HR) to fix the nicked DNAꎬ which may
result in a small deletion or insertion. It has been re ̄
ported that silencing genes in the NHEJ pathwayꎬ such
as ku70ꎬ will increase the ratio of HR repair that can
knock ̄in specific exogenous sequencesꎬ which could
replace transposon based random genomic insertion
(Ma et al. ꎬ2014).
3􀆰 2􀆰 2 Delivery methods
Genome editing with the CRISPR / Cas9 system in
various species can carried out with several delivery
methods. Most of the CRISPR / Cas9 studies in cells
were facilitated by transfection of Cas9 and sgRNA ex ̄
pression vectors (Cong et al. ꎬ2013). For in vivo mu ̄
tationꎬ there are many ways to deliver the functional u ̄
nitsꎬ such as direct injection of synthesized Cas9 mR ̄
NA and sgRNAꎬ plasmids expressing these RNAs and
a cross of two established transgenic cell lines ( one
line for ubiquitous or specific Cas9 expression and the
other line for sgRNA production with Pol Ⅲ promot ̄
ers) (Kondo & Uedaꎬ2013ꎻWang et al. ꎬ2013). In ̄
terestinglyꎬ sgRNA obtained by feeding in Cas9 ex ̄
pressed transgenic C. elegans showed efficient gene
disruption ( Liu et al. ꎬ2014). In plantsꎬ both Cas9
and sgRNA expression cassettes in a single vector were
integrated into the genome and were capable of promo ̄
ting specific genomic mutation ( Feng et al. ꎬ2013).
Currentlyꎬ several online programs or downloadable
software are readily available to design sgRNAs that ac ̄
count for the PAM sequenceꎬ lengthꎬ GC contentꎬ po ̄
tential nicking efficiency and low off ̄target ratioꎬ etc.
(Naito et al. ꎬ2015). The goal of coding genesꎬ non ̄
coding genes and even groups of gene knock ̄outs have
already become accessible in vitro and / or in vivo with
the help of CRISPR / Cas9 system (Hsu et al. ꎬ2014).
4 Regulatory Hurdles
4􀆰 1 Regulatory concerns for RNAi ̄based geneti ̄
cally modified crops
As debates ensue over the safety of transgenic
crops by the general public and the scientific communi ̄
tyꎬ one should take regulatory concerns into considera ̄
tion when performing genetically modified (GM) relat ̄
ed work and research. Before the commercial release of
RNAi engineered cropsꎬ biosafety issues should be an ̄
alyzed and a series of risk assessment studies should be
performed. The media and the anti ̄GMO community e ̄
rupted when Losey et al. (1999) published a study
that showed the susceptibility of monarch butterfly lar ̄
vae to Bt ̄toxins expressed in pollen of transgenic corn.
By pointing out several flaws of the research to prevent
the misuse by anti ̄GMO groups misrepresenting the re ̄
searchꎬ research community criticized the work pub ̄
lished by Rosi ̄Marshall et al. (2007)ꎬ in which she
stated that “widespread planting of Bt crops has unex ̄
pected ecosystem ̄scale consequences” (Waltzꎬ2009).
Assessing risks for the GM crops and products as ̄
sociated with RNAi is currently at an early stage and
debates are ongoing concerning the necessary improve ̄
ments of the risk assessment framework. Current eco ̄
logical risk assessment (ERA) guidelines are designed
1865 期 Xu Linghuaꎬ et al. : The coming of RNA ̄based pest controls
for the first generation GM crops ( e. g. ꎬ Bt crops).
Howeverꎬ the predictive properties of ERA for RNAi ̄
mediated crops and the unique nature of non ̄coding
RNA (ncRNA) based genetically modified plants re ̄
quire special considerations ( Auer and Frederickꎬ
2009ꎻLundgren & Duanꎬ2013ꎻRameshꎬ2013). RNAi
modifications involve essentially reprogramming the way
plants express their genesꎬ an uncharted territory as far
as their consequences to the environment. Auer &
Frederick (2009 ) discussed the predictive ERA for
RNAi ̄based crops using a transgenic crop expressing
Bt endotoxin and a host ̄delivered ( HD) ̄RNAi crop
producing a small RNA with toxicity to insect pests as
inferences.
Several potential risks of RNAi transgenic crops
should be considered due to the unique nature of
ncRNA ̄mediated gene manipulationꎬ in addition to
prevalent risks associated with the first generation Bt
GM crops. These risks include increased invasivenessꎬ
intra ̄ and inter ̄specific hybridization resulting in gene
transferꎬ and potential adverse effect on human health
and other non ̄target organisms ( Heinemann et al. ꎬ
2013ꎻ Lundgren & Duanꎬ 2013ꎻ Casacuberta et al. ꎬ
2015). As RNAi effect depends on the sequence iden ̄
tityꎬ bioinformatics analysis is crucial for predicting the
potential effects associated with the RNAi ̄generated
GM crops (Rameshꎬ2013).
In summaryꎬ RNAi ̄based gene silencing technolo ̄
gies have shown enormous potential for insect pest con ̄
trols. When employing RNAi ̄based technology for the
development of the next generation of transgenic cropsꎬ
not only technical challenges need to be addressedꎬ but
more consideration and attention should be given to the
biosafety concernsꎬ specificallyꎬ how do weꎬ as a sci ̄
entific communityꎬ assess the potential risks involved
with these new GM plants and how are we to reassure
the general public that these transgenic plants are safe
for consumption. Tailoring an environmental risk as ̄
sessment framework specifically designed for the emer ̄
ging RNAi ̄mediated pesticides is essential.
4􀆰 2 Regulatory concerns for RNA guide genome
editing technologies
Over three generations of genome editing technolo ̄
giesꎬ costꎬ timeꎬ and labor limit further development of
ZFNs and TALENs. ZFNs are the earliest genome edi ̄
ting platform to be commercializedꎬ but were quickly
replaced by TALENs. Laterꎬ with the discovery and
understanding of the CRISPR / Cas9 systemꎬ genome
editing became a rapid platform for many non ̄model
organisms. As target recognition for current genome
technologies are based on the matching of protein ̄DNA
or DNA ̄RNAꎬ the first consideration will be the off ̄
target effect. Compared with ZFNs and TALENsꎬ
CRISPR / Cas9 shows the most off ̄target effect because
of the short 20 bp match and its tolerance of mismat ̄
ches. Ran et al. (2013) reported that inducing double
nicks using a pair of sgRNAs and Cas9 D10A nickase
(Cas9n) can enhance the genome editing specificity.
Guilinger et al. (2014) and Tsai et al. (2014) sug ̄
gested that fusion of dCas9 and FokIꎬ combined with
two sgRNAsꎬ improves specificity and decreases the
off ̄target ratio.
Another important issue should be considered is
the target limitation of CRISPR / Cas9 system. The
PAM sequence is the basis of CRISPR recognitionꎬ
which makes less available targets in some genes with
shorter sequences or small RNAs. In addition to the
conventional NGG sequenceꎬ Hou et al. (2013) iden ̄
tified that a Cas9 protein from Neisseria meningitides
required the other type of PAM sequenceꎬ GATT. Be ̄
sides finding more PAM sequencesꎬ another way to ex ̄
pand the CRISPR sites is by alternative promoters. For
exampleꎬ the common U6 promoter needs a guanine to
initiate transcriptionꎬ which in turn limits target mis ̄
matches. Ranganathan et al. (2014) reported that the
mammal H1 promoter drove the expression of sgRNAs
with a G7AN19NGG sequence.
As genome editing technologies become broadly
applied in agricultureꎬ the potentially unwanted / unex ̄
pected ecological effects need to be assessed for each
application. Not only are the concerns associated with
these gene ̄drives in the fieldꎬ possibly leading to the
mutant populationsꎬ but also changes in how these ex ̄
periments are regulated warrant further investigation.
More strict confinement strategies are needed at the
molecular level (separate units of gene drivers on dif ̄
ferent loci)ꎬ through ecological and reproductive sce ̄
nariosꎬ while implementing various barriers to prevent
286 植  物  保  护  学  报 42 卷
unintentional releases into the wild ( Akbari et al. ꎬ
2015). Regulatory concernsꎬ especially with emerging
biotechnologiesꎬ need to be assessed prior to their ap ̄
plication in the field. These impediments along with
continuousꎬ long ̄term testing to ensure drive ̄functions
are confinedꎬ the altered organisms do not invade and
occupy new nichesꎬ and ensure the gene ̄drives are as ̄
sessed in a case ̄by ̄case basis are vital in assessing risk
of this technology in both transgenic crops and GM ̄in ̄
sects (Esvelt et al. ꎬ2014ꎻOye et al. ꎬ2014ꎻAkbari et
al. ꎬ2015).
5 Summary and Perspectives
5􀆰 1 RNAi ̄based genetic manipulations
As the global populations grows exponentiallyꎬ es ̄
pecially in developing countries with the greatest popu ̄
lation and malnutrition problemsꎬ the need for GM
crops is urgent for several reasonsꎬ includingꎬ but not
limited to: i) increase agriculture productivityꎻ ii) im ̄
prove the nutritional value of cropsꎻ iii) provide more
benefits to famersꎻ iv) save and limit the use of availa ̄
ble arable land. The ultimate goal for agricultural prac ̄
tices is to achieve high crop yieldsꎬ limit the use of re ̄
sources while reducing possible adverse effects on the
environment. RNAi technology could serve as an alter ̄
native solution to tackle many agricultural problems.
RNAi has been shown to be a conserved mechanism
that can be used to control pest insects with a high de ̄
gree of specificity. One of the advantages of RNAi over
other genetic technologies is that the suppressed pheno ̄
type produced by RNAi transgenes can be stably inher ̄
ited as far as the 5th generation (Singh et al. ꎬ2011).
In additionꎬ manipulating the degree of target gene
suppression by tittering the level of dsRNA expression
can be controlled by tissue ̄specific promoters to con ̄
fine RNAi in highly specific regions of the plants
(Singh et al. ꎬ2011).
Excessive exposure to pesticides increases the
likelihood that pests rapidly develop resistanceꎬ allo ̄
wing for resistant insects to reproduce and leading to
decreased product efficiency and sustainability (Chris ̄
tou et al. ꎬ2006). Since the first commercial release of
Bt cropsꎬ some insect pests have evolved resistance a ̄
gainst an array of Bt Cry ̄proteins ( Bates et al. ꎬ
2005). The success of dietary and in planta RNAi
have led to the speculation that crop protection by engi ̄
neering plants to express dsRNAs that targeting insect
genes are highly efficient ( Gordon & Waterhouseꎬ
2007). One would expect that the efficiency of RNAi
GM crops should obtain similar or better results than Bt
cropsꎬ but there is always a possibility for the develop ̄
ment of insect resistance to RNAi. Even though Bach ̄
man et al. (2013) demonstrated that insect resistance
to DvSnf7 is highly unlikely because even with the
presence of more than three 21 nt matchesꎬ the or ̄
tholog dsRNA would be active and theoretically could
have as many as 221 potential 21 nt matches. Single
nucleotide polymorphisms ( SNPs) in the target se ̄
quence of 240 nt would not likely change the biological
impacts of dsRNA on the target ( Bachman et al. ꎬ
2013).
To develop plant resistance to plant diseases
caused by virusesꎬ pathogen ̄derived resistance (PDR)
was achieved by transforming plants with gene se ̄
quences from the pathogen and was determined to be
mediated by PTGS of RNAs (Mansoor et al. ꎬ2006).
Intriguinglyꎬ once triggeredꎬ the gene silencing elici ̄
tors can spread throughout the plantꎬ providing system ̄
ic resistance to pathogens (Mansoor et al. ꎬ2006). For
the purpose of insect pest controlꎬ the systemic spread
of gene silencing within the plant can be achieved theo ̄
retically. Howeverꎬ plant viruses have evolved counter ̄
silencing strategies by producing so ̄called “ suppres ̄
sors” of gene silencing ( Mansoor et al. ꎬ 2006ꎻ
Rameshꎬ2013). Suppressor proteins are found in plant
viruses allowing the virus to circumvent plant anti ̄viral
defense mechanisms. Hereꎬ VIGS can disrupt RNAi
silencing process at various stages (Rameshꎬ2013).
As siRNA ̄mediated gene silencing is an ancient and
conserved defense mechanismꎬ a similar and even more
complex situation exists between plant ̄insect interac ̄
tions. As these RNAi based pest controls are being
generatedꎬ management of RNAi resistance should be
employed to ensure the long ̄term sustainability of
RNAi GM crops.
5􀆰 2 Future directions for genome editing
With more than two decades of rapid develop ̄
mentsꎬ genome editing technologies present powerful
3865 期 Xu Linghuaꎬ et al. : The coming of RNA ̄based pest controls
applications that can be used in various species ranging
from bacteria to mammals. Particularlyꎬ the readily ac ̄
cessible CRISPR / Cas9 system has been widely used in
many areasꎬ such as functional genomics researchꎬ
gene therapyꎬ virus controlꎬ and insect pest manage ̄
ment. Detailed understanding of the mechanism and
reducing the off ̄target ratio is the first obstacle in the
future research. Increasing precise regulation of these
technologies is noteworthy during clinical translation.
Dow et al. (2015) reported a doxycycline regulated
Cas9 expression system ( inducible CRISPRꎬ iC ̄
RISPR) and Polstein & Gersbach (2015) engineered
a light ̄activated CRISPR / Cas9 effector ( LACE) sys ̄
tem to demonstrate the importance of regulated genome
editing technologies.
Table 1 Regulatory considerations associate with gene silencing and genome editing biotechnologies
Risk assessment Gene silecning1 Genome editing2 Control
Genetic /
bioinformatics
Define target site specificity and how
many base pairing matches exist be ̄
tween target and potential non ̄target
species. Numerate possible cross in ̄
teractions.
Specificity to edit genome in specific
regions only. Determineꎬ in silicoꎬ
any possible concerns with normal
genomic contentꎻ evaluate region and
transcriptional activation.
1Determine nt matches (19ꎬ 20ꎬ and 21
mer sequence overlaps).
2Design multiple loci for genomic editing
modules and those specific lab strains.
Laboratory Test dsRNAs via standard protocols
using feedingꎬ injection and drenc ̄
hing / soaking methods in target and
non ̄target species. Quantify possible
interactions using qRT ̄PCR and life
history analyses.
Assess performance of GM ̄organism
using biotic and abiotic conditions.
Determine stability of genome editing
and determine new gene function
and / or performance of individuals
with genome additions / deletions.
1Assess risk in lab and semi ̄field settings
prior to field approvalꎻ design new regula ̄
tory framework off existing protocols.
2Multipleꎬ physical barriers to GM ̄organ ̄
ism and approved biosafety level clearance
and protocols for handling and disposal of
spent materials.
Ecological Stability of expressed dsRNAs in a
given vector ( in plantaꎬ bacteriaꎬ
virusesꎬ etc. ) . Determine half ̄life
of dsRNAsꎬ siRNAsꎬ or miRNAs in
field ̄level substrate.
Forecast range expansion over set
number of years and determine po ̄
tential hybridization patterns with in ̄
dividuals within species and across
sister taxa.
NA
Release facili ̄
ties
Controlled field plot releases on
smallꎬ large and full field scales.
Controlled releases on small and
large scales.
NA
Profiling and
genetic mixing
Quantify effects and document loss
( if seenꎬ or observable) on target
and non ̄target species.
Random sampling of wild populations
to monitor for interbreeding or herita ̄
ble genomic elements from population
hybridizing.
NA
Reversibility Ensure half ̄life of dsRNA effect in
target can be lost in 1 - 2 generations
of defined target.
Impediments according to reversing
effects of a given “ knock ̄in ” or
“knock ̄out” are easily introduced if
needed.
NA
Federal and /
or regulatory
agencies
Strict regulation of dsRNA cropsꎻ re ̄
lease crops in cycles and measure
quantifiable risks according to ERA
framework to determine suitability of
other crops.
Continuous monitoring and random
sampling to ensure genome edits are
not lostꎬ additions are not acquired
and genomic content is not mixing in
multiple populations / species outside
target organism.
NA
As the basic function of genome modificationꎬ ge ̄
nome editing technology will eventually replace the cur ̄
rent transposon ̄based transgenic methods with accurate
insertion of functional cassettes. Although there are
some reportsꎬ the successful trails of gene knock ̄ins
with TALENs and CRISPR / Cas9 are relatively low. To
improve the homology ̄directed repair (HDR) after DS ̄
Bs could induce exogenous sequence insertions into the
genome. Basu et al. ( 2015 ) demonstrated efficient
gene insertion after TALEN / CRISPR mutagenesis by
silencing the NHEJ pathway in A. aegypti.
In conclusionꎬ much work is needed to perfect the
genome editing system. One of the advantages of ge ̄
nome editing over other genetic methods is the modified
phenotype is stable and heritable. When these technol ̄
ogies are under the commercial developmentꎬ effective
detecting and tracking systems are required. There ̄
486 植  物  保  护  学  报 42 卷
foreꎬ research concerning the reduction of off ̄target
effectsꎬ the improvement of HDR and the assessment of
the ecological risks associated with genome editing
technologies will be needed in the near future.
5􀆰 3 Assessment of these RNA ̄based pest controls
Both dsRNA ̄based gene silencing and CRISPR /
Gas9 ̄based genome editing are derived from internal
biological processesꎬ one for the regulation of gene ex ̄
pression and the other involving in the immune re ̄
sponseꎬ respectively. With decades of modification and
optimizationꎬ RNAi and CRISPR / Gas9 ̄based genome
editing are powerful tools to manipulate genetic ele ̄
ments in reverse genetics and have been broadly ap ̄
plied in many different fields. The dsRNA ̄based gene
silencing and CRISPR / Gas9 ̄mediated genome editing
methods are the most effective and easiest ̄to ̄implement
strategies when compared with other RNAi methods
(shRNA or siRNA ̄basedꎬ etc. ) and genome editing
technologies (ZFNs and TALENsꎬ etc. ) . For agricul ̄
tural applicationsꎬ dsRNA ̄based RNAi has now been
tested in pest management through transgenic plantsꎬ
which express dsRNA targeting insect pests (Mao et
al. ꎬ2007ꎻWang et al. ꎬ2011). Meanwhileꎬ genetically
modified wheatsꎬ whose genome has been modified
with the CRISPR / Cas9 systemꎬ are resistant to certain
pathogens (Wang et al. ꎬ2014b).
There are fundamental differences between the
dsRNA ̄based gene silencing and CRISPR / Gas 9 ̄medi ̄
ated genome editing technologies (Table 1). The regu ̄
lation of target genes expression by dsRNA ̄based RNAi
is mainly focused on mRNA levels without any change
to the genomic DNAꎬ which is the target of CRISPR /
Gas 9 ̄mediated genome editing. Although the regula ̄
tion of gene expression by these two methods is induc ̄
ibleꎬ only RNAi methods are reversibleꎬ while genomic
manipulations are permanent. Another issueꎬ which is
different between RNAi and genome editingꎬ is the le ̄
thal effect. Due to the partial loss of gene functions af ̄
ter RNAi applicationꎬ only a few genes are potentially
lethal though RNAiꎬ whereas more genes might cause
death by genome editing. The length of dsRNA is usu ̄
ally about 300 - 500 bpꎬ but sgRNA targets are 23 bp
in length. A shorter target region indicates that the po ̄
tential off ̄target effect will be much higher in genome
editing. Despite these differencesꎬ both systems have
tremendous impacts on agricultureꎬ the environment
and human health.
Acknowledgements
Authors would like to thank Drs. Xiangrui Liꎬ
Kenneth Haynesꎬ and John Obrycki for their comments
on the earlier drafts. This is publication No. 15 ̄08 ̄106
of the Kentucky Agricultural Experiment Station and is
published with the approval of the Director.
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