Pathogen populations evolve to greater race complexity in agricultural systems--evidence from analysis of Rhynchosporium secalis virulence data

Fitness cost associated with pathogens carrying unnecessary virulence alleles is the fundamental assumption for preventing the emergence of complex races in plant pathogen populations but this hypothesis has rarely been tested empirically on a temporal and spatial scale which is sufficient to distinguish evolutionary signals from experimental error. We analyzed virulence characteristics of ≈ 1000 isolates of the barley pathogen Rhynchosporium secalis collected from different parts of the United Kingdom between 1984 and 2005. We found a gradual increase in race complexity over time with a significant correlation between sampling date and race complexity of the pathogen (r(20) = 0.71, p = 0.0002) and an average loss of 0.1 avirulence alleles (corresponding to an average gain of 0.1 virulence alleles) each year. We also found a positive and significant correlation between barley cultivar diversity and R. secalis virulence variation. The conditions assumed to favour complex races were not present in the United Kingdom and we hypothesize that the increase in race complexity is attributable to the combination of natural selection and genetic drift. Host resistance selects for corresponding virulence alleles to fixation or dominant frequency. Because of the weak fitness penalty of carrying the unnecessary virulence alleles, genetic drift associated with other evolutionary forces such as hitch-hiking maintains the frequency of the dominant virulence alleles even after the corresponding resistance factors cease to be used.     

Epidemiology and disease-control under gene-for-gene plant-pathogen interaction

An introduction of disease-resistant variety of a crop plant often leads to the development of a virulent race in pathogen species that restores the pathogenicity to the resistant crop. This often makes disease control of crop plants extremely difficult. In this paper, we theoretically explore the optimal 'multiline' control, which makes use of several different resistant varieties, that minimizes the expected degree of crop damages caused by epidemic outbreaks of the pathogen. We examine both single-locus and two-locus gene-for-gene (GFG) systems for the compatibility relationship between host genotypes and pathogen genotypes, in which host haplotype has either susceptible or resistant allele in each resistance locus, and the pathogen haplotype has either avirulent or virulent allele in the corresponding virulence locus. We then study the optimal planting strategy of host resistant genotypes based on standard epidemiological dynamics with pathogen spore stages. The most striking result of our single-locus GFG model is that there exists an intermediate optimum mixing ratio for the susceptible and resistant crops that maximizes the final yield, in spite of the fact that the susceptible crop has no use to fight against either avirulent or virulent race of the pathogen. The intermediate mixture is optimum except when the initial pathogen spore population in the season consists exclusively of the virulent race. The optimal proportion of resistant crops is approximately 1/R(0), where R(0) is the basic reproductive ratio of pathogen--the rest (the vast majority if R(0) is large) of crops should be the susceptible genotype. By mixing susceptible and resistant crops, we can force the pathogen races to compete with each other for their available hosts. This competition between avirulent and virulent races prevents the fatal outbreak of the virulent race (the super-race) that can infect all the host genotypes. In the two-locus GFG control, there again exists the optimal mixing ratio for the fraction of universally susceptible genotype and the total fraction of various resistant genotypes, with the ratio close to 1/R(0).     

Race Profiling and Molecular Diversity Analysis of Fusarium oxysporum f.sp. ciceris Causing Wilt in Chickpea

Seventy isolates of Fusarium oxysporum f.sp. ciceris (Foc) causing chickpea wilt representing 13 states and four crop cultivation zones of India were analysed for their virulence and genetic diversity. The isolates of the pathogen showed high variability in causing wilt incidence on a new set of differential cultivars of chickpea, namely C104, JG74, CPS1, BG212, WR315, KWR108, GPF2, DCP92‐3, Chaffa and JG62. New differential cultivars for each race were identified, and based on differential responses, the isolates were characterized into eight races of the pathogen. The same set of isolates was used for molecular characterization with four different molecular markers, namely random amplified polymorphic DNA, universal rice primers, simple sequence repeats and intersimple sequence repeats. All the four sets of markers gave 100% polymorphism. Unweighted paired group method with arithmetic average analysis grouped the isolates into eight categories at genetic similarities ranging from 37 to 40%. The molecular groups partially corresponded to the states of origin/chickpea‐growing region of the isolates as well as races of the pathogen characterized in this study. The majority of southern, northern and central Indian populations representing specific races of the pathogen were grouped separately into distinct clusters along with some other isolates, indicating the existence of variability in population predominated by a single race of the pathogen. The present race profiling for the Indian population of the pathogen and its distribution pattern is entirely new. The knowledge generated in this study could be utilized in resistance breeding programme. The existence of more than one race, predominated by a single one, in a chickpea cultivation zone as supported by the present molecular findings is also a new information.     

