Genetic background matters: a plant-virus gene-for-gene interaction is strongly influenced by genetic contexts

The Naturally Occurring Amino Acid Substitution in the VPg α1-α2 Loop Breaks eIF4E-Mediated Resistance to PRSV by Enabling VPg to Re-Hijack Another eIF4E Isoform eIF(iso)4E in Watermelon

Plant resistance, which acts as a selective pressure that affects viral population fitness, leads to the emergence of resistance-breaking virus strains. Most recessive resistance to potyviruses is related to the mutation of eukaryotic translation initiation factor 4E (eIF4E) or its isoforms that break their interactions with the viral genome-linked protein (VPg). In this study, we found that the VPg α1-α2 loop, which is essential for binding eIF4E, is the most variable domain of papaya ringspot virus (PRSV) VPg. PRSV VPg with the naturally occurring amino acid substitution of K105Q or E108G in the α1-α2 loop fails to interact with watermelon (Citrullus lanatus) eIF4E but interacts with watermelon eIF(iso)4E instead. Moreover, PRSV carrying these mutations can break the eIF4E-mediated resistance to PRSV in watermelon accession PI 244019. We further revealed that watermelon eIF(iso)4E with the amino acid substitutions of DNQS to GAAA in the cap-binding pocket could not interact with PRSV VPg with natural amino acid substitution of K105Q or E108G. Therefore, our finding provides a precise target for engineering watermelon germplasm resistant to resistance-breaking PRSV isolates.

Within-plant genetic drift to control virus adaptation to host resistance genes

Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These PVY populations exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term.

Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis

Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.

Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses

Potyviruses are the largest group of plant-infecting RNA viruses that affect a wide range of crop plants. Plant resistance genes against potyviruses are often recessive and encode translation initiation factors eIF4E. The inability of potyviruses to use plant eIF4E factors leads to the development of resistance through a loss-of-susceptibility mechanism. Plants have a small family of eIF4E genes that encode several isoforms with distinct but overlapping functions in cell metabolism. Potyviruses use distinct eIF4E isoforms as susceptibility factors in different plants. The role of different members of the plant eIF4E family in the interaction with a given potyvirus could differ drastically. An interplay exists between different members of the eIF4E family in the context of plant-potyvirus interactions, allowing different eIF4E isoforms to modulate each other's availability as susceptibility factors for the virus. In this review, possible molecular mechanisms underlying this interaction are discussed, and approaches to identify the eIF4E isoform that plays a major role in the plant-potyvirus interaction are suggested. The final section of the review discusses how knowledge about the interaction between different eIF4E isoforms can be used to develop plants with durable resistance to potyviruses.

Virus Evolution Faced to Multiple Host Targets: The Potyvirus-Pepper Case Study

The wealth of variability amongst genes controlling immunity against potyviruses in pepper (Capsicum spp.) has been instrumental in understanding plant-virus co-evolution and major determinants of plant resistance durability. Characterization of the eukaryotic initiation factor 4E1 (eIF4E1), involved in mRNA translation, as the basis of potyvirus resistance in pepper initiated a large body of work that showed that recessive resistance to potyviruses and other single-stranded positive-sense RNA viruses resulted from mutations in eukaryotic initiation factors in many plant crop species. Combining mutations in different eIF4Es in the same pepper genotype had complex effects on the breadth of the resistance spectrum and on resistance durability, revealing a trade-off between these two traits. In addition, combining eIF4E1 mutations with a quantitatively resistant genetic background had a strong positive effect on resistance durability. Analysing the evolutionary forces imposed by pepper genotypes onto virus populations allowed identifying three key factors improving plant resistance durability: the complexity of mutational pathways involved in virus adaptation to the plant resistance, the decrease of competitivity induced by these mutations on the virus and the intensity of genetic drift imposed by plant genotypes on the virus during its infection cycle.

Narcissus Plants: A Melting Pot of Potyviruses

Our paper presents detailed evolutionary analyses of narcissus viruses from wild and domesticated Narcissus plants in Japan. Narcissus late season yellows virus (NLSYV) and narcissus degeneration virus (NDV) are major viruses of Narcissus plants, causing serious disease outbreaks in Japan. In this study, we collected Narcissus plants showing mosaic or striped leaves along with asymptomatic plants in Japan for evolutionary analyses. Our findings show that (1) NLSYV is widely distributed, whereas the distribution of NDV is limited to the southwest parts of Japan; (2) the genomes of NLSYV isolates share nucleotide identities of around 82%, whereas those of NDV isolates are around 94%; (3) three novel recombination type patterns were found in NLSYV; (4) NLSYV comprises at least five distinct phylogenetic groups whereas NDV has two; and (5) infection with narcissus viruses often occur as co-infection with different viruses, different isolates of the same virus, and in the presence of quasispecies (mutant clouds) of the same virus in nature. Therefore, the wild and domesticated Narcissus plants in Japan are somewhat like a melting pot of potyviruses and other viruses.

Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic

Scallion mosaic virus (ScaMV) belongs to the turnip mosaic virus phylogenetic group of potyvirus and is known to infect domestic scallion plants (Allium chinense) in China and wild Japanese garlic (Allium macrostemon Bunge) in Japan. Wild Japanese garlic plants showing asymptomatic leaves were collected from different sites in Japan during 2012–2015. We found that 73 wild Japanese garlic plants out of 277 collected plants were infected with ScaMV, identified by partial genomic nucleotide sequences of the amplified RT-PCR products using potyvirus-specific primer pairs. Sixty-three ScaMV isolates were then chosen, and those full genomic sequences were determined. We carried out evolutionary analyses of the complete polyprotein-coding sequences and four non-recombinogenic regions of partial genomic sequences. We found that 80% of ScaMV samples have recombination-like genome structure and identified 12 recombination-type patterns in the genomes of the Japanese ScaMV isolates. Furthermore, we found two non-recombinant-type patterns in the Japanese population. Because the wild plants and weeds may often serve as reservoirs of viruses, it is important to study providing the exploratory investigation before emergence in the domestic plants. This is possibly the first epidemiological and evolutionary study of a virus from asymptomatic wild plants.

First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process

Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity.

Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants

The efficiency of plant major resistance genes is limited by the emergence and spread of resistance-breaking mutants. Modulation of the evolutionary forces acting on pathogen populations constitutes a promising way to increase the durability of these genes. We studied the effect of four plant traits affecting these evolutionary forces on the rate of resistance breakdown (RB) by a virus. Two of these traits correspond to virus effective population sizes (N_e ) at either plant inoculation or during infection. The third trait corresponds to differential selection exerted by the plant on the virus population. Finally, the fourth trait corresponds to within-plant virus accumulation (VA). These traits were measured experimentally on Potato virus Y (PVY) inoculated to a set of 84 pepper doubled-haploid lines, all carrying the same pvr2³ resistance gene, but having contrasting genetic backgrounds. The lines showed extensive variation for the rate of pvr2³ RB by PVY and for the four other traits of interest. A generalized linear model showed that three of these four traits, with the exception of N_e at inoculation, and several pairwise interactions between them had significant effects on RB. RB increased with increasing values of N_e during plant infection or VA. The effect of differential selection was more complex because of a strong interaction with VA. When VA was high, RB increased as the differential selection increased. An opposite relationship between RB and differential selection was observed when VA was low. This study provides a framework to select plants with appropriate virus evolution-related traits to avoid or delay RB.

Role of the Genetic Background in Resistance to Plant Viruses

In view of major economic problems caused by viruses, the development of genetically resistant crops is critical for breeders but remains limited by the evolution of resistance-breaking virus mutants. During the plant breeding process, the introgression of traits from Crop Wild Relatives results in a dramatic change of the genetic background that can alter the resistance efficiency or durability. Here, we conducted a meta-analysis on 19 Quantitative Trait Locus (QTL) studies of resistance to viruses in plants. Frequent epistatic effects between resistance genes indicate that a large part of the resistance phenotype, conferred by a given QTL, depends on the genetic background. We next reviewed the different resistance mechanisms in plants to survey at which stage the genetic background could impact resistance or durability. We propose that the genetic background may impair effector-triggered dominant resistances at several stages by tinkering the NB-LRR (Nucleotide Binding-Leucine-Rich Repeats) response pathway. In contrast, effects on recessive resistances by loss-of-susceptibility-such as eIF4E-based resistances-are more likely to rely on gene redundancy among the multigene family of host susceptibility factors. Finally, we show how the genetic background is likely to shape the evolution of resistance-breaking isolates and propose how to take this into account in order to breed plants with increased resistance durability to viruses.

Local adaptation of plant viruses: lessons from experimental evolution

For multihost pathogens, adaptation to multiple hosts has important implications for both applied and basic research. At the applied level, it is one of the main factors determining the probability and severity of emerging disease outbreaks. At the basic level, it is thought to be a key mechanism for the maintenance of genetic diversity both in host and pathogen species. In recent years, a number of evolution experiments have assessed the fate of plant virus populations replicating within and adapting to one single or to multiple hosts species. A first group of these experiments tackled the existence of trade-offs in fitness and virulence for viruses evolving either within a single hosts species or alternating between two different host species. A second set of experiments explored the role of genetic variability in susceptibility and resistance to infection among individuals from the same host species in the extent of virus local adaptation and of virulence. In general, when a single host species or genotype is available, these experiments show that local adaptation takes place, often but not always associated with a fitness trade-off. However, alternating between different host species or infecting resistant host genotypes may select for generalist viruses that experience no fitness cost. Therefore, the expected cost of generalism, arising from antagonistic pleiotropy and other genetic mechanisms generating fitness trade-offs between hosts, could not be generalized and strongly depend on the characteristics of each particular pathosystem. At the genomic level, these studies show pervasive convergent molecular evolution, suggesting that the number of accessible molecular pathways leading to adaptation to novel hosts is limited.

Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y

The evolution of resistance-breaking capacity in pathogen populations has been shown to depend on the plant genetic background surrounding the resistance genes. We evaluated a core collection of pepper (Capsicum annuum) landraces, representing the worldwide genetic diversity, for its ability to modulate the breakdown frequency by Potato virus Y of major resistance alleles at the pvr2 locus encoding the eukaryotic initiation factor 4E (eIF4E). Depending on the pepper landrace, the breakdown frequency of a given resistance allele varied from 0% to 52.5%, attesting to their diversity and the availability of genetic backgrounds favourable to resistance durability in the plant germplasm. The mutations in the virus genome involved in resistance breakdown also differed between plant genotypes, indicating differential selection effects exerted on the virus population by the different genetic backgrounds. The breakdown frequency was positively correlated with the level of virus accumulation, confirming the impact of quantitative resistance loci on resistance durability. Among these loci, pvr6, encoding an isoform of eIF4E, was associated with a major effect on virus accumulation and on the breakdown frequency of the pvr2-mediated resistance. This exploration of plant genetic diversity delivered new resources for the control of pathogen evolution and the increase in resistance durability.

Amino acid substitution in P3 of Soybean mosaic virus to convert avirulence to virulence on Rsv4-genotype soybean is influenced by the genetic composition of P3

The modification of avirulence factors of plant viruses by one or more amino acid substitutions converts avirulence to virulence on hosts containing resistance genes. Limited experimental studies have been conducted on avirulence/virulence factors of plant viruses, in particular those of potyviruses, to determine whether avirulence/virulence sites are conserved among strains. In this study, the Soybean mosaic virus (SMV)-Rsv4 pathosystem was exploited to determine whether: (i) avirulence/virulence determinants of SMV reside exclusively on P3 regardless of virus strain; and (ii) the sites residing on P3 and crucial for avirulence/virulence of isolates belonging to strain G2 are also involved in virulence of avirulent isolates belonging to strain G7. The results confirm that avirulence/virulence determinants of SMV on Rsv4-genotype soybean reside exclusively on P3. Furthermore, the data show that sites involved in the virulence of SMV on Rsv4-genotype soybean vary among strains, with the genetic composition of P3 playing a crucial role.

Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population

RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3' untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity.

IMPORTANCE

This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence.

Emerging viruses: why they are not jacks of all trades?

In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that is, the negative fitness effect in the primary host of mutations allowing the infection of and the multiplication in a new host, has long been thought to be the main limitation to the evolution of generalist viruses and thus to emergence. However, the accumulation of experimental examples contradicting the hypothesis of antagonistic pleiotropy has highlighted the importance of other factors such as the epistasis between mutations increasing the adaptation to a new host. Epistasis is pervasive in viruses, affects the shape of the adaptive landscape and consequently the accessibility of evolutionary pathways. Finally, recent studies have gone steps further in the complexity of viral fitness determinism and stressed the potential importance of the epistatic pleiotropy and of the impact of host living conditions.

Evolutionary Pathways to Break Down the Resistance of Allelic Versions of the PVY Resistance Gene va

Emergence of viral genotypes can make control strategies based on resistance genes ineffective. A few years after the deployment of tobacco genotypes carrying alleles of the Potato virus Y (PVY) recessive resistance gene va, virulent PVY isolates have been reported, suggesting the low durability of va. To have a broader view of the evolutionary processes involved in PVY adaptation to va, we studied mutational pathways leading to the emergence of PVY resistance-breaking populations. The viral genome-linked protein (VPg) has been described to be potentially involved in va adaptation. Analyses of the VPg sequence of PVY isolates sampled from susceptible and resistant tobacco allowed us to identify mutations in the central part of the VPg. Analysis of the virulence of wild-type isolates with known VPg sequences and of mutated versions of PVY infectious clones allowed us to (i) validate VPg as the PVY virulence factor corresponding to va, (ii) highlight the fact that virulence gain in PVY occurs rapidly and preferentially by substitution at position AA₁₀₅ in the VPg, and (iii) show that the 101G substitution in the VPg of a PVY^C isolate is responsible for cross-virulence toward two resistance sources. Moreover, it appears that the evolutionary pathway of PVY adaptation to va depends on both virus and host genetic backgrounds.

Key mutations in the cylindrical inclusion involved in lettuce mosaic virus adaptation to eIF4E-mediated resistance in lettuce

We previously showed that allelic genes mol¹ and mo1² used to protect lettuce crops against Lettuce mosaic virus (LMV) correspond to mutant alleles of the gene encoding the eukaryotic translation initiation factor 4E. LMV resistance-breaking determinants map not only to the main potyvirus virulence determinant, a genome-linked viral protein, but also to the C-terminal region of the cylindrical inclusion (CI), with a key role of amino acid at position 621. Here, we show that the propagation of several non-lettuce isolates of LMV in mo1¹ plants is accompanied by a gain of virulence correlated with the presence in the CI C terminus of a serine at position 617 and the accumulation of mutations at positions 602 or 627. Whole-genome sequencing of native and evolved isolates showed that no other mutation could be associated with adaptation to mo1 resistance. Site-directed mutagenesis pinpointed the key role in the virulence of the combination of mutations at positions 602 and 617, in addition to position 621. The impact of these mutations on the fitness of the virus was evaluated, suggesting that the durability of mo1 resistance in the field relies on the fitness cost associated with the resistance-breaking mutations, the nature of the mutations, and their potential antagonistic effects.

Interaction patterns between potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae

The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations.

IMPORTANCE

The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.

The Potyviridae cylindrical inclusion helicase: a key multipartner and multifunctional protein

A unique feature shared by all plant viruses of the Potyviridae family is the induction of characteristic pinwheel-shaped inclusion bodies in the cytoplasm of infected cells. These cylindrical inclusions are composed of the viral-encoded cylindrical inclusion helicase (CI protein). Its helicase activity was characterized and its involvement in replication demonstrated through different reverse genetics approaches. In addition to replication, the CI protein is also involved in cell-to-cell and long-distance movements, possibly through interactions with the recently discovered viral P3N-PIPO protein. Studies over the past two decades demonstrate that the CI protein is present in several cellular compartments interacting with viral and plant protein partners likely involved in its various roles in different steps of viral infection. Furthermore, the CI protein acts as an avirulence factor in gene-for-gene interactions with dominant-resistance host genes and as a recessive-resistance overcoming factor. Although a significant amount of data concerning the potential functions and subcellular localization of this protein has been published, no synthetic review is available on this important multifunctional protein. In this review, we compile and integrate all information relevant to the current understanding of this viral protein structure and function and present a mode of action for CI, combining replication and movement.

Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants

The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.

Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity

TAXONOMY

Potato virus Y (PVY) is the type member of the genus Potyvirus in the family Potyviridae. VIRION AND GENOME PROPERTIES: PVY virions have a filamentous, flexuous form, with a length of 730 nm and a diameter of 12 nm. The genomic RNA is single stranded, messenger sense, with a length of 9.7 kb, covalently linked to a viral-encoded protein (VPg) at the 5' end and to a 3' polyadenylated tail. The genome is expressed as a polyprotein of approximately 3062 amino acid residues, processed by three virus-specific proteases into 11 mature proteins.

HOSTS

PVY is distributed worldwide and has a broad host range, consisting of cultivated solanaceous species and many solanaceous and nonsolanaceous weeds. It is one of the most economically important plant pathogens and causes severe diseases in cultivated hosts, such as potato, tobacco, tomato and pepper, as well as in ornamental plants.

TRANSMISSION

PVY is transmitted from plant to plant by more than 40 aphid species in a nonpersistent manner and, in potato, by planting contaminated seed tubers. DIVERSITY: Five major clades, named C1, C2, Chile, N and O, have been described within the PVY species. In recent decades, a strong increase in prevalence of N × O recombinant isolates has been observed worldwide. A correlation has been observed between PVY phylogeny and certain pathogenicity traits. GENETIC CONTROL OF PVY: Resistance genes against PVY have been used widely in breeding programmes and deployed in the field. These resistance genes show a large diversity of spectrum of action, durability and genetic determinism. Notably, recessive and dominant major resistance genes show highly contrasting patterns of interaction with PVY populations, displaying rapid co-evolution or stable relationships, respectively.

Epistasis between mutations is host-dependent for an RNA virus

How, and to what extent, does the environment influence the way mutations interact? Do environmental changes affect both the sign and the magnitude of epistasis? Are there any correlations between environments in the variability, sign or magnitude of epistasis? Very few studies have tackled these questions. Here, we addressed them in the context of viral emergence. Most emerging viruses are RNA viruses with small genomes, overlapping reading frames and multifunctional proteins for which epistasis is abundant. Understanding the effect of host species in the sign and magnitude of epistasis will provide insights into the evolutionary ecology of infectious diseases and the predictability of viral emergence.

Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown

Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper-Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant-pathogen systems and their importance in plant breeding are discussed.

Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus

BACKGROUND

Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus).

RESULTS

Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G → T: C → A.

CONCLUSIONS

While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.

Evaluation of North American isolates of Soybean mosaic virus for gain of virulence on Rsv-genotype soybeans with special emphasis on resistance-breaking determinants on Rsv4

Resistance to Soybean mosaic virus (SMV) in soybean is conferred by three dominant genes: Rsv1, Rsv3 and Rsv4. Over the years, scientists in the USA have utilized a set of standard pathotypes, SMV-G1 to SMV-G7, to study interaction with Rsv-genotype soybeans. However, these pathotypes were isolated from a collection of imported soybean germplasm over 30 years ago. In this study, 35 SMV field isolates collected in recent years from 11 states were evaluated for gain of virulence on soybean genotypes containing individual Rsv genes. All isolates were avirulent on L78-379 (Rsv1), whereas 19 were virulent on L29 (Rsv3). On PI88788 (Rsv4), 14 of 15 isolates tested were virulent; however, only one was capable of systemically infecting all of the inoculated V94-5152 (Rsv4). Nevertheless, virulent variants from 11 other field isolates were rapidly selected on initial inoculation onto V94-5152 (Rsv4). The P3 cistrons of the original isolates and their variants on Rsv4-genotype soybeans were sequenced. Analysis showed that virulence on PI88788 (Rsv4) was not associated, in general, with selection of any new amino acid, whereas Q1033K and G1054R substitutions were consistently selected on V94-5152 (Rsv4). The role of Q1033K and G1054R substitutions, individually or in combination, in virulence on V94-5152 (Rsv4) was confirmed on reconstruction in the P3 cistron of avirulent SMV-N, followed by biolistic inoculation. Collectively, our data demonstrate that SMV has evolved virulence towards Rsv3 and Rsv4, but not Rsv1, in the USA. Furthermore, they confirm that SMV virulence determinants on V94-5152 (Rsv4) reside on P3.

Cucumber mosaic virus

Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution.

Viruses of pepper crops in the Mediterranean basin: a remarkable stasis

Compared to other vegetable crops, the major viral constraints affecting pepper crops in the Mediterranean basin have been remarkably stable for the past 20 years. Among these viruses, the most prevalent ones are the seed-transmitted tobamoviruses; the aphid-transmitted Potato virus Y and Tobacco etch virus of the genus Potyvirus, and Cucumber mosaic virus member of the genus Cucumovirus; and thrips-transmitted tospoviruses. The last major viral emergence concerns the tospovirus Tomato spotted wilt virus (TSWV), which has undergone major outbreaks since the end of the 1980s and the worldwide dispersal of the thrips vector Frankliniella occidentalis from the western part of the USA. TSWV outbreaks in the Mediterranean area might have been the result of both viral introductions from Northern America and local reemergence of indigenous TSWV isolates. In addition to introductions of new viruses, resistance breakdowns constitute the second case of viral emergences. Notably, the pepper resistance gene Tsw toward TSWV has broken down a few years after its deployment in several Mediterranean countries while there has been an expansion of L³-resistance breaking pepper mild mottle tobamovirus isolates. Beyond the agronomical and economical concerns induced by the breakdowns of virus resistance genes in pepper, they also constitute original models to understand plant-virus interactions and (co)evolution.

Simultaneous mutations in multi-viral proteins are required for soybean mosaic virus to gain virulence on soybean genotypes carrying different R genes

BACKGROUND

Genetic resistance is the most effective and sustainable approach to the control of plant pathogens that are a major constraint to agriculture worldwide. In soybean, three dominant R genes, i.e., Rsv1, Rsv3 and Rsv4, have been identified and deployed against Soybean mosaic virus (SMV) with strain-specificities. Molecular identification of virulent determinants of SMV on these resistance genes will provide essential information for the proper utilization of these resistance genes to protect soybean against SMV, and advance knowledge of virus-host interactions in general.

METHODOLOGY/PRINCIPAL FINDINGS

To study the gain and loss of SMV virulence on all the three resistance loci, SMV strains G7 and two G2 isolates L and LRB were used as parental viruses. SMV chimeras and mutants were created by partial genome swapping and point mutagenesis and then assessed for virulence on soybean cultivars PI96983 (Rsv1), L-29 (Rsv3), V94-5152 (Rsv4) and Williams 82 (rsv). It was found that P3 played an essential role in virulence determination on all three resistance loci and CI was required for virulence on Rsv1- and Rsv3-genotype soybeans. In addition, essential mutations in HC-Pro were also required for the gain of virulence on Rsv1-genotype soybean. To our best knowledge, this is the first report that CI and P3 are involved in virulence on Rsv1- and Rsv3-mediated resistance, respectively.

CONCLUSIONS/SIGNIFICANCE

Multiple viral proteins, i.e., HC-Pro, P3 and CI, are involved in virulence on the three resistance loci and simultaneous mutations at essential positions of different viral proteins are required for an avirulent SMV strain to gain virulence on all three resistance loci. The likelihood of such mutations occurring naturally and concurrently on multiple viral proteins is low. Thus, incorporation of all three resistance genes in a soybean cultivar through gene pyramiding may provide durable resistance to SMV.