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Genetics of Plant Virus Resistance
Genetics of Plant Virus Resistance
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10.1146/annurev.phyto.43.011205.141140
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853;
email: [email protected], [email protected], [email protected]
INTRODUCTION
Viruses are among the most agriculturally important and biologically intriguing
groups of plant pathogens. Plant viral diseases cause serious economic losses in
many major crops by reducing yield and quality and often determine whether
and when a crop is planted in a cropping system. Although viruses are relatively
simple genetic entities, still largely unknown are the mechanisms by which the
many symptoms of disease are generated, and by which plants resist these effects.
In this chapter, we review the literature pertaining to genetic resistance to plant
viruses.
Genetic resistance is one of a number of approaches to protect crops from
virus infection that also include control of biotic vectors, use of virus-free seed or
plant materials, and cultural practices that minimize transmission (106). Resistant
varieties, where available, however, are still considered the most cost-effective
and reliable approach. Considerable time and cost may be involved in developing
varieties with the appropriate range of resistances. If resistance proves durable,
then the use of resistant crop varieties is clearly the preferred method to control
agricultural losses.
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The study of plant resistance genes (R genes), namely, plant genes in which
genetic variability occurs that alters the plants suitability as a host, also raises
many fundamental questions regarding the molecular, biochemical, cellular, and
physiological mechanisms involved in the plant-virus interaction and the evolution
of these interactions in natural and agricultural ecosystems. Over the past decade,
the cloning and analysis of numerous plant R genes (84, 134) have stimulated
attempts to develop unifying theories about mechanisms of resistance and susceptibility, and coevolution of plant pathogens and their hosts. The focus has been
mainly on monogenic dominant resistance to fungal and bacterial pathogens (84);
however, there is clear evidence that common mechanisms can be involved in virus
resistance.
Considerable progress is evident in the areas of R gene structure, identification
of molecular interactions important in plant viral infection, and elucidation of
mechanisms of resistance and viral evolution since the last Annual Review of plant
virus resistance genes was published in 1990 (64). For this review, we emphasize
the current status of R genes that have been characterized at a molecular level,
possible connections to down-stream host responses, and factors that may influence
durability of resistance in agricultural ecosystems.
TYPES OF RESISTANCE
Resistance to disease of plants has historically been divided into two major categories (64): nonhost resistance and host resistance. The former, which encompasses the case where all genotypes within a plant species show resistance or fail
to be infected by a particular virus, specifically signifies the state where genetic
polymorphism for susceptibility to a particular virus has not been identified in a
host taxon. Clearly, most plant species are resistant to most plant viruses. Susceptibility is the exception to the more general condition of resistance or failure
to infect. Although underlying mechanisms of nonhost resistance to viruses are
largely unknown and are likely as diverse for viruses as they are for other classes
of plant pathogens (152), improved understanding of the ways in which infection
fails in these interactions may be particularly important for breakthroughs in the
development of plants with durable broad-spectrum disease resistance.
Host resistance to plant viruses has been more thoroughly investigated, at least
in part because, unlike nonhost resistance, it is genetically accessible. This general
case, termed host resistance, specific resistance, genotypic resistance, or cultivar
resistance, occurs when genetic polymorphism for susceptibility is observed in
the plant taxon, i.e., some genotypes show heritable resistance to a particular
virus whereas other genotypes in the same gene pool are susceptible. In resistant
individuals, the virus may or may not multiply to some extent, but spread of the
pathogen through the plant is demonstrably restricted relative to susceptible hosts,
and disease symptoms generally are highly localized or are not evident.
The distinction between resistance to the pathogen and resistance to the disease
is important to articulate. Resistance to the pathogen typically leads to resistance
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possible mechanisms, where known, are included. Genes reported to show dominant inheritance are listed in Supplementary Table 1 (Follow the Supplemental Material link from the Annual Reviews home page at http://www.annualreviews.org);
genes reported to show recessive inheritance are listed in Supplementary Table 2
(Follow the Supplemental Material link from the Annual Reviews home page at
http://www.annualreviews.org).
This discussion highlights key observations drawn primarily from studies of
dicot species, the focus of most work to date. [For reviews on general trends
regarding inheritance of naturally occurring plant virus R genes, see (64, 65, 106,
175).] Within the dicots, information regarding several plant families, notably
the Solanaceae, Cucurbitaceae, and Leguminosae, predominate for historical and
agricultural reasons. R genes reported from monocot species are almost exclusively
limited to major crop species, e.g., barley, wheat, and rice.
More than 80% of reported viral resistance is monogenically controlled; the
remainder shows oligogenic or polygenic control. Only slightly more than half of
all reported monogenic resistance traits show dominant inheritance. In most but
not all (63) cases, dominance has been reported as complete. The heterozygote
may show a clearly different response from that of the homozygote, however this
is rarely checked carefully in inheritance studies. Where incomplete dominance
is observed, there are important implications for mechanisms that may involve
gene dosage effects. The relatively high proportion of recessive viral R genes is in
marked contrast to fungal or bacterial resistance where most reported resistance is
dominant.
About one third of the R genes listed in Supplentary Tables 1 and 2 (Follow the Supplemental Material link from the Annual Reviews home page at
http://www.annualreviews.org) have been tagged with molecular genetic markers
including RFLP, AFLP, RAPD, and various other PCR-based markers. Molecular
markers linked to R genes can be used for indirect selection via genotype, for locating R genes in plant genomes, and for gene isolation. Relatively few quantitative
trait loci (QTL) for plant viral resistance have been tagged or genetically mapped
(3, 12, 26, 30, 127).
Both pathogen and host taxa are composed of dynamic populations and therefore
unambiguous identification of host and pathogen genotypes is essential, ideally
with representative genotypes archived in a stable and reliable location such as the
USDA National Plant Germplasm System or the American Type Culture Collection. Historically, important collections of plant germplasm and viral cultures have
been maintained at universities and research institutes, where shifts in staffing and
resource allocation may put critical genetic resources at risk.
Within a host gene pool, there may be several to many independent sources
of resistance to a single virus or viral pathotype (a set of viral genotypes that
interact similarly with a set of host lines showing differential response) (81, 115,
159, 166). The advent of molecular methods has demonstrated that these R genes
may represent different loci with shared or independent evolutionary histories, or
different alleles at the same locus. Numerous early studies concluded that R genes
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and discussed in terms of R gene evolution and plant breeding (142). Two distinct
types of gene clusters are clearly evident. One type of R gene cluster contains a
set of genes, showing similar inheritance and resistance phenotypes that control
very closely related viral genotypes. Presumably this type of cluster arose from
the classic evolutionary trend of gene duplication, followed by divergence. This
mechanism classically results in genes with related but slightly altered function. A
notable example of this pattern occurs in Pisum sativum where recessive resistance
has been mapped to two R gene clusters on linkage groups II and VI. In LG II, six
very tightly linked monogenically inherited recessive loci (bcm, cyv1, mo, pmv,
sbm2, and wmv) for resistance to BCMV, Bean yellow mosaic virus (BYMV),
Clover yellow vein virus (ClYVV), Pea mosaic virus (PMV), Pea seed-borne
mosaic virus (PSbMV-L1), and WMV, respectively, occur in a cluster but are
separable by recombination. On LG VI, five distinct but very tightly linked loci
have been identified that overlap with the specificities observed for the cluster on
LG II. In this cluster, the loci cyv2, sbm1, sbm3, sbm4, and wlv confer resistance
to ClYVV, PSbMV-P1, PSbMV-L1 or -P2, PSbMV-P4, and White lupin mosaic
virus, respectively (172175).
The second type of R gene cluster contains viral resistance along with R genes
that control unrelated pathogens. These clusters may include a relatively large
number of R genes and span megabases of genomic sequence (76). This type of R
gene cluster occurs widely in monocots and dicots. For example, the wheat Bdv1
allele conferring resistance to Barley yellow dwarf virus (BYDV) is linked to fungal
R genes Lr34 and Yr18 (197). This type of cluster may, in fact, emerge as the most
common genomic context for plant disease R genes, as more complete information
about plant genome structure develops. Information regarding the content and
distribution of R gene clusters is probably best understood in the dicot family,
Solanaceae, the focus of major investments in genetic and genomic analyses. As
tomato, potato, pepper, tobacco, and many minor solanaceous crops are affected
by well-known viruses, extensive information is available regarding inheritance
and mapping of viral R genes and many other R genes (70, 76). A comprehensive
genome-wide analysis of R gene clusters and their distribution within a series of
crop genomes linked by comparative genetic mapping has been published for the
Solanaceae (76). This study clearly demonstrated that R gene clusters often occur
at homologous positions in related genomic regions, even in genera that diverged
tens of millions of years ago. Furthermore, across genera, clusters contained either
dominant R genes and QTL, or recessive genes and QTL, but not both dominant
and recessive genes. These clusters may therefore consist of evolutionarily related
sequences that diverged to control very different pathogen groups. When the sets
of pathogens controlled by R genes in a given cluster were compared across taxa,
no overlap of resistance specificities (i.e., the group of pathogen taxa controlled by
R genes in the cluster) was initially observed, except in two cases on chromosomes
4 and 11. Both of these involved Phytophthora pathogens, P. capsici in pepper and
P. infestans in potato. As additional R genes have been mapped, a striking pattern
that includes viral R genes has now emerged (Table 1). On potato chromosome
Hero (n)
R2 (p),
Ny (v)
Phyto5.2 (p)
Tomato
Potato
Pepper
Chr 5
Gro1 (n),
Rpi1, R9 (p)
Ph-1 (p)
Chr 7
Gro1.2 (n)
Ph-2 (p)
Chr 10
Gpa2 (n),
Rx1 (v)
Chr 12
References
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(b) bacteria, (f) fungi, (n) nematode, (p) Phytophthora spp., (v) virus.
Gene names are followed by letters designating the major pathogen group controlled:
Chr 11
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Positions are inferred, therefore the precise linkage relationships of these loci remain unclear in many cases.
Chr 4
Plant
Some cross-generic R gene groups that include virus resistance genes in Solanaceae
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TABLE 1
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12, the Rx1 gene conferring resistance to Potato virus X (PVX) is tightly linked to
the Gpa2 locus for resistance to the cyst nematode Globodera pallida (208). This
pair of specificities is also found very tightly linked in a second R gene cluster
on potato chromosome 5. This cluster on chromosome 5 also contains resistance
to P. infestans. When the inferred positions of all mapped R genes from tomato,
potato, and pepper are collected on one comparative genetic map, at least five R
gene groups can be discerned that contain a dominant R gene to Globodera and
a dominant gene for resistance to Phytophthora, several of which also contain
R genes or QTL for plant viruses including PVX, as mentioned above, TMV,
CMV, Tomato yellow leaf curl virus (TYLCV), and potato virus Y. A prediction,
based on this observation, but not yet confirmed, is that despite these striking
differences in pathogen specificity, the basic molecular structure of these genes
will be generally similar, even between relatively distantly related host genera.
This similarity may facilitate the molecular cloning and characterization of genes
that reside in these clusters. Insofar as this prediction has been examined within
a single R gene cluster in one plant taxon, e.g., Rx and Gpa2, it has been upheld
(208).
Dominant resistance is often, although not always, associated with the hypersensitive response (HR) (63), possibly due to the frequent use of HR as a diagnostic
indicator for field resistance by plant breeders. HR, induced by specific recognition
of the virus, localizes virus spread by rapid programmed cell death surrounding the
infection site, which results in visible necrotic local lesions. HR-mediated resistance is a common resistance mechanism for viruses and for other plant pathogens.
Because the extent of visible HR may be affected by gene dosage (37), genetic
background, environmental conditions such as temperature, and viral genotype,
etc., schemes that classify or name virus R genes based on presence or absence of
HR may obscure genetic relationships (see discussion of the Ry-mediated resistance to PVY in potato below).
Over the past 10 years significant advances have been made in the understanding of the molecular basis of the HR-mediated resistance. More than 40 plant
R genes showing monogenic dominant inheritance have been cloned. Several of
these confer resistance to plant viruses (134). These include N for resistance to
TMV in tobacco (211), Rx1 and Rx2 for resistance to PVX in potato (14, 16), Sw5
for resistance to Tomato spotted wilt virus (TSWV) in tomato (21), and RTM1,
RTM2 to TMV (34, 212), and HRT for resistance to Turnip crinkle virus (TCV)
(38), RCY1 for resistance to CMV (204), respectively, in Arabidopsis (see below).
In contrast to dominant R genes, many recessive R genes appear to function
at the single cell level or affect cell-to-cell movement. More than half of the
recessive R genes identified to date confer resistance to potyviruses, members of
the largest and perhaps the most economically destructive family of plant viruses
(195). This may be a consequence of some bias that affects the scope of our
knowlege, or may be due to specific features of potyvirus biology. In general,
considerably less is known regarding the mechanisms that account for recessively
inherited resistance mechanisms. Several recessive R genes have recently been
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cloned and/or characterized including pvr1 (=pvr2 ), mo11 , sbm1, and rym4/5 (67,
102, 154, 186, 215), as described below.
Despite the possibility of bias affecting the comprehensiveness of available
data, trends can be noted in the types of genetic resistance available to control
viruses belonging to specific plant virus families. For example, resistance to CMV
often shows complex inheritance. Very few monogenically inherited R genes are
known (22), despite the enormous host range of this virus and its economic impact.
Most resistance or tolerance of economic significance to this pathogen is quantitatively inherited. In contrast, resistance to tobamoviruses is widespread and is often
monogenic dominant. For some viral families of extreme agricultural importance,
most notably the Geminiviridae, naturally occurring genetic resistance can be difficult to locate, and is often highly strain-specific and/or quantitatively inherited
(i.e., each gene has a relatively slight positive effect on host response), making
resistant varieties extremely difficult or impossible to develop without molecular
markers and/or transgenic approaches.
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Suppression
Knock-out
Pectin methylesterase
Acetyl transferase
Plastid-localized stearoyl-ACP
desaturase
Translation initiation factor,
eIF(iso)4E
Essential constituent of
replication complex
Formation of RNA replication
complex
SUMO-conjugating enzyme
(32, 33)
(222224)
(222224)
(29)
(207)
(92, 93)
(121)
(28, 136)
(193)
References
a
CLCV, Cabbage leaf curl geminivirus; CMV, Cucumber mosaic virus; TEV, Tobacco etch virus; TGMV, Tomato golden mosaic virus; TMV, Tobacco mosaic virus; TuMV, Turnip mosaic
virus.
PME
cum2-1
TCV
Knock-out
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Systemic movement
Arabidopsis TMV
cum1-1
Suppression
Knock-out
tom2A
NbSCE1
Knock-out
tom1
Cell-to-cell movement
Arabidopsis CMV
TGMV
Knock-out
1sp1
Over expression
Knock out
Gene
expression
control
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Nicotiana
TEV
TuMV
TMV
Virusa
Gene or
protein
Examples of host factors involved in plant viral life cycles and resistance mechanisms
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TABLE 2
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observations from pepper, lettuce, pea, and tomato that implicate host translation
factors in resistance to potyviruses and CMV (102, 154, 163, 167, 186).
The second type of mechanism that can result in resistance at the single-cell
level involves an active resistant response to virus infection that occurs rapidly
enough to limit virus replication before cell-to-cell movement occurs. Plants with
this response may show no symptoms or extremely limited necrosis (pinpoint lesions). Well-known examples of this response include resistance controlled by
Tm-1 for TMV in tomato (147, 209), the R gene against CPMV in cowpea (171),
Nx and Rx for PVX and Ry for Potato virus Y (PVY) in potato (199), Sw5 in
tomato (21), and Rsv1 in soybean (80). This response has been studied in some
detail using the Ry gene for ER in potato as a model. Plants carrying the Ry gene do
not show any visible symptoms when challenged with PVY. Virus accumulation
is not detected in the inoculated leaves by either RNA hybridization or ELISA.
Furthermore, protoplasts isolated from resistant genotypes do not support viral
replication. Because HR was not evident, it was postulated that these genes might
encode inhibitors of virus accumulation (64). However, there may be no mechanistic distinction between reactions previously categorized as ER and HR. When
each of the PVY-encoded proteins was expressed in leaves of PVY-resistant plants,
the nuclear inclusion of a protease (NIaPro) induced HR, demonstrating that the
HR mechanism may be a component of the ER response. The same trends hold
true for Rx/PVX-CP in potato (14), Sw5 in tomato (21), and Rsv in soybean (79).
For elicitation of Ry-mediated resistance, the protease domain of PVY NIaPro,
specifically the integrity of the protease active site, is required (140). Mutant analysis of NIaPro, however, demonstrated that NIa protease activity is not sufficient
for elicitation of resistance because elicitor-defective mutants still retained a high
level of protease activity (141). The location of Ry in a genomic region containing
many NBS-LRR sequences is consistent with the possibility that Ry may encode
a NBS-LRR-type protein typical of genes controlling HR (82).
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for replication and export progeny genomes back to the cytoplasm for translation
and virion assembly. The viral proteins required for these functions are known,
at least for some viruses. For example, the nuclear import and export of bipartite
geminivirus DNA is mediated by the BV1 (BR1) protein (27), but interference
with these processes by host factors resulting in resistance has not yet been reported. With respect to intercellular movement, it is well established that movement
proteins (MP), identified for most families of both DNA and RNA plant viruses
[for reviews, see (42, 73, 132, 188)], perform dedicated functions required for
cell-to-cell movement by modifying pre-existing pathways in the plant for macromolecular movement such that viral material can translocate between plant cells
(27, 117). In the case of potyviruses, which do not encode a dedicated MP, the
movement functions have been allocated to several proteins, including CP, HCPro, the cylindrical inclusion (CI) protein, and the genome-linked protein (VPg)
(180). In mutant viruses defective in these proteins, movement from the initially
infected cell to adjacent noninfected cells did not occur.
A number of mutations in host genes are known that prevent cell-to-cell movement of plant viruses. The Arabidopsis cum1 and cum2 mutations inhibit CMV
movement (223, 224). In protoplasts prepared from plants homozygous for these
alleles, CMV RNA and CP accumulate to wild-type levels, but the accumulation of
the CMV 3a protein, necessary for cell-to-cell movement of the virus, is strongly
reduced. Positional cloning demonstrated that CUM1 and CUM2 encode eukaryotic translation initiation factors 4E and 4G, respectively (222). Similar results
for members of a different viral family have been obtained from tobacco, pepper, and pea. In tobacco, the movement of Tobacco vein mottling virus and PVY
is controlled by the recessive gene va (71). In pepper and pea, pvr11 (formerly
pvr21 ) and sbm1 were identified as mutations at a locus encoding eIF4E (67, 186).
A functional analysis of the product of the dominant allele suggested a function
for eIF4E in cell-to-cell movement, in addition to its proposed role in viral RNA
replication or translation (102, 121).
The HR also serves to disrupt cell-to-cell movement of plant viruses. Recognition of the viral elicitor results in the induction of a cascade of host defense
responses that include oxidative H2 O2 bursts and up-regulation of hydrolytic enzymes, PR proteins, and callose and lignin biosynthesis. As a consequence, viral
movement may be limited to a small number of cells, illustrated by such classic
examples as the tobacco N gene (160) and the tomato Tm-2 and Tm-22 alleles
(147). Protoplasts isolated from the plants carrying these R genes allowed replication of TMV; no cell death was observed. Despite the strong correlation of HR
and disease resistance, necrotic cell death is now thought to be an ancillary consequence of the resistant response, not necessary for pathogen suppression. For
example, in Phaseolus vulgaris carrying the I allele to BCMV, a continuum of viral
infection phenotype responses that range from no necrosis to a lethal systemic response can be manipulated by allele dosage and temperature (37). The defense no
death (dnd1) mutant in Arabidopsis is another example of independent resistance
and HR (225), consistent with results from several viral-host systems including
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but the mechanism by which TEV movement in this system is restricted is not
understood.
A. thaliana
A. thaliana
A. thaliana
A. thaliana
S. lycopersicum
Sw5
HRT
RTM1
RTM2
RCY1
Tm22
P. sativum
sbm1
Replication
Tolerance
Replication
Cell-to-cell movement
Systemic movement
Systemic movement
Replication
Candidate approach
Candidate approach
Candidate approach
Transposon tagging
Positional cloning
Positional cloning
Positional cloning
Positional cloning
Positional cloning
Positional cloning
Positional cloning
Transposon tagging
Cloning method
eIF4E
eIF4E
eIF4E
CC-NBS-LRR
CC-NBS-LRR
LZ-NBS-LRR
CC-NBS-LRR
CC-NBS-LRR
CC-NBS-LRR
TIR-NBS-LRR
Predicted
domains
2004
2003
2002
2003
2002
2000
2000
2000
2000
2000
1999
1994
Year
isolated
(67)
(154)
(102, 186)
(116)
(204)
(212)
(34)
(38)
(21)
(16)
(14)
(211)
References
CMV, Cucumber mosaic virus; LMV, Lettuce mosaic virus; PSbMV, Pea seed borne mosaic virus; PVY, Potato virus Y; PVX, Potato virus X; TCV, Turnip crinkle virus; ToMV, Tomato
mosaic virus; TEV, Tobacco etch virus; TMV, Tobacco mosaic virus; TSWV, Tomato spotted wilt virus.
PSbMV Replication
LMV
PVY
ToMV
CMV
TEV
TEV
TCV
TSWV
PVX
Replication
Resistance mechanism
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L. sativa
mo11
mo12
C. annuum
S. esculentum
Rx2
PVX
TMV
Virusa
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pvr1, pvr1
pvr11
S. tuberosum
Rx1
N. tabacum
S. tuberosum
Plant
AR
Gene
16:42
TABLE 3 Naturally occurring plant virus resistance genes for which nucleotide sequences are known
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domains such that they are no longer held inactive (P. Moffet & G. Rairdan, personal communication). In experiments designed to determine the biochemistry of
Rx function, segments of the protein were expressed independently in an elegant
system where phenotypic response could be easily assayed. PVX CP-dependent
HR was observed after fragments of Rx (CC and NBS-LRR domains) and PVXCP were expressed transiently in N. benthamiana via agroinfiltration (143). These
results indicate that a functional Rx protein can be reconstituted through physical
interactions between domains, even when the domains are expressed in different
molecules. Furthermore, PVX CP disrupted the interaction between these Rxderived domains. The current model suggests that CP recognition induces sequential conformational changes in Rx, disrupting intramolecular interactions, thereby
activating Rx-mediated signaling (143).
Experiments using virus-induced gene silencing (VIGS) showed that Rxmediated resistance does not require EDS1 (164) and RAR1. Bieri et al., however,
have shown that silencing Rar1 actually reduces the levels of Rx (18). Therefore,
Rar1 is likely a cochaperone required to varying degrees by different R proteins
(P. Moffet, personal communication). Silencing of tobacco MAP kinase kinase
kinase (MAPKKK) interferes with the function of the Rx gene (99, 100). Similar to results described above for the N gene, silencing SGT1 also compromised
Rx-mediated resistance (165), and HSP90 is required, presumably acting as a
cochaperone to stabilize Rx (129) (Figure 2B).
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of virus infection, and restriction of virus to the inoculated leaves. This resistance
response in C24 is controlled by a single dominant RCY1 (resistance to cucumber
mosaic virus strain Y) gene. The analysis of a series of chimeric viruses constructed
from the avirulent isolate CMV-Y and the virulent isolate CMV-B2 revealed that
the coat protein of CMV-Y serves as the avirulent determinant of resistance in
C24 (204). The RCY1 gene has been mapped in Arabidopsis within the MRC-5
region on chromosome 5, in which nine other defined resistance genes (RAC3,
RPS4, HRT, TTR1, and five distinct RPP loci) are located (204). Fine mapping
and sequence comparison of this region from C24 and a CMV-Y susceptible C24
mutant identified the RCY1 gene encoding 104-kDa CC-NBS-LRR type protein.
RCY1 is allelic to the resistance gene RPP8 against Peronospora parasitica in
the ecotype Lansberg erecta and HRT against TCV in the ecotype Dijon-17. The
RCY1-conferred resistance requires both salicylic acid and ethylene signaling but
not jasmonic acid signaling (202, 203).
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(102, 121). The role of eIF4E and eIF(iso)4E in the potyvirus infection cycle is not
known. However, the negative effects of mutations in these host factors on the infectivity of various potyviruses in various host plants imply that the effect of these
host factors upon potyvirus infection cycle is probably conserved. The common
feature linking pvr1/2, sbm1, and mo1 is that the viral avirulence determinants map
to a specific region in the VPg, the protein covalently linked to the 5 end of the viral
RNA and perhaps mimicking the m7 G cap of eukaryotic mRNAs (19, 104, 105,
148). In eukaryotic cells, eIF4E binds to the m7 G cap as the first step in recruiting
mRNA into the translational preinitiation complex. A similar role for eIF4E might
be predicted when potyvirus infects plant cells (102). Although eIF4E has never
been shown to bind VPg in infection, VPg or its precursor VPg-Pro interacted with
eIF4E or eIF(iso)4E in yeast two-hybrid and in vitro pull-down assays (102, 122,
190, 217).
In the 1950s, pvr1 and pvr2 in pepper (Capsicum annuum and C. chinense)
were initially considered allelic but then two loci were distinguished because of
differences in resistance spectra. The allele formerly known as pvr21 is effective
only against PVY-0, and pvr22 is effective against both PVY-0 and PVY-1. The
allele pvr1 was relatively broad in effect, controlling TEV, PepMoV, and PVY)
(115). We now know that only one locus is involved, pvr1, at which at least three
resistance alleles and two susceptibility alleles occur (186). Point mutations in
eIF4E that fall near critical positions for cap-binding function abolish interaction
with TEV VPg and determine the range of isolates across three potyviral species
that are controlled (102). Two of these alleles when homozygous block accumulation of the virus in protoplasts (43, 150). The narrower spectrum allele retards
movement of the virus through the plant but has no effect at the protoplast level
(5). In a fourth case, Pepper veinal mottle virus, it appears eIF4E and probably
eIF(iso)4E must be mutated to control the virus (102).
In lettuce, mo11 and mo12 control common isolates of LMV. In the homozygous
state, mo11 confers resistance, i.e., absence of LMV accumulation; mo12 results in
reduced LMV accumulation and lack of symptoms (180). As observed in pepper,
allelic variants of eIF4E, Ls-eIF4E0 , Ls-eIF4E1 , and Ls-eIF4E2 contained point
mutations that result in predicted amino acid substitutions near the cap-binding
pocket of the protein (154).
In pea, sbm1 confers resistance to PSbMV pathotypes P1 and P4 as described
above, now known to be a consequence of mutations in an eIF4E homolog (67).
Transient expression of susceptible-eIF4E in a resistant background complemented
PSbMV infection by supporting both virus multiplication in primary target cells
and cell-to-cell movement. Processes that account for cell-to-cell movement are
not well understood, and therefore it is difficult to speculate on a plausible role
for eIF4E in virus movement. Nevertheless, in both the pepper and pea systems,
variants at an eIF4E locus result in inhibition of movement, as well as extreme
resistance. Again, point mutations in the resistant eIF4E allele are located in and
around the cap-binding pocket. Similar to pvr1, cap-binding ability of the eIF4E
protein is abolished in the resistant eIF4E variant. Recently, rym4/5 for resistance
to BaYMV in barley has also been shown to encode eIF4E (215). In contrast
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mo1
mo12
Lettuce
PVA-M
PSbMV
PSbMV
Nicandra physaloides
Pea
VPg
P3 and 6K1 cistron
62 K and VPg
3 half of genome
Replication
Systemic movement
Replication
movement
HR
Replication
2a polymerase
3 portion of MNSV genome
Gene VI product
Replication
HR
P3
P3
CI
Not available
Not avialable
Four aa
Not available
3 UTR
Single aa
Not available
Single aa
Single aa
Single aa
Single aa
Not available
Not available
Not available
(105)
(101)
(177)
(178)
(45)
(108)
(109, 191)
(98)
(97)
(96)
(69)
(157, 218)
(204)
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sbm-1
sbm-2
MNSV
Cucumis melo L.
LMV
CMV
nsv
Cowpea
CaMV
C. amaranticolor
HR
CI
HR
HR
HR
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TuRBO1,
TuMV
TuRBO1b
TuRBO3
TuMV
TuRBO4,
TuMV
TuRBO5
Brassica napus
BV1 protein
Coat protein
Coat protein
BDMV
Bdm
Bean
TCV
CMV
HRT
RCY1
References
YEAM
Arabidopsis
Avirulence gene
Plant
Resistancebreaking
change
KANG
Reported mesistance
mechanism
AR
Resistance
gene
Virusa
604
TABLE 4
JAHN
ToMV
N
N
va
Tobacco
Tobacco
Rsv1
Soybean
HR
Single aa
Mutiple aa
Two aa
Two aa
Not available
Several aa
Single aa
Single aa
Single aa
Single aa
Two aa
Not known
Not available
Single aa
(57)
(148)
(87)
(138)
(139, 210)
(35, 192)
(162)
(155)
(110, 187)
(133)
(189)
(15)
(140)
a
BYMV, Bean yellow mosaic virus; CaMV, Cauliflower mosaic virus; CMV, Cucumber mosaic virus; LMV, Lettuce mosaic virus; MNSV, Melon necrotic spot virus; PSbMV, Pea seed
borne mosaic virus; PVA-M, Potato virus A strain M; PVY, Potato virus Y; PVX, Potato virus X; TBSV, Tomato bush stunt virus; TCV, Turnip crinkle virus; TuMV, Turnip mosic virus;
ToMV, Tomato mosaic virus; TMV, Tobacco mosaic virus; TVMV, Tobacco vein mottling virus; TSWV, Tomato spotted wilt virus; SMV, Soybean mosaic virus.
VPg
M RNA
PVY
TSWV
Replication
HR
Cell-to-cell
movement
HR
Cell-to-cell
HR
HR
HR
Replication/HR
Replication
HR
Movement
Replication
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SMV
Replicase
30 kD movement protein
ToMV
ToMV
Tm-1
Tm-2,
Tm-22
pot-1
Sw-5
Tomato
TBSV
N. clevelandii
Coat protein
25 K movement protein
Coat protein
Coat protein
NIa protease
Coat protein
VPg
AR250-PY43-23.tex
TMV
PVY
PVX
PVX
PVX
PVX
Nb
Nx
Rx1, Rx2
Ry
Potato
TMV
PVY
L1 , L2 , L3
pvr11
pvr12
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Pepper
605
606
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interaction of MNSV with melon (45). In the eight cases where the viral elicitor is protein, host recognition of these viral proteins that serve as pathogenicity
determinants is altered by amino acid substitutions that do not appear to significantly compromise the function of the protein in pathogenesis. For other microbial
pathogens, there often appears to be a fitness penalty association with mutations
from avirulence to virulence (128). Although this type of fitness/avirulence tradeoff has not been noted generally for plant viruses, there are specific examples where
this occurs. Isolates of ToMV capable of overcoming Tm22 gene were found to
multiply poorly on resistant plants (116). If the Tm22 resistant protein targets a
domain of the viral MP such that this protein is mutated to overcome resistance,
these mutations could result in diminished fitness.
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TABLE 5
607
Resistance genes
Host
Virus
Reported
mechanisms
Selected
references
Tm-22
Tomato
ToMV
Impaired fitness
(116)
Sw-5
Tomato
TSWV
Multiple aa changes
(21)
sbm1 + sbm2
Soybean
SMV
Multiple aa changes
(86)
TuRB03 + TuRBO4
Turnip
TuMV
Multiple aa changes
(97)
Tobacco
TMV
Multiple aa changes
(161, 162)
Rx
Potato
PVX
Replication
(1, 119)
Ry
Potato
PVY
Replication
(86)
pvr1
Pepper
PVY, TEV
Replication
(150)
Common bean
BCMV
Replication
(114)
Tu
Lettuce
TuMV
Unknown
(227)
BCMV; Bean common mosaic virus, PVY; Potato virus Y, PVX; Potato virus X, Tobacco etch virus; TEV, TuMV; Turnip
mosaic virus, ToMV; Tomato mosaic virus, TMV; Tobacco mosaic virus, TSWV; Tomato spotted wilt virus, SMV; Soybean
mosaic virus.
608
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host and viral genes and genomes have all contributed to significant shifts in our
understanding of the structure and function of genetic resources for plant virus
resistance. Nonetheless, our knowledge of plant genetic variability relevant to viral interactions remains far from comprehensive. To date, research efforts have
focused disproportionately on a few viral and plant families, with strong bias toward viruses with RNA genomes that infect dicots and host responses that show
monogenic control. Continued evaluation of plant genetic diversity with respect
to interactions with viruses is needed, as is characterization of the inheritance of
contrasting responses in diverse host species.
A striking area of progress has been the identification at the molecular level of
a number of viral R genes from a wide array of plants. In contrast to early speculation that mutations that result in resistance would occur in many different types of
genes, these studies to date have shown a remarkable degree of conservation evident in both monocot and dicot hosts for both dominant and recessive resistance.
The extent to which this will remain true is unknown as more comprehensive information drawn from diverse host-pathogens interactions accumulates. The trends
resolved to date, however, are very clear. In plant viral resistance showing dominant
inheritance, most of the genes isolated and characterized to date fall into a series
of related categories that involve proteins containing NBS-LRR domains, similar
to those that control a wide array of other plant pathogens. In recessively inherited
resistance, 7 of 9 examples known to date affect loci that encode 1 of 2 isoforms of
the eukaryotic translation factor eIF4E. The degree of conservation observed will
clearly accelerate the pace of gene discovery via candidate gene approaches, e.g.,
the bc-u, bc-1, bc-2, and bc-3 system in Phaseolus vulgaris and other systems in
which one or more recessive loci are involved in resistance to RNA viruses. These
systems represent clear opportunities to examine the extent to which eIF4E-related
sequences may serve as candidates for diverse recessive R genes.
Given this observation of striking overall conservation among many R genes
identified to date, how these genes actually function to produce resistance becomes
very compelling because insights drawn from one system are likely to be broadly
applicable. Equally compelling, and perhaps of considerably more applied significance, will be research directions that aim to elucidate the sources of specificity
in these interactions.
Progress has lagged in the identification of R genes that control plant viruses
with genomes comprised of DNA, and that contribute to quantitatively inherited
(polygenically controlled) viral resistance or tolerance. One promising area of
current activity is the identification of host proteins that interact with viral genes
or gene products during infection. This work is primarily aimed at understanding
mechanisms of viral infection and pathogenesis, rather than viral resistance and
has exploded with the advent of such techniques as yeast two- and three-hybrid
assays and those that canvas for specific protein-protein interactions. Numerous
proteins identified this way using viral gene products as bait have relevance to the
viral life cycles and pathogenicity, even in viral systems about which relatively
little is known. An important limitation to these studies is the degree to which an
interaction identified in yeast or in vitro can be demonstrated in planta. The next
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generation of candidate genes for viral R genes and QTL will undoubtedly come
from these studies.
A major discovery of the past decade resulting from these types of studies
with profound implications in virology, plant biology, and biotechnology is gene
silencing and its role in pathogenesis and resistance. In addition to elucidating
central aspects of cellular metabolism with profound effects on gene expression
and regulation, these studies have allowed for the development of vectors, based
on viral genomes, most notably the tobravirus Tobacco rattle virus, for viralinduced gene silencing (VIGS) (10, 125). These tools provide the basis for powerful
genetic approaches through which genes are identified by the phenotypes produced
when they are silenced. This approach, known as reverse genetics, is becoming
increasingly important in projects involving high-throughput functional genomic
analyses of plant genomes.
Despite landmark advances over the past 15 years with respect to both fundamental understanding of the structure and, to some extent function, of plant viral
R genes, and major milestones in their applications in agriculture, much remains
to be done. With expanding agricultural monocultures, particularly in the developing world, have come rising threats from viral pathogens for which the necessary
resistance resources are not known. Although virus resistance was among the first
objectives addressed by transgenic crops in the United States, the ways in which
mutations in plant genes interfere with viral infection and biology of resistance
specificity and durability are still poorly understood. Elucidation of the mechanisms by which broadly effective and durable host-resistant responses can be
induced by a wide array of plants, and the ways in which these responses may
be deployed in agriculture will surely be a major focus of investigation for the
future.
ACKNOWLEDGMENTS
We gratefully acknowledge the contributions of George Bruening, Christiane Gebhardt, Andy Jackson, Peter Moffett, and John Murphy who provided critical review
of this chapter; Helen Griffiths for assistance with manuscript preparation; and
Rosario Provvidenti for helpful discussions. Support was provided in part from
USDA IFAFS Award No. 2001-52100-113347 and NSF Plant Genome Award No.
0218166.
The Annual Review of Phytopathology is online at
http://phyto.annualreviews.org
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Figure 2 (A) Structure and location of the six main classes of plant disease resistance proteins. Virus resistance genes are indicated in bold letters. Classes 15 are
defined based on combinations of a limited number of structural motifs. Class 6
includes R proteins that do not fit into classes 15. LRR, leucine-rich repeat; NBS,
predicted nucleotide binding site; CC, predicted coiled coil domain; TIR, Toll and
interleukin 1 receptor domain. (B) Downstream components of virus resistance
genes. Left panel is modified from (124). Question marks indicate unknown signaling steps.
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Annual Reviews
AR250-FM
CONTENTS
FRONTISPIECE, Robert K. Webster
BEING AT THE RIGHT PLACE, AT THE RIGHT TIME, FOR THE RIGHT
REASONSPLANT PATHOLOGY, Robert K. Webster
FRONTISPIECE, Kenneth Frank Baker
KENNETH FRANK BAKERPIONEER LEADER IN PLANT PATHOLOGY,
R. James Cook
REPLICATION OF ALFAMO- AND ILARVIRUSES: ROLE OF THE COAT PROTEIN,
John F. Bol
RESISTANCE OF COTTON TOWARDS XANTHOMONAS CAMPESTRIS pv.
MALVACEARUM, E. Delannoy, B.R. Lyon, P. Marmey, A. Jalloul, J.F. Daniel,
J.L. Montillet, M. Essenberg, and M. Nicole
PLANT DISEASE: A THREAT TO GLOBAL FOOD SECURITY, Richard N. Strange
and Peter R. Scott
VIROIDS AND VIROID-HOST INTERACTIONS, Ricardo Flores,
Carmen Hernandez, A. Emilio Martnez de Alba, Jose-Antonio Dar`os,
and Francesco Di Serio
PRINCIPLES OF PLANT HEALTH MANAGEMENT FOR ORNAMENTAL PLANTS,
Margery L. Daughtrey and D. Michael Benson
THE BIOLOGY OF PHYTOPHTHORA INFESTANS AT ITS CENTER OF ORIGIN,
Niklaus J. Grunwald and Wilbert G. Flier
PLANT PATHOLOGY AND RNAi: A BRIEF HISTORY, John A. Lindbo
and William G. Doughtery
CONTRASTING MECHANISMS OF DEFENSE AGAINST BIOTROPHIC AND
NECROTROPHIC PATHOGENS, Jane Glazebrook
LIPIDS, LIPASES, AND LIPID-MODIFYING ENZYMES IN PLANT DISEASE
RESISTANCE, Jyoti Shah
PATHOGEN TESTING AND CERTIFICATION OF VITIS AND PRUNUS SPECIES,
Adib Rowhani, Jerry K. Uyemoto, Deborah A. Golino,
and Giovanni P. Martelli
MECHANISMS OF FUNGAL SPECIATION, Linda M. Kohn
xii
1
25
39
63
83
117
141
171
191
205
229
261
279
vii
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CONTENTS
309
337
361
395
437
459
491
523
545
581
623
661