HOST-PATHOGEN INTERACTIONS IN NATURAL POPULATIONS OF LINUM MARGINALE AND MELAMPSORA LINI: I. PATTERNS OF RESISTANCE AND RACIAL VARIATION IN A LARGE HOST POPULATION

Populations of wild flax, Linum marginale and its associated rust fungus Melampsora lini growing at Kiandra, New South Wales, Australia, were sampled during the 1986–1987 growing season. Thirteen different races of M. lini were detected in a sample of 96 isolates. The distribution of isolates was uneven: race A comprised 73% of the samples; race N, 8%; and race H, 5%; while the remaining races were represented by only one or two samples. The dominance of race A increased over the course of the growing season, comprising 67% of the early season samples and increasing to 78% for those collected late in the season. The overall diversity of the pathogen population decreased late in the growing season, but this trend was not statistically significant. The average virulence of individual isolates of the pathogen population increased during the growing season. This trend was most pronounced among the minor races, where the mean number of differential hosts infected increased from 4.58 for early season samples to 5.12 and 5.08 for mid and late season samples, respectively. In contrast to the virulence pattern in the pathogen, the L. marginale population displayed a more even distribution of resistance. In a sample of 67 plants 10 resistance phenotypes were detected from their pattern of resistance/susceptibility to seven pathogen isolates. No phenotype had a frequency that exceeded 30%. Resistance phenotypes were randomly distributed on both a population level and on a fine scale.     

Reaction of Some Coffea arabica Genotypes to Strains of Colletotrichum kahawae, the Cause of Coffee Berry Disease

Pathogenicity tests were performed on 11 genotypes of Coffea arabica using single‐isolate suspensions of Colletotrichum Kahawae obtained from 90 monoconidial isolates. The objective of this study was to estimate the proportion of pathogenic variation corresponding 10 differences in aggressiveness and virulence (races). A large part of the variation in the pathogen population was due to aggressiveness. The differential effects were too small to suggest conclusively that races exist. This paper discusses the possible causes for the observed small differential interaction and suggests breeding strategies that not only prevent possible adaptation of the pathogen to resistant varieties but also limit variation for resistance due to differences in aggressiveness of the pathogen.     

Identification of a New Race of Sporisorium reilianum and Characterization of the Reaction of Sorghum Lines to Four Races of the Head Smut Pathogen

Sporisorium reilianum is the causal agent of head smut on sorghum and maize. In order to effectively utilize host resistance to control this important disease in crops, it is necessary to monitor changes in disease dynamics and virulence of the pathogen. An outbreak of head smut was recently observed in a sorghum field, near Gaoping, Shanxi, China, and research was undertaken to characterize a putative new race of S. reilianum. A set of differential sorghum lines with resistance to several conventional races was used to characterize the newly collected isolate of S. reilianum. The reactions of differential cultivars/germplasm lines to the new isolate indicate that it is a new physiological race of S. reilianum. The new race is highly virulent on sorghum line A₂V4 and its hybrid, Jinza 12, that are known as resistant to all existing Chinese races of S. reilianum, including races 1, 2, and 3. The new isolate of S. reilianum is different from all of the described races of the pathogen; thus, it is designated as race 4 of S. reilianum. Furthermore, a collection of 34 sorghum genotypes including commercial cultivars and germplasm lines was evaluated for disease reaction to the newly described race and the three known races of the pathogen.     

Predation Determines Different Selective Pressure on Pea Aphid Host Races in a Complex Agricultural Mosaic

Field assessments were conducted to examine the interplay between host plant and predation in complex agricultural mosaic on pea aphid clover and alfalfa races. In one experiment, we examined the relative fitness on clover race (CR) and alfalfa race (AR) pea aphids on broad bean, red clover and alfalfa alone. But because clover is typically grown in a more complex agricultural mosaic with alfalfa and broad bean, a second experiment was conducted to assess the fitness consequences under predation in a more complex agricultural field setting that also included potential apparent competition with AR pea aphids. In a third experiment we tested for the effect of differential host race density on the fitness of the other host race mediated by a predator effect. CR pea aphids always had fitness losses when on broad bean (had lower fitness on broad bean relative to red clover) and fitness benefits when on red clover (higher fitness on red clover relative to broad bean), whether or not in apparent competition with alfalfa race aphids on bean and alfalfa. AR suffered fitness loss on both alfalfa and bean in apparent competition with CR on clover. Therefore we can conclude that the predation rate between host races was highly asymmetrical. The complexity of the agricultural mosaic thus can influence prey selection by predators on different host plants. These may have evolutionary consequences through context dependent fitness benefits on particular host plants.     

Spatially structured superinfection and the evolution of disease virulence

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.     

Modelling the evolution of common cuckoo host‐races: speciation or genetic swamping?

Co‐evolutionary arms races have provided clear evidence for evolutionary change, especially in host–parasite systems. The evolution of host‐specific races in the common cuckoo (Cuculus canorus), however, is also an example where sexual conflict influences the outcome. Cuckoo females benefit from better adaptation to overcome host defences, whereas cuckoo males face a trade‐off between the benefits of better adaptation to a host and the benefits of multiple mating with females from other host‐races. The outcome of this trade‐off might be genetic differentiation or prevention of it by genetic swamping. We use a simulation model to test which outcome is more likely with three sympatric cuckoo host‐races. We assume a cost for cuckoo chicks that express a host adaptation allele not suited to their foster host species and that cuckoo males that switch to another host‐race experience either a fitness benefit or cost. Over most of the parameter space, cuckoo male host‐race fidelity increases significantly with time, and gene flow between host‐races ceases within a few thousand to a hundred thousand generations. Our results hence support the idea that common cuckoo host‐races might be in the incipient stages of speciation.     

Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in a plant pathosystem

Abstract Virulence is thought to be a driving force in host–pathogen coevolution. Theoretical models suggest that virulence is an unavoidable consequence of pathogens evolving towards a high rate of intrahost reproduction. These models predict a positive correlation between the reproductive fitness of a pathogen and its level of virulence. Theoretical models also suggest that the demography and genetic structure of a host population can influence the evolution of virulence. If evolution occurs faster in pathogen populations than in host populations, the predicted result is local adaptation of the pathogen population. In our studies, we used a combination of molecular and physiological markers to test these hypotheses in an agricultural system. We isolated five strains of the fungal pathogen Mycosphaerella graminicola from each of two wheat cultivars that differed in their level of resistance to this pathogen. Each of the 10 fungal strains had distinct genotypes as indicated by different DNA fingerprints. These fungal strains were re‐inoculated onto the same two host cultivars in a field experiment and their genotype frequencies were monitored over several generations of asexual reproduction. We also measured the virulence of these 10 fungal strains and correlated it to the reproductive fitness of each fungal strain. We found that host genotypes had a strong impact on the dynamics of the pathogen populations. The pathogen population collected from the moderately resistant cultivar Madsen showed greater stability, higher genotype diversity, and smaller selection coefficients than the pathogen populations collected from the susceptible cultivar Stephens or a mixture of the two host cultivars. The pathogen collection from the mixed host population was midway between the two pure lines for most parameters measured. Our results also revealed that the measures of reproductive fitness and virulence of a pathogen strain were not always correlated. The pathogen strains varied in their patterns of local adaptation, ranging from locally adapted to locally maladapted.     

Social immunity modulates competition between coinfecting pathogens

Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.     

Population Dynamics of Virulence Genes of Xanthomonas campestris pv. malvacearum on Cotton

Population genetic principles in relation to the pathogenicity genes have been applied on the genotypes (races) of Xanthomonas campestris pv. malvacearum(Xcm) which are characterized on the basis of bacterial blight resistant host genes ( B -genes) attacked. Observed (OF) and expected (EF) frequencies were determined to predict the intensity of selection pressure operating in the pathogen population due to the introduction of particular host resistant gene(s). Race 32 (V_p, V₇ V₂ V₁₀ V_N) was the most prevalent genotype representing 41.55% of the Xcm population. Other prevalent genotypes were race 30 (11.08%, V_p V₂ V_in V_N), race 20 (8.56%, V_p V₂ V_N), race 9 (6.80%, V_p V_in) and race 8 (11.59%, V_p V₂). The OF (observed frequency) of race 32 was 41.55%, whereas EF (expected frequency) was 15.74% indicating a strong selection pressure favouring this highly virulent genotype. Whereas, race 31 (V₇ V₂ V_in V_N) also overcomes four major genes like race 32 but not the polygene complex, it was less fit and possessed low EF and OF, i.e. 0.25% and 1.18% respectively. Xcm genotypes capable of attacking 3–4 major B -genes were prevalent on G. hirsutum , while genotypes with virulence against 1–2 B -genes favoured G. barbadense cottons. High virulence level in pathogen genotypes, was maintained on resistant/tolerant host genotypes of G. arboreum and G. hirsutum whereas, it was diluted on the highly susceptible G. barbadense.     

A Pathotype System to Describe Intraspecific Variation in Pathogenicity of Meloidogyne chitwoodi

Tests of eight Dutch Meloidogyne chitwoodi isolates to the differential set for host races 1 and 2 in M. chitwoodi provided no evidence for the existence of host race 2 in the Netherlands. The data showed deviations from expected reactions on the differential hosts, which raised doubts of the usefulness of the host race classification in M. chitwoodi. The term ''''pathotype'''' is proposed for groups of isolates of one Meloidogyne sp. that exhibit the same level of pathogenicity on genotypes of one host species. We recommend that the pathotype classification be applied in pathogen-host relationships when several genotypes of a Meloidogyne sp. are tested on several genotypes of one host species. Three pathotypes of M. chitwoodi were identified on Solanum bulbocastanum, suggesting at least two different genetic factors for virulence and resistance in the pathogen and the host species, respectively. The occurrence of several virulence factors in M. chitwoodi will complicate the successful application of resistance factors from S. bulbocastanum for developing resistant potato cultivars.     

Virulence cost in Plasmopara halstedii (sunflower downy mildew)

Virulence cost (trade-off between virulence and aggressiveness) was studied in seven Plasmopara halstedii (sunflower downy mildew) isolates of races 100, 300, 304, 314, 710, 704 and 714. The seven isolates were divided, according to their virulence and aggressiveness, into two main groups as more aggressive isolates of the 100 and 3xx races that do not overcome the sunflower differential host D3, and less aggressive isolates of 7xx races that can overcome D3. Consequently, the 100 and 3xx avirulent races had a virulence cost measured by differences in aggressiveness (from 58.3 to 78.2%) compared to 7xx virulent races carrying unnecessary virulence gene.     

Experimental manipulation of population‐level MHC diversity controls pathogen virulence evolution in Mus musculus

The virulence levels attained by serial passage of pathogens through similar host genotypes are much higher than observed in natural systems; however, it is unknown what keeps natural virulence levels below these empirically demonstrated maximum levels. One hypothesis suggests that host diversity impedes pathogen virulence, because adaptation to one host genotype carries trade‐offs in the ability to replicate and cause disease in other host genotypes. To test this hypothesis, with the simplest level of population diversity within the loci of the major histocompatibility complex (MHC), we serially passaged Friend virus complex (FVC) through two rounds, in hosts with either the same MHC genotypes (pure passage) or hosts with different MHC genotypes (alternated passage). Alternated passages showed a significant overall reduction in viral titre (31%) and virulence (54%) when compared to pure passages. Furthermore, a resistant host genotype initially dominated any effects due to MHC diversity; however, when FVC was allowed to adapt to the resistant host genotype, predicted MHC effects emerged; that is, alternated lines show reduced virulence. These data indicate serial exposure to diverse MHC genotypes is an impediment to pathogen adaptation, suggesting genetic variation at MHC loci is important for limiting virulence in a rapidly evolving pathogen and supports negative frequency‐dependent selection as a force maintaining MHC diversity in host populations.     

Detecting local adaptation in a natural plant-pathogen metapopulation: a laboratory vs. field transplant approach

Antagonistic coevolution between hosts and parasites in spatially structured populations can result in local adaptation of parasites. Traditionally parasite local adaptation has been investigated in field transplant experiments or in the laboratory under a constant environment. Despite the conceptual importance of local adaptation in studies of (co)evolution, to date no study has provided a comparative analysis of these two methods. Here, using information on pathogen population dynamics, I tested local adaptation of the specialist phytopathogen, Podosphaera plantaginis, to its host, Plantago lanceolata at three different spatial scales: sympatric host population, sympatric host metapopulation and allopatric host metapopulations. The experiment was carried out as a field transplant experiment with greenhouse-reared host plants from these three different origins introduced into four pathogen populations. In contrast to results of an earlier study performed with these same host and parasite populations under laboratory conditions, I did not find any evidence for parasite local adaptation. For interactions governed by strain-specific resistance, field studies may not be sensitive enough to detect mean parasite population virulence. Given that parasite transmission potential may be mediated by the abiotic environment and genotype-by-environment interactions, I suggest that relevant environmental variation should be incorporated into laboratory studies of parasite local adaptation.     

Detection of Cochliobolus heterostrophus races in South China

Cochliobolus heterostrophus is the causal pathogen of the southern corn leaf blight (SCLB). There are three known races: race O, race C and race T. To determine which C. heterostrophus races comprise the field population in southern China and to assess diversity of these strains in terms of virulence, 200 isolates from diseased plants were collected in nine provinces/municipalities. All were race O, that is, no race T or race C isolates were found. Sixty race O isolates that sporulated well were chosen for further analysis. Virulence was measured using the integral optical density (IOD) of leaf lesions on four maize inbred lines. UPGMA cluster analysis of AFLP markers was applied to the 60 race O isolates plus control race O, T and C strains. Phylogenetic distribution, geographic location and virulence were not correlated. These results can provide valuable information for guidance in early warning and disease control.     

Population structure of a vector‐borne plant parasite

Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector‐borne desert mistletoe (Phoradendron californicum) across two legume host tree species (Senegalia greggii and Prosopis velutina) in the Sonoran desert using microsatellites. Consistent with host race formation, we found strong host‐associated genetic structure in sympatry, little genetic variation due to geographic site and weak isolation by distance. We hypothesize that genetic differentiation results from differences in the timing of mistletoe flowering by host species, as we found initial flowering date of individual mistletoes correlated with genetic ancestry. Hybrids with intermediate ancestry were detected genetically. Individuals likely resulting from recent, successful establishment events following dispersal between the host species were detected at frequencies similar to hybrids between host races. Therefore, barriers to gene flow between the host races may have been stronger at mating than at dispersal. We also found higher inbreeding and within‐host individual relatedness values for mistletoes on the more rare and isolated host species (S. greggii). Our study spanned spatial scales to address how interactions with both vectors and hosts influence parasitic plant structure with implications for parasite virulence evolution and speciation.     

The genetic relationship between races of Bremiae lactucae and cultivars of Lactuca sativa

The reactions of lettuce cultivars to physiologic races of Bremia lactucae are interpreted in terms of a gene-for-gene relationship between pathogen and host. The hypothesis takes into account the parentage of cultivars and the origins of their resistance, the characteristