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Plant Biotechnology Journal (2012) 10, pp. 150–163 doi: 10.1111/j.1467-7652.2011.00647.x

Resistance to Wheat streak mosaic virus generated by

expression of an artificial polycistronic microRNA in wheat
Muhammad Fahim1,2,†, Anthony A. Millar2, Craig C. Wood1 and Philip J. Larkin1,*
1
CSIRO Plant Industry, Canberra, ACT, Australia
2
Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia

Received 16 April 2011; Summary

revised 26 May 2011; Wheat streak mosaic virus (WSMV) is a persistent threat to wheat production, necessitating
accepted 7 July 2011. novel approaches for protection. We developed an artificial miRNA strategy against WSMV,
*Correspondence (Tel 61 2 6246 5060; incorporating five amiRNAs within one polycistronic amiRNA precursor. Using miRNA
fax 61 2 6246 5000; sequence and folding rules, we chose five amiRNAs targeting conserved regions of WSMV
email Philip.larkin@csiro.au) but avoiding off-targets in wheat. These replaced the natural miRNA in each of five arms of
†
Present address: Lecturer, Department of
the polycistronic rice miR395, producing amiRNA precursor, FanGuard (FGmiR395), which
Microbiology, Hazara University Mansehra,
was transformed into wheat behind a constitutive promoter. Splinted ligation detected all five
KPK, Pakistan. Tel +92 997 414130;
email mfahim@hu.edu.pk
amiRNAs being processed in transgenic leaves. Resistance was assessed over two generations.
Three types of response were observed in T1 plants of different transgenic families: completely
immune; initially resistant with resistance breaking down over time; and initially susceptible
followed by plant recovery. Deep sequencing of small RNAs from inoculated leaves allowed
the virus sequence to be assembled from an immune transgenic, susceptible transgenic, and
susceptible non-transgenic plant; the amiRNA targets were fully conserved in all three isolates,
indicating virus replication on some transgenics was not a result of mutational escape by the
Keywords: wheat streak mosaic
virus. For resistant families, the resistance segregated with the transgene. Analysis in the T2
generation confirmed the inheritance of immunity and gave further insights into the other
virus, artificial microRNA, multiplex
phenotypes. Stable resistant lines developed no symptoms and no virus by ELISA; this resis-
amiRNA, transgenic resistance, tance was classified as immunity when extracts failed to transmit from inoculated leaves to
Triticum aestivum, Tritimovirus, test plants. This study demonstrates the utility of a polycistronic amiRNA strategy in wheat
Potyviridae. against WSMV.

et al., 2002; Smith et al., 2000; Waterhouse et al., 1998). It is

Introduction
now established that RNAi is a natural surveillance mechanism
Wheat streak mosaic virus (WSMV; Genus Tritimovirus; Family conserved across eukaryotic organisms, where small RNAs either
Potyviridae) has remained a threat to wheat production wher- repress or cleave the complementary mRNAs in sequence-spe-
ever it occurs, and its distribution is expanded as evidenced by cific manner (Baulcombe, 2004). Since then, the strategy has
its confirmed presence in Australia in 2003. Although no data been successfully employed to confer resistance in various
are available for seed transmission of other isolates of WSMV, plants against invading pathogens.
the Australian isolate is transmitted both through its natural Previously, we have shown that transgene constructs capable
vector wheat curl mite Aceria tosichella (Slykhuis, 1955; Harvey of forming dsRNA transcripts are more likely to result in immu-
and Seifers, 1991; Seifers et al., 1998) and through seed (Jones nity against WSMV (Fahim et al., 2010) than either of the previ-
et al., 2005). The virus spread rapidly across the Australian con- ous two strategies that involved sense expression of the nuclear
tinent between 2003 and 2007 (Dwyer et al., 2007). The virus inclusion b or coat protein genes (Sivamani et al., 2000, 2002).
poses a new threat to the wheat production and required However, the use of long hairpin RNA (hpRNA) from conven-
development of new bio-security practices. The widespread tional RNAi vectors as in Fahim et al.’s (2010) study theoretically
occurrence of the virus and its vector, the potential major entails an increased risk of ‘off-target’ effects, i.e. silencing of
impacts on yield, and the impracticality of managing the mites unintended genes (Jackson et al., 2003). Furthermore, some
add to the priority of breeding virus-resistant varieties and express concern that agricultural-scale deployment of antivirus
developing alternative methods of virus control through devel- hpRNA-expressing transgenic plants might lead to evolution of
opment of virus-resistant transgenic wheat. new virus biotypes via heterologous recombination or comple-
Pathogen-derived resistance was pioneered with the expres- mentation between the relatively long viral sequences expressed
sion of viral coat protein in transgenic tobacco plants (Abel from the transgene and RNA from a non-target virus infecting
et al., 1986) and developed into more efficient and effective the same plant. Although the likelihood of such events seems
transgenic protection against viruses in plants utilizing double- remote and could be further reduced by judicious selection of
stranded RNA (dsRNA)-induced RNA interference (RNAi) (Abbott smaller sequences for the hpRNA constructs, nevertheless the

ª 2011 CSIRO
150 Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd
 Virus resistance via multiple artificial miRNAs 151

utility of other approaches is worth exploring. One such Petrie, P. Shrestha, M. Fahim, Q. Liu, C. C. Wood and S. P.
approach, amiRNA-mediated gene silencing, has recently been Singh, unpublished).
developed specifically to address the risk of off-target effects Here, we expressed five pre-amiRNA, potentially generating
and transgene–virus recombination to form new biotypes ten amiRNA species, to different conserved regions of the
(Schwab et al., 2006). WSMV genome from a modified version of rice miRNA precur-
The amiRNA approach utilizes a naturally occurring miRNA sor miR395. The polycistronic amiRNA strategy is able to pro-
precursor as a backbone, with the mature miRNA sequence duce marker-free transgenic wheat plants immune to WSMV,
being replaced to gain new targeting ability (Ossowski et al., demonstrating that this is a viable strategy for a major crop spe-
2008; Vaucheret et al., 2004). In plants, amiRNAs have been cies. Moreover, it alleviates the concerns of recombinant novel
successfully used to down-regulate endogenous genes (Alvarez viral entities forming and also produces plants predicted to
et al., 2006; Khraiwesh et al., 2008; Molnar et al., 2009; avoid the loss of resistance caused by virus mutation. The reso-
Schwab et al., 2006; Warthmann et al., 2008) and also for lution of technological problems and concerns implies this strat-
developing transgenic virus resistance against Turnip yellow egy has a strong biotechnological potential for agriculture.
mosaic virus (TYMV), Turnip mosaic virus (TuMV) (Niu et al.,
2006), Cucumber mosaic virus (CMV) (Duan et al., 2008), Results
Potato virus X (PVX), and Potato virus Y (PVY) (Ai et al., 2011)
Design of polycistronic amiRNA construct
in Arabidopsis; against CMV (Qu et al., 2007) in tobacco;
against CMV (Zhang et al., 2011) in tomato; and against We chose pre-miR395 as the backbone for simultaneous
Cassava brown streak virus (CBSV) and Cassava brown streak expression of multiple amiRNAs targeting various conserved
Uganda virus (CBSUV) in cassava (Wagaba et al., 2010). regions in the WSMV genome. We combined published ami-
It has been argued that the use of short viral sequences in RNA selection criterion (http://wmd3.weigelworld.org/cgi-bin/
this amiRNA approach is less likely to enable the emergence of webapp.cgi) into a software application we call ‘miR Mate’.
novel viral entities through recombination and trans-encapsida- Applying this to the available full WSMV genome sequences
tion (Schnippenkoetter et al., 2001). However, when only a (five at the time) identified approximately 120 potential target
small viral sequence is used, the virus is more likely to evolve in sites for amiRNA. As a final selection filter, we searched Wheat
the amiRNA target sequence via transition mutation and enable TIGR mRNA databases for potential off-targets of these poten-
avoidance of amiRNA complementarity and defence (Simon- tial WSMV amiRNAs using the online miRU program (http://
Mateo and Garcia, 2006; Lin et al., 2009). Other examples plantgrn.noble.org/psRNATarget/). No expressed sequences
include HIV escape mutants to avoid RNAi (Boden et al., 2003; were found as potential targets when three mismatches were
Das et al., 2004; Westerhout et al., 2005). To substantially allowed. Through this process, five amiRNA were chosen and
reduce the risk of viruses evolving to avoid degradation, a strat- designated amiRNA-1, amiRNA-2, amiRNA-3, amiRNA-4, and
egy would be very useful where an amiRNA precursor gene amiRNA-5; their WSMV genome targets and their target coordi-
expressed multiple amiRNAs targeting different conserved struc- nates are given in Table 1 and Figure 1. The target of amiRNA-
tural and functional portions of the viral genome. Resistance to 1 lies in 5¢ UTR region, amiRNA-2 targets the newly described
this protection would require simultaneous mutations to avoid open reading frame (ORF) pipo region of P3 cistron (Chung
all the amiRNA sequences. A similar rationale was invoked in et al., 2008), amiRNA-3 targets P1 gene, amiRNA-4 targets P3
the work of Israsena et al. (2009) where they designed precur- cistron (upstream of pipo), and amiRNA-5 targets the HCpro
sor genes encoding three amiRNA against rabies virus and gene on WSMV genome (Figure 1). We deliberately chose a
tested them in cell culture. Likewise, multiple siRNA were devel- mix of targets on the genomic and replicative strands of the
oped from a multiplex miRNA directed against HIV in cultured virus in case one strand was more available for the amiRNA sur-
cells (Liu et al., 2008; ter Brake et al., 2006). veillance than the other. While further good targets could be
miRNA precursors that have been used for the delivery of identified in the 3¢ genes, the bias to the 5¢ genes is simply a
amiRNAs in plants include miR159a (Niu et al., 2006); miR171a result of beginning the screening for potential off-targets from
(Qu et al., 2007), miR172a (Schwab et al., 2006), miR30 (Zeng that end. Surprisingly, no 21-nt sequence in the extreme 3¢
et al., 2002), miR528 (Warthmann et al., 2008), and miR167b region of the virus could be identified, which was both con-
(Ai et al., 2011). In plants, Niu et al. (2006) demonstrated that served and met the design rules. The endogenous miRNAs and
a dimeric amiRNA precursor in Arabidopsis could be effective miRNA* that are derived from the miR395 precursor were
against two different viruses. Others have successfully targeted replaced with these amiRNA and amiRNA* sequences to con-
two endogenous transcripts with dimeric amiRNA precursors in serve the secondary structure of the transcript. The predicted
Arabidopsis (Park et al., 2009) and Chlamydomonas (Zhao secondary structure of the polycistronic miR395 and the modi-
et al., 2009) using different miRNA precursors. Here, in our fied artificial miR395 were almost identical (Figure 2), presum-
studies, we used the multiplex precursor of rice miR395 family ably enhancing the prospect of the predicted biogenesis of
of miRNAs that was identified in both Arabidopsis thaliana and mature amiRNAs. This artificial polycistronic precursor was
Oryza sativa computationally and was later experimentally veri- named FanGuard395 (FGmiR395).
fied (Guddeti et al., 2005; Kawashima et al., 2009). OsmiR395
Generation of wheat carrying the FanGuard395
targets ATP sulphurylases that are involved in sulphate assimila-
transgene
tion (Rotte and Leustek, 2000) and is induced in sulphur starva-
tion to regulate a low-affinity sulphate transporter and two ATP FGmiR395 was synthesized by Geneart and cloned into pWubi
sulphurylases (Allen et al., 2005; Jones-Rhoades and Bartel, vector, to generate FGWS-pWubi, where FGmiR395 was behind
2004). The rice miR395 is a single 1-kb transcript that gener- a constitutive maize polyubiquitin promoter separated from the
ates a convoluted RNA structure that generates seven fully pro- transgene by a spliceable ubiquitin intron. FGWS-pWubi was
cessed miRNA (Jones-Rhoades and Bartel, 2004; S. Belide, J. R. cobombarded into wheat immature embryos along with

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
 Table 1 Conservation of amiRNA targets in WSMV Genome. The alignment used to design amiRNA against conserved targets in WSMV genome. AlignX was used with default settings using Vec-
tor NTI 10. (a) Alignment of the five chosen target regions in the five published WSMV genomes at the time of the design of the amiRNA. (b) Alignment in the five target regions in the ten new
WSMV genomes that became available subsequent to amiRNA design. (c) Alignment of the amiRNA target regions in the WSMV-ACT isolate (unpublished and obtained subsequent to the design
152 Muhammad Fahim et al.

of FGmiR395 and production of the transgenic plants). The mismatched nucleotides with other isolates are highlighted. amiRNA-1 and amiRNA-2 target the replicating strand, signified by number-
ing 1–21 from left to right; amiRNA-3, amiRNA-4 and amiRNA-5 target the genomic strand of the WSMV, signified by numbering 1–21 from right to left. The chosen targets remain absolutely
conserved in all five target regions of the WSMV-ACT isolate, when virus population RNA was resequenced from inoculated plants in the study including )S, +R, and the transgenic breakdown
plants +S

amiRNA-1 Target sequence amiRNA-2 Target sequence amiRNA-3 Target sequence amiRNA-4 Target sequence amiRNA-5 Target sequence
AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
Accession Description Origin 1 21 1 21 21 1 21 1 21 1

(a)
AF057533 Sydney 81 Nebraska AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
1AF285169 Type Strain Kansas AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF285170 El Batan Mexico AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATACCACTATGTACCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF454454 Czech Czech AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTTCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF454455 Turkish Turkey AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
(b)
AF511614 H95S Kansas AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGGTTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF511615 H98 Kansas AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CTGCGAACGTCTTGCAAGTTA
AF511618 ID96 Idaho AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF511619 ID99 Idaho AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
AF511630 Mon96 Montana AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
EU914917 Naghadeh Iran AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTTCATTATGTACCAA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
EU914918 Sadat-Saher Iran AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
F511643 WA99 WA, USA AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTTCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
FJ348358 WA94 WA, USA AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTTCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCAAACGTCTTGCAAGTTA
FJ348359 ARG2 Argentina AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA
(c)
Unpublished ACT Australia AGCTCTCGCATAGAGATAAGC TCGAGCAAGATCTTTCACACG GAAGATTCCATTATGTGCCGA CCAGGAAGCATTTTCTGGTCA CCGCGAACGTCTTGCAAGTTA

WSMV, Wheat streak mosaic virus.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
 Virus resistance via multiple artificial miRNAs 153

Figure 1 Structure of the Wheat streak mosaic virus (WSMV) genome (approximately 9400 nt), the target sites for amiRNAs and the FGmiR395
transgene. (a) Genome map of WSMV showing the five conserved regions (indicated by scissors) targeted by amiRNAs, amiRNA-1 to amiRNA-5. (b)
Design of FGmiR395 construct (1400 nt) used to transform wheat using biolistics; shown are the probe region for Southern blot and primer sequences
FgPf1 and M13RevP used in PCR. (c) Diagram of pCMneoSTLS2 containing the nptII gene for geneticin resistance, used in the cotransformation of
immature wheat embryos and showing the position of the PCR primers pNeo3 and pNeo5.

(a) (b)

Figure 2 amiRNA Secondary Structure. A com-

parison of truncated Osa-miR395 and FGmiR395 3
secondary structures. (a) Predicted secondary
structure of miR395 truncated to include only 5
the first five native miRNAs. (b) Predicted second-
ary structure of FGmiR395 replacing the first five
natural miRNA sequences with amiRNAs design
against Wheat streak mosaic virus, numbered
1

1
1–5. These are the predicted fold structures of
transcripts using RNAfold. Bars showing regions
1 2
corresponding to amiRNA guide strand. Second-
0

0
ary structure probabilities are indicated by heat
map (Blue, weak; Red, strong).

plasmid pCMneoSTLS2 (Maas et al., 1997) that contained neo- within the promoter region, full ubiquitin intron and all of the
mycin phosphotransferase gene (nptII), conferring resistance to FGmiR395 transgene including the nos terminator (Figure 1b).
geneticin (G418). From a wheat transformation of 379 PCR analysis of T1 families confirmed that 14 of the 23 families
embryos, a total of 23 T0 transgenic wheat plants were gener- had FGmiR395 as well as nptII (Figure 3a, PCR data not shown)
ated from 16 different embryos; therefore, there were at least and 10 of these were from different embryos and were there-
16 independent events. fore independent transgenic events. Southern blot analysis of T2
The transgenic lines were designated FanGuard plasmid (FGP) plants from a subset of these lines confirmed the presence of
plus a number corresponding to the bombarded embryo. transgene (Figure 4). Nine families were negative for FGmiR395
Where multiple T0 plants were obtained from a single embryo, and positive for nptII. The latter lines were discarded after the
they were distinguished with lower-case letters, e.g. FGP1a and preliminary assessment for resistance (next section).
FGP1b. All T0, T1, and T2 transgenic plants were morphologi-
Preliminary assessment of FGmiR395 transgenic wheat
cally indistinguishable from the wild-type parental cultivar, Bob
in T1
White selection 26 (BW26), implying that the FGmiR395 does
not influence growth or development (Figure 3b). The T1 generation was subsequently challenged with WSMV
Plants recovered from the transformation selection cultures through mechanical inoculation at the three-leaf stage (4–17
were screened through PCR for the nptII selectable marker from plants per family) using the spray gun. Wheat streak mosaic dis-
the pCMneoSTLS2 cotransformation vector (Figure 1c). This ease is characterized by light-green-to-faint-yellow streaks in
confirmed that all 23 plants coming through the antibiotic wheat leaves parallel to the veins. The virus arrests growth, and
selection were true transgenics carrying the selectable marker. plants show moderate-to-severe stunting with prostrated tillers
Genomic PCR screening for the presence of FGmiR395 was car- often with empty spikes or spikes with shrivelled kernels.
ried out using primers, fgPf1 and M13RevP, that span from Serological characterization of the transgenic families involved

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
154 Muhammad Fahim et al.

p.i. Virus accumulation in leaves was determined using ELISA

and expressed as a ratio of inoculated plants to non-inoculated
controls.
The progeny of nine geneticin-resistant nptII positive lines
were negative by PCR for FGmiR395 and were completely sus-
ceptible to the challenged virus. The T1 families from all the
other transgenic lines included plants inheriting FGmiR395 and
plants resistant to the virus. The transgenic (signified by +),
resistant (signified by R) segregants were designated as
FGmiR395+R. These plants were completely free of virus symp-
toms at all four data points 7, 14, 21, and 28 d p.i. They were
indistinguishable from uninfected wild-type BW26 plants. Such
phenotypes were observed in segregating families of all
FGmiR395-carrying events except FGP18.
In several transgenic families, some FGmiR395-carrying indi-
viduals were incompletely resistant, characterized as either: (i)
intermediate phenotype between susceptible and resistant aris-
ing from either resistance breakdown or plant recovery from
virus infection, or (ii) fully susceptible phenotype identical to
infected wild-type BW26. The intermediate phenotype was
characterized by intermediate plant height and a lower virus
titre compared to susceptible control BW26; these types of
transgenic segregants were designated as moderately resistant
or FGmiR395+MR (Figure 3b). The fully susceptible FGmiR395-
carrying plants were designated as FGmiR395+S; these were
indistinguishable from infected BW26 or the null segregant
FGmiR395)S phenotype.
Figure 3 Preliminary assessment of resistance in T1 families of
In this preliminary analysis, most FGmiR395 families segre-
FGmiR395 expressing transgenic wheat. (a) Wheat streak mosaic virus
gated for all three phenotypes (Figure 3a); however, in four
ELISA-based bioassay analysis of resistance in segregating populations.
Virus levels were detected by double-antibody sandwich enzyme-linked
events, FGP1b, FGP4b, FPG5a, and FGP6, all FGmiR395-inherit-
immunosorbent assay at 14 d p.i. (days postinoculation). )S indicated ing segregants were fully resistant. The numbers of plants were
FGmiR395 transgene–negative susceptible segregants, +S indicated variable and low (4–17), so little attention was paid to the
transgene-carrying susceptible segregants, while +R indicated the trans- segregation ratios at this stage.
gene-carrying resistant segregants. (b) Resistance phenotypes: Hea., All segregants in FGP18 displayed either FGmiR395+S or
healthy control; Inf., infected control; R., FGP15a2.10, an inoculated FGmiR395)S phenotype in this preliminary assessment and
transgenic immune; M., FGP15a2.7, an inoculated moderate resistant; showed no resistance. These susceptible transgenic plants along
S., FGP15a2.2, an inoculated susceptible negative segregant ()S). with other FGmiR395-S from other families exhibited character-
istic virus symptoms and were comparable with virus-infected
wild-type control BW26 plants.
inoculating each individual plant with WSMV and assaying with The initial analysis revealed a variety of phenotypes in
a double-antibody sandwich enzyme-linked immunosorbent response to WSMV inoculation. Transgenic families FGP4a, 6,
assay (DAS-ELISA) at 14 days postinoculation (d p.i.) and 28 d 8c, 15a, and 18 were selected as representative of the range of

Figure 4 Southern blot analysis of families in T2 generation. (a) BamHI digested wheat DNA for transgene copy number. (b) HindIII-digested wheat
DNA for transgene copy size. FC is full copy insert size 3 KB; TC is truncated copy inserts. Plant FGP18.6 is labelled )S by PCR and bioassay; it has FG
sequence present, but that sequence is truncated so that it is not detected by the PCR.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
 Virus resistance via multiple artificial miRNAs 155

phenotypes to be studied in greater numbers and detail in T1 inoculated transgenic individuals and ELISA readings very simi-
and T2 generations. lar to the ELISA readings of uninoculated controls, suggesting
the complete absence of virus from the inoculated transgenic
Analysis of transgenic family FGP6 for resistance
plants. Experiments were conducted to see whether infectious
to WSMV
virus or viral RNA could be recovered from the resistant inocu-
The preliminary analysis indicated that all FGmiR395-positive lated transgenic plants. Leaf sap from inoculated plants in
segregants in FGP1b, FGP4b, FGP5a, and FGP6 were resistant three transgenic families (FGP8c, FGP13b, and 15a) was
(Figure 3a). Subsequently, a bioassay on 26 T1 individuals of extracted and inoculated onto test plants of control BW26 at
FGP6 showed that all 13 FGmiR395-carrying segregants were 1 ⁄ 10 (w ⁄ v) dilution to investigate the presence of any infec-
symptom free at all four time points (7, 14, 21, and 28 d p.i.) tious WSMV particles. Results from these test inoculation
and had background ELISA ratio at 14 and 28 d p.i. One of the experiments revealed that all FGmiR395+R phenotypes were
major effects of virus infection on plant physiology is the severe immune to WSMV, as no infectious virus could be recovered
stunting and extreme reduction in plant height. When we plot- and carried over to control wheat through mechanical inocula-
ted the virus concentration (ELISA ratio of virus inoculated tion with the most concentrated leaf extract inoculum. Sap
plant) in segregating FGP6 progeny, we found that they clearly from inoculated segregants with FGmiR395 transgenes failed
grouped into two clusters (Figure 5b), showing that the plant to transmit infection to susceptible BW26 as judged by symp-
height is inversely related to the virus concentration. toms and ELISA, whereas sap from segregants with no trans-
PCR analysis of selectable marker nptII in this family revealed gene and non-transformed controls (BW26) did transmit
that 17 of 26 plants carried the selectable marker (Table 2). One infection in every case. Examples of these tests are shown in
immune FGmiR395 transgenic plant FGP6.22 was negative for Figure 6.
selectable marker nptII, while five FGmiR395-negative segregants
The formation of amiRNAs from the FGmiR395
were carrying nptII, and eight segregants were negative for both
transcript
transgenes. It is worth noting that the approach and technique
utilized in this work can yield marker-free immune transgenics. The expression of the amiRNAs was analysed in virus-free
Southern blot analysis carried out on T2 segregants confirmed transgenic wheat leaves and detected by splinted ligation using
stable integration of FGmiR395 transgene(s) into the wheat miRtect IT (Maroney et al., 2007). Potentially, from the five
genome (Table 2) and apparently multiple copies of the trans- duplex arms of the precursor FGmiR395, five guide strands
gene (BamHI digest: Figure 4a). (amiRNA) could be produced; moreover, if one also considers
the loading of passenger strand (amiRNA*) into RNA Induced
Efficacy of viral suppression in transgenic families
Silencing Complex (RISC), then a total of ten amiRNA could
The analyses reported thus far for the resistant transgenic potentially be produced against the virus. To detect both
families showed the complete absence of symptoms in amiRNA and amiRNA* sequences using splinted ligation, we

Figure 5 Segregation of resistance in FGP families expressing FGmiR395 transgene. Virus levels were detected by double-antibody sandwich enzyme-
linked immunosorbent assay at 28 d p.i. postinoculation and expressed as ratio of inoculated and healthy control. The plant height (in cm) was
measured at the heading stage and plotted against the corresponding ELISA ratio. )S indicated the FGmiR395 transgene–negative susceptible segre-
gant, +S indicated transgene-carrying susceptible segregant, +MR indicated segregants that carried the transgene but accumulated virus titre owing to
resistance breakdown, while +R indicated the transgene-carrying resistant segregants. Transgenic families are shown as (a) FGP4a, (b) FGP6, (c) FGP8c,
(d) FGP15a, and (e) FGP18. MR, moderate resistance.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
156 Muhammad Fahim et al.

Table 2 Segregation of transgene and resistance in T1 and T2. Analysis of six selected FGmiR395 families in T1 and T2. Recorded for T1 are
the results of Southern hybridisation, segregation for genomic PCR, and resistance. Segregation for resistance in T2 is also shown for a series
of selected derivative families. Selected T2 families were derived as shown from T1 individuals that were transgene carrying and resistant (+R);
transgene-carrying susceptible (+S); and transgene-negative susceptible ()S). Southern blots are shown in Figure 4

T0 (NT) T1 T2

FGmiR395 Copy no. FGmiR395 ELISA phenotype in

Southern blot no. of loci PCR ptII PCR GmiR395 ELISA WSMV ELISA-based T2 segregants
T0 Parent (examples Figure 4a) (segregation) +:) +:) R:S T1 parent phenotype in T1 R:S

FGP4a 2 1 21 : 11 24 : 8 15 : 9 4a.18 +S 20 : 15
4a.22 +R 29 : 0
4a.31 )S 0:8
FGP6 4 – 17 : 9 13 :173 13 : 13 6.3 )S 0 : 14
6.10 +R 22 : 15
FGP8c 3 1 49 : 21 51 : 19 30 : 21 8c.10 +S 14 : 21
8c.11 +R 24 : 8
8c.27 )S 0 : 19
FGP15a 1 1 39 : 13 39 : 13 32 : 7 15a.1 +R 34 : 1
15a.2 +S 24 : 4
15a.11 )S 0:6
FGP18 3 – 26 : 12 17 : 21 0 : 38 18.6 )S 0 : 15
18.10 +S 12 : 32

WSMV, Wheat streak mosaic virus.

designed the ten bridging oligos accordingly (Table S1). All five
designed anti-WSMV miRNAs, amiRNA-1, amiRNA-2, amiRNA-
3, amiRNA-4, and amiRNA5, were expressed in the plant. Using
an immune plant in T2 generation, seven of the potential ten
amiRNA were generated from FGmiR395 and accumulated suf-
ficiently to be readily detected (Figure 7). At least these seven
amiRNAs would be loaded into RISC and would be expected to
target the invading virus at both the genomic RNA and replica-
tive RNA levels in four viral regions, the 5¢ UTR, P1, P3, and
HCpro regions.
Investigating the resistance breakdown phenotype
In addition to stable immunity FGmiR395+R, other phenotypes
were observed in some transgenic events described previously
as FGmiR395+MR and FGmiR395+S. These also were studied
in more detail in the five families chosen for closer examina-
tion. Negative segregants FGmiR395)S along with wild-type
BW26 were used as negative (susceptible) controls in all
assays.
Transgenic event FGP4a
In the T1 generation of FGP4a, 24 of 32 plants carried the
transgene; however, only 15 of these showed strong resistance
throughout the experiment. The resistance in nine individuals
Figure 6 Virus transmission from the inoculated transgenic plants onto
broke down with time, and symptoms began to appear as faint
Bobwhite26. Sap was extracted from inoculated transgenic plants at
streaks at 14 d p.i. Two of these nine individuals showed a
1 ⁄ 10 (w ⁄ v). Each sap extract was inoculated onto three wild-type BW26
plants. At 28 d p.i., samples were collected and processed for Wheat
moderate resistance (MR) as judged by no symptoms at 14 d
streak mosaic virus ELISA. (a) Plotted is the average ELISA ratio (inocu- p.i., but the gradual development of leaf symptoms, growth to
lated divided by healthy) for the three test-inoculated plants. (b) Also only intermediate height, and accumulated virus titre at 28 d
tabulated are the molecular analyses of the inoculated T1 individuals p.i.; these segregants were characterized as FGmiR395+MR
whose sap extracts were being tested. Shown for each sap donor is the (Figure 5a). PCR, ELISA ratio, and plant height plot suggested
FGmiR395 PCR result, the bioassay result for that donor plant (as 28 d four groups in this family. The third cluster (FGmiR395+S) accu-
p.i. ELISA ratio), and the symptom score at 28 d p.i. (0–4 scale). Control mulated less virus than the null segregants but was equally
BW(i) is inoculated BW26. BW(h) is the uninoculated BW26. affected in height.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
 Virus resistance via multiple artificial miRNAs 157

of nptII, and both segregate in simple Mendelian proportions

(Table 2). Most of 32 tested FGmiR395 + segregants were
strongly resistant (+R), but six had moderate resistance (+MR)
(Figure 5d). These six segregants had lower virus accumulation
and were less stunted compared to the FGmiR395 null segre-
gants (Figure 5d).
Figure 7 Expression analysis of Wheat streak mosaic virus-specific amiR- Three different FGP15a T1 segregants were selected for anal-
NAs: Levels of the amiRNAs in immune transgenic segregant FGP4a.22 ysis in T2, and once again, resistant phenotypes were recovered
were examined using the MiRtect IT splinted ligation assay. Assays with from a susceptible transgene-positive T1 parent (FGP15a.2). The
bridge oligonucleotides specific for (a) amiRNA, (b) amiRNA*, and (c) family had one site of insertion of the transgene; however, a
internal controls. The numbers in the bottom panel correspond to strong signal might suggest concatamerization at this site; there
amiRNA-1 to -5, respectively. was also evidence of a truncated copy (Figure 4). From the +R
T1 individual FGP15a.1, only one of 35 T2 was not immune.
Transgenic event FGP8c
In FGP8c, four classes of phenotype were observed. A total of
70 individuals were analysed for the transgenes, and 51 were
assayed in T1 for WSMV resistance (Table 2). Of T1 plants tested
(Figure 5c), 30 were +R with average plant height of 45.56 cm;
seven were +MR where resistance held up at 14 d p.i. but grad-
ually broke down with the virus titre ratio above ten at 28 d
p.i. and average plant height of 28.5 cm; 14 segregants were
+S despite carrying a full copy of FGmiR395, with average plant
height of 16.92 cm and indistinguishable from the 19 )S segre-
gants with average plant height 14.26 cm.
Seeds were collected from three T1 individuals representing
Figure 8 Segregation of resistance in T2 progeny of T1 individual
+R, +S, and )S classes (Table 2). From the immune +R individ-
FGP4a.18: (a) Inoculated T2 plants and FGmiR395 PCR results. (i) and (v) ual FGP8c.11, resistance segregated normally (24 : 8) in T2.
transgene-negative susceptibles; (ii) transgene carrying moderately resis- Again, the T2 progeny of a +S plant, FGP8c.10, segregated
tant; (iii) (iv) (vi) and (vii) transgene-carrying immunes. (b) Southern blot some strongly resistant plants (14 : 21). The Southern blot anal-
for copy size of FGP4a (+R) and FGP4a ()S), where FC shows the ysis revealed the presence of three copies (Table 2, Figure 4)
expected full size, and TC shows a truncated copy. (c) Southern blot for that appeared to be of equal size but segregated together at
copy number FGP4a (+R) and FGP4a ()S). one insertion locus.
Leaf saps from the strongly resistant segregants of event FGP
8c were back-inoculated to susceptible controls and found to
Seeds collected from three FGP4a T1 individuals, representing be immune; this is illustrated in Figure 6 by T1 individual
immune (FGmiR395+R), resistance breakdown (FGmiR395+MR), FGP8c.2. However, individuals such as FGP8c.7 showed some
and susceptible phenotypes (FGmiR395)S) were analysed in T2 breakdown of resistance after 14 d p.i., and sap from this plant
generation (Table 2 and Table S2). was infective to the same extent as the null segregant FGP 8c.1
A total of 29 plants were grown and bioassayed from the (Figure 6).
seed collected from T1 segregant FGP4a.22 (+R), and when
Transgenic event FGP18
challenged with WSMV, all 29 T2 individuals proved to be
immune to WSMV and no virus was retrieved on BW26 Event FGP18 was examined further because the apparent full-
through back-assay. The progeny of intermediate phenotype length insertions of the FGmiR395 gene failed to confer any
FGP4a.18 (+MR) with resistance breakdown phenotype in T1 plants with a high level of resistance in T1 (Figure 3a, Figure
produced 15 resistant progeny in T2 plants (of 35 total). This T2 5e). In 38 T1 segregants, the nptII gene segregated simply, but
segregation for resistance in FGP4a.18 is also illustrated in segregation was significantly distorted away from the
Figure 8a. We hypothesize this may indicate the segregation of FGmiR395 transgene (17 : 21, Table 2). While none of the T1
an antagonistic factor such as an interfering truncated trans- individuals were strongly resistant, Figure 5e shows that the
gene copy away from a functional copy of FGmiR395 resulting FGmiR395-carrying plants clustered distinctly from the null
in more stable resistance. Southern blot analysis for copy size segregants, with average plant height of +S being 26.1 cm,
did reveal the presence of a truncated copy (Figure 8b). Further- compared to 14.6 cm in )S segregants (Figure 5e, Table S2).
more, it is also possible that the zygosity of FGmiR395 might be Southern blot analysis revealed the presence of four copies (Fig-
involved in the amiRNA production where the homozygous level ure 4a) including truncated copies (Figure 4b). The T2 progeny
of expression may result in more stable resistance. The T2 prog- from a +S and )S T1 parent were analysed for virus resistance.
eny propagated from a negative segregant parent FGP4a.31 Resistance was evident in 12 T2 individuals from FGP18.10 of
(FGmiR395)S) were fully susceptible and indistinguishable from 44 tested (Table 2). It is noteworthy that even in this multi-
the wild-type susceptible BW26 controls. insertion transgenic event, which appeared in T1 generation to
be ineffective, by T2, it was possible to identify fully resistant
Transgenic event FGP15a
transgenic segregants. Plant FGP18.6 is noteworthy. Using PCR
In FGP15a, a total of 52 individuals were analysed in T1 genera- and bioassay, it was classified as )S; it did have transgenic
tion. There appears to be one copy of FGmiR395 and one copy sequence present (Figure 4a), but the sequence is truncated

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
158 Muhammad Fahim et al.

(Figure 4b). Presumably, the truncation has eliminated one or

both of the primer sites so that the PCR gave no product.
When only the truncated copy is present, the plants are suscep-
tible in both T2 and T3 generations (Table 2).
The possibility that the virus was evolving to avoid all five
amiRNA species can be dismissed based on two lines of evi-
dence. T2 transgenics were challenged with the infected sap
derived from both susceptible and transgene-carrying suscepti-
ble segregants in T1. Leaf sap collected from FGmiR395+S T1
plants was used to inoculate T2 progeny. These potentially
evolved virus populations continued to be controlled by resistant
transgenics. Furthermore, in a number of families (Table 2), +R
and +MR phenotypes emerged from +S T1 parents. Therefore,
the original +S susceptibility was not the result of virus muta-
tion; otherwise, resistance would not have emerged in T2 when
challenged with the putatively mutant virus preparations. In
addition, deep sequencing was carried out of small RNA frac-
tions extracted from virus-inoculated plants of the three pheno-
types, +R, +S, and )S. This allowed the full virus genomic
sequence to be reconstructed from each of these virus popula-
tions. As reported in Table 1, the virus sequence of WSMV-ACT
recovered from the non-transgenic plant ()S), in each of the
five target regions, was exactly the sequence as used in the
construction of the amiRNA. Furthermore, the sequence in
these regions was entirely unchanged in the virus population
from both the transgenic resistant plant (+R) and the transgenic
susceptible plant (+S).
The recovery phenotype
Individuals with a recovery phenotype were observed in trans-
genic family FGP13b. These plants had virus symptoms at 14 d Figure 9 Recovery phenotype. (a) Inoculated leaf (b) leaf showing symp-
p.i. and a high virus titre; however, when assayed at 28 d p.i., toms (c) newly emerged healthy leaf. In this transgenic FGP13b.2 indi-
virus was not detected through ELISA nor were there any symp- vidual, we inoculated the leaf with spray gun (necrotic spots shows
toms observed on the newly emerged leaves. An example of mechanical injury resulting from spray inoculation); at 14 d p.i., the
this phenomenon is displayed in transgenic segregant FGP13b.2 plants showed symptoms and accumulated virus by ELISA ratio. How-
(Figure 9), where the new leaf displayed characteristic virus ever, at 28 d p.i., newly emerged leaves were completely symptom-free
symptoms at 14 d p.i. (still evident at 28 d p.i., Figure 9b) and with no virus detected by ELISA. When sap from new leaves of this
had an ELISA ratio of 2.5. However, as the plant developed fur- plant was test-inoculated onto BW26, no infectious virus could be
recovered (Figure 5).
ther, no virus symptoms were observed on the newly emerged
leaves at 28 d p.i. (Figure 9c). Moreover, no WSMV-specific
PCR product could be amplified from reverse-transcribed RNA transcript would be processed upon expression to produce five
from the newly emerged leaves. This suggests that the amiRNA 21-bp amiRNA duplexes and then up to ten species of amiRNA,
was ineffective in the young plant but expressed better and because secondary structure of the plant precursor miRNAs
became effective in overcoming virus multiplication as the plant appears to be more important for processing by DCL1 than the
developed further. sequence of the mature miRNA itself (Schwab et al., 2006;
Sap was extracted from the newly emerged leaves and inocu- Ossowski et al., 2008). WSMV has a +ssRNA single-stranded
lated onto susceptible BW26 plants to test whether the virus (monopartite) genome that replicates through a dsRNA interme-
has been completely eliminated from the newly emerged leaves. diate to generate a negative ()) strand during this replication
No infectious virus could be recovered in this back-assay process. This monopartite genome provides the opportunity to
(Figure 6, FGP13b.2). This lead to the conclusion that in some target the virus at any accessible position that would result in
resistant transgenic events, the virus was able to get away to homology-dependent degradation of the viral genome or the
initial establishment but that the amiRNA expression sub- replicative strand. amiRNA-1 and amiRNA-2 were designed to
sequently was able to completely eliminate the virus from the be complementary to and target the replicating strand, while
recovering plant. amiRNA-3, amiRNA-4, and amiRNA-5 were designed to be com-
plementary to and target the genomic strand of the virus. It has
been shown that both positive and negative strands of hepatitis
Discussion
C virus may be targeted by siRNAs (Wilson and Richardson,
We engineered a complex rice-derived miR395 with five artificial 2005). The amiRNA* (passenger strand) might also get loaded
miRNA precursors designed to target WSMV genome, to into RISC and thus mediate the degradation of the opposite
achieve amiRNA-mediated resistance in wheat. We retained the strand of the virus (either genomic or replicative strand) than
predicted secondary structure of miR395 in the synthetic the predicted one. In fact, our results showed that seven of the
FGmiR395 transgene and hypothesized that the FanGuard potential ten types of amiRNA could be readily detected.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
 Virus resistance via multiple artificial miRNAs 159

Resistance cosegregated with the transgene in most of the online (NCBI) had grown from five to 13. An alignment of all 13
transgenic events of this study. However, analysis of T1 families revealed that three of five chosen amiRNA targets are still
revealed a range of phenotypes. (i) Immune individuals were completely conserved in the WSMV genome (Table 1). This
obtained, which remained symptomless and with no viral coat highlights the importance of having multiple targets in polycis-
protein accumulation all the way through to maturity. Sap pre- tronic amiRNA and the importance of aligning as many virus ge-
pared from these inoculated plants failed to transmit infection nomes as possible to select highly conserved regions.
to susceptible controls. Such immunity was evident across two One of the targets in FGmiR395 was the functional region
generations, (ii) In other cases, the plants were resistant without called pipo (pretty interesting Potyviridae ORF) within the gene
symptoms or ELISA detected coat protein at 14 d p.i., but sub- encoding the P3 protein. Pipo was initially identified as a small
sequently, the resistance broke down, allowing virus to accumu- ORF embedded in the P3 cistron of Turnip mosaic virus (TuMV;
late by 28 d p.i., (iii) A third transgenic phenotype may be genus Potyvirus; family Potyviridae) (Chung et al., 2008), and its
called plant recovery, in which early susceptibility is followed by presence was confirmed in 48 viruses representing all genera in
full recovery and resistance, (iv) The forth phenotype is where the family Potyviridae, including WSMV. Mutation in pipo hin-
the presence of multiple copies of the transgene confers only ders various important functions; in the case of WSMV that
moderate resistance. We challenged the transgenic families with includes effects on replication and movement in the plant.
high-titre virus inoculum at two time points 0 and 10 d p.i. and When mutations are introduced into the pipo region of P3,
therefore suggest that the breakdown of resistance in some without affecting the amino acid sequence of the translated
events might result from an excessive virus pressure that over- protein, the virus loses the ability to replicate in protoplasts
whelms the amiRNA-mediated resistance. Such a phenomenon (Chung et al., 2008) or it is restricted to only a few cells in inoc-
has been observed in transgenic barley against Barley yellow ulated plants (Wen and Hajimorad, 2010).
dwarf virus (BYDV) where an increase in viruliferous aphid infes- As one would expect, the presence of one full copy of the
tation resulted in breakdown of RNAi resistance to BYDV (M.-B. transgene can be enough to confer resistance (immunity)
Wang, pers. commun.). Ai et al. (2011) showed that although against WSMV. However, we saw evidence in some transgenic
amiRNAs were detectable and resistance to PVX or PVY evident events of additional truncated FGmiR395 insertions and
in their transgenic plants, the resistance was overcome by rein- behaviour in T1 and T2 generations suggestive that the
oculation at 35 d p.i., resulting in increased viral pressure. The truncated copy may be interfering with the expression of the
pressure of inoculation in our experiments was very high and full-length copy; subsequent loss of the truncated copy restores
may be responsible for some of the more complex resistance effective resistance. This interpretation will require further
phenotypes. It would be interesting to investigate the efficiency experimentation to confirm. We sometimes observed resistance
of the FGmiR395-expressing wheat plants in the field under the segregation ratios inconsistent with Mendelian expectation
milder pressures expected from natural wheat curl mite infesta- based on the inferred insert locus number. Usually, this involved
tions. lower than expected numbers of resistant individuals and is
It could also be informative to quantify the level of amiRNA likely associated with some inserts of the transgene being inef-
expression in the various transgenic phenotypes to observe fective or conditionally effective (Matzke et al., 2009).
whether there is a correlation with the degree or stability of Previously, we have reported the use of long hairpin dsRNA-
resistance. Such an analysis would need to follow all ten of the mediated WSMV immunity in wheat (Fahim et al., 2010). The
potential amiRNA species and would ideally include the various comparison to the present study is a rare opportunity to con-
phases of resistance breakdown and various phases of recovery. trast the two approaches in the same genetic background
Previous studies have shown some degree of correlation against the same virus. Compared to amiRNA, long hairpin RNA
between amiRNA expression and virus resistance (PVX and PVY had the advantage of a very high frequency of insertion events
in Arabidopsis, Ai et al., 2011; CMV in tobacco, Qu et al., with stable heritable immunity. In this respect, long hairpin
2007). When there are at least five and potentially ten species RNAi is very attractive from a biotechnology application per-
of amiRNA attacking the virus, as with FGmi395, the analysis of spective. However, long hpRNA would have a higher probability
correlation with resistance will be complex. of unintended silencing of off-target genes in the host (Xu
One potential risk with amiRNA-mediated resistance is the et al., 2006; Duan et al., 2008; Khraiwesh et al., 2008). Fur-
generation of virus mutants that escape the amiRNA surveillance thermore, long hpRNA approaches are seen by some as posing
(Simon-Mateo and Garcia, 2006; Lin et al., 2009). We addressed a risk in the field of heterologous recombination with other
this issue in our studies by selecting amiRNA targets based upon virus genomes and resulting in new virus biotypes. Low temper-
conserved regions in five full WSMV genome sequences avail- atures can also compromise the efficacy of RNAi silencing strat-
able. We observed no evidence that the virus was evolving egies (Szittya et al., 2003). On the other hand, miRNAs appear
(mutating) during the course of the experiment. This was evi- to be completely temperature independent, and the transgenic
dent because virus populations collected from FGmiR395+S T1 lines expressing virus-derived amiRNA retain their resistance at
plants was used to inoculate T2 progeny. Not only did the resis- low temperatures (Niu et al., 2006; Szittya et al., 2003). We
tant transgenic continue to be resistant to these inoculations, were able to achieve immunity in wheat to WSMV from both
but progeny from some +S T1 parents included +R and +MR the long hairpin dsRNA and the amiRNA strategies. We con-
phenotypes. We take this as evidence that the original +S sus- clude that amiRNA-based viral resistance, especially polycistronic
ceptibility was not the result of virus mutation; otherwise, resis- amiRNA as advocated here, deserves and needs further in-depth
tance would not have emerged in T2 when challenged with the studies to improve the amiRNA efficiency. An even better com-
putatively mutant virus preparation. Furthermore, deep sequenc- parison would be achieved if the long hpRNA was designed to
ing of virus populations from infected transgenic plants con- cover the same regions as the amiRNA used in this study.
firmed no mutations in the target sequences. By the end of this The work described here exemplifies the utility of miR395
study, the number of full-length WSMV genomes available and similar miRNA clusters as a carrier of multiple amiRNAs.

ª 2011 CSIRO
Plant Biotechnology Journal ª 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd, Plant Biotechnology Journal, 10, 150–163
160 Muhammad Fahim et al.

They can be used to target multiple regions of the one virus (as The stemloop backbone
here), multiple viruses, or multiple endogenous mRNA species
For the delivery of the final five amiRNAs as a polycistronic
(S. Belide, J. R. Petrie, P. Shrestha, M. Fahim, Q. Liu, C. C.
transgene, we selected the precursor of rice miR395 that is
Wood and S. P. Singh, unpublished). Mixed viral infections are
expressed under sulphur stress conditions (Guddeti et al., 2005;
common in the field especially in fruits and vegetables. Using
Jones-Rhoades and Bartel, 2004; Kawashima et al., 2009).
the polycistronic amiRNA, it will be possible to target highly
A synthetic gene called FanGuard (FG) was designed by replac-
conserved regions of multiple viruses. Similarly, polycistronic
ing the five native miRNA sequences in the first five duplex
pre-amiRNA genes will be effective in targeting multiple plant
arms of native miR395 with five amiRNA designed to target
endogenous genes for functional genomics and in applications
WSMV. In a parallel study, a similar construct was used to
such as redirecting plant metabolism into novel products.
simultaneously silence five endogenous genes in Arabidopsis
We conclude that polycistronic amiRNAs can be utilized to
(Belide et al. submitted). The designed FGmiR395 was synthe-
induce virus resistance in commercially valuable plants, where
sized through GENEART GmbH (http://www.geneart.com)
there are limited options of natural resistance. We anticipate
flanked by restriction sites for BamHI and KpnI in the carrier
ongoing improvements in the understanding of miRNA biogene-
plasmid. The FG gene was excised from the carrier plasmid
sis and design of amiRNA to further enhance the utility for virus
using appropriate restriction enzymes and ligated between the
resistance and engineering other agronomically important traits.
Ubiquitin promoter and tm1 terminator of vector pWubi-tm1
Furthermore, the expression of multiple amiRNAs from a single
vector (Wang and Waterhouse, 2000) generating cereal trans-
precursor transgene will minimize the difficulties of repeated
formation plasmid FG-pWubi.
transformations, need for multiple selectable markers, and the
constraint of breeding with multiple independent loci. Wheat transformation
Transgenic wheat plants were generated following microparticle
Experimental procedures bombardment of 186 immature cv. Bob White 26 (BW26)
wheat embryos. The embryos were cobombarded with two
Designing WSMV-specific amiRNA
plasmids, FG-pWubi and a selectable marker plasmid
To select conserved regions in WSMV genome as targets for arti- pCMneoSTLS2, as described previously (Fahim et al., 2010;
ficial miRNAs, full-genome sequences of WSMV were retrieved Pellegrineschi et al., 2002).
from NCBI (Table 1). The sequences were aligned with Clustal
Analysis of T0 transgenic plants—PCR
W ⁄ AlignX (a component of Vector NTI Advance 10.3.0) to
screen for highly conserved regions in the viral genome. The DNA extraction was carried out using DNAeasy Plant Mini Kit
possible amiRNA sequences were generated from the highly following manufacturer’s instructions (Qiagen Inc, Valencia,
conserved regions (20 nt or more in length) using the basic crite- CA). For PCR-based genotyping of the FGmiR395 transgene,
ria defined at WMD3 (http://wmd3.weigelworld.org/, a web DNA was amplified (Figure 1b) using FgPf1 5¢-TGCAGCATC-
microRNA design tool) and incorporated into a software algo- TATTCATATGC-3¢ and M13RevP 5¢-CATGGTCATAGCTGTT-3¢,
rism called miR Mate developed specifically for this study. The that generated approximately 1.4 kb of FG-pWubi amplicon
algorithm was developed using Microsoft. NET Framework and covering promoter, transgene, and terminator regions, under
also incorporates the Vienna RNA Package 1.7 algorithm RNA- the following thermocycler conditions 94 C for 30 s, 60 C for
fold.exe (Hofacker et al., 1994; McCaskill, 1990; Zuker and Stie- 45 s, 72 C for 60 s for 35 cycles with a final extension at
gler, 1981). The miRNA design criteria used include A ⁄ U at 72 C for 10 min. For the selectable marker nptII (Figure 1c), a
position 1 (Mi et al., 2008; Eamens et al., 2009; Takeda et al., 700-bp nptII fragment was amplified using the forward primer
2008), A at position 10 (Reynolds et al., 2004; Mallory et al., Neo3 5¢-TACGGTATCGCCGCTCCCGAT-3¢ and reverse primer
2004), and G ⁄ C at position 21 (P. Waterhouse, pers. commun.). Neo5 5¢-GGCTATTCGGCTATGACTG-3¢, both sequences being
miR Mate utilizes the RNAfold algorithm to calculate minimal in the nptII coding region, using the following thermocycler
free energy (mfe) values for the formation of the candidate miR- conditions: 94 C for 30 s, 55 C for 30 s, 72 C for 60 s for
NA’s folded structure; values of £)30 kcal ⁄ mol represent opti- 40 cycles with a final extension at 72 C for 10 min.
mal stability. The negative values reflect the fact that stored
Analysis of T1 and T2 transgenic plants—Virus bioassay
energy is released during the formation of the structure;
the more negative the value, the more energy is released and Virus inoculum was prepared by grinding WSMV-infected tissue
the more favourable is the formation of the structure. Candidate in a mortar and pestle at a 1 : 10 w ⁄ v ratio in 0.02 M potas-
amiRNAs with the lowest mfe value (the highest stability) were sium phosphate buffer (pH 7). After filtering through four lay-
then assessed for potential off-targets in wheat and barley. ers of Miracloth (Calbiochem, La Jolla, CA), abrasive celite
The set of potential virus target sequences were used to (Johns-Manville, Denver, CO) was added at 2% w ⁄ v to serve
search for genes that may be potential off-targets in wheat or as an abrasive. For the analysis in T1 plants, the inoculum was
barley, using miRU: Plant microRNA Potential Target Finder prepared from virus-infected non-transgenic BW26; for the
http://bioinfo3.noble.org/miRNA/miRU.htm (a recent version analysis of T2 plants, sap from a mixture of FGmiR395 carrying
psRNATarget: A Plant Small RNA Regulator Target Analysis Ser- susceptible and FGmiR395-negative segregant susceptible
ver is available at http://bioinfo3.noble.org/psRNATarget/) (Bren- plants was used. The sap–celite mixture was first applied with
necke et al., 2005; Jones-Rhoades and Bartel, 2004; Lim et al., an air-powered spray gun, and then, leaves were gently rubbed
2005; Mallory et al., 2004). WSMV-derived amiRNAs were with fingers to ensure the infection of plant by the virus. At
selected having the least probability of targeting any sequence 10 d p.i., plants were reinoculated with the virus-infected sap
in the gene or EST databases of wheat or barley. to ensure high inoculum pressure.

ª 2011 CSIRO
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 Virus resistance via multiple artificial miRNAs 161

The plants were scored for symptoms at 7, 14, 21, and 28 d 15–50 bp was dissected and small RNA was extracted from
p.i. on a scale of 0–4 with 0 as healthy, 1 as mild with very excised gel overnight in 4 M NaCl. The RNA concentration was
few streaks, 2 as moderate with streaks that coalesce, 3 as measured in 1 lL of solution using Nanodrop (Thermo Scien-
severe with approximately 50% leaf area with streaks, and 4 as tific, Wilmington). The splinted ligation was performed on the
the most severe or lethal symptoms where the streaks develop purified fraction with miRtect-IT miRNA Labeling and Detec-
into chlorosis of more than 70% of leaf area based on visual tion Kit (USB, Cleveland, OH) (Maroney et al., 2007). Specific
observation. WSMV-specific ELISA was performed on leaf sam- bridge oligonucleotides (Table S1) were designed according to
ples collected at 14 d p.i. and 28 d p.i., using Agdia reagents the manufacturer’s directions. Using 50 ng of enriched smRNA
(Agdia, Elkhart, IN) following the manufacturer’s instructions. per reaction, amiRNAs were captured by a specific bridge oligo-
Plates were read at A405nm in ELISA Reader Spectra Max 340 nucleotide and ligated to the P32-labelled detection oligonucleo-
PC (Molecular Devices, Sunnyvale, CA) 60 min after the addi- tide with T4 DNA ligase. Ligated products were separated on
tion of substrates. Healthy controls were included on every 17% urea–polyacrylamide gel and visualized using Fujifilm FLA-
plate, every sample was duplicated, and duplicate value means 5000 phosphor imager.
were used in calculating the ELISA value ratio between inocu-
Small RNA library preparation and deep sequencing
lated and healthy controls.
Small RNAs were enriched using the mirVana miRNA Isolation
Segregation analysis of FanGuard transgene and
Kit (Invitrogen) following manufacturer instructions. Small RNA-
resistance in T1 and T2 generations
Seq libraries were prepared based on Illumina’s alternative v1.5
For detailed segregation analysis of selected events in T1 gen- protocol and a published method (Lu et al., 2007) and run on
eration, 25–35 seeds were germinated in pots. Leaf samples the Illumina’s GAIIx platform at the Genome Discovery Unit of
were collected, and DNA was extracted as described previ- Australian National University. WSMV sequences were assem-
ously, and genomic PCR was conducted to detect both bled with assistance from Dr Stephen Ohms, JCSMR, The
FGmiR395 and nptII amplicons. The cosegregation of resistance Australian National University.
with the transgene was assessed by challenging with WSMV
as described earlier. ELISA was performed 14 and 28 d p.i. in
Acknowledgements
T1 and only 28 d p.i. for T2 generations on inoculated plants.
Plant heights and symptoms were recorded at 7, 14, 21, and We are thankful to Dr Peter Waterhouse and Dr Ming-Bo Wang
28 d p.i. for their technical advice at various stages of these studies,
Mr. Zarman Mazhar Rizvi for his assistance with putting
Test inoculation to detect infectious virus in leaf sap
together various algorithms under one miR Mate, Drs. James
Sap was extracted at 28 d p.i. from each inoculated transgenic Petrie and Qing Liu for technical supervision in amiRNA detec-
plant to be tested, using 0.02 M potassium phosphate buffer at tion, and Dr Jun Fan, The John Curtin School of Medical
1 : 10 (1 g leaf per 10 mL buffer) concentration and mixed with Research, The Australian National University, for providing
celite abrasive and then inoculated onto three control BW26 excellent training and technical supervision in small RNA library
plants. This test inoculation (or back-inoculation) method was preparation. Dr Stephen Ohms is gratefully acknowledged for
used to evaluate the effectiveness of the FanGuard (FGmiR395) his assistance with bioinformatic analysis of small RNAs. The
transgene in eliminating viral replication and preventing the for- first author thankfully acknowledges AusAID for financial
mation of infectious particles. Symptoms were scored on the assistance as PhD studentship.
test-inoculated plants and leaf samples collected 28 d p.i. for
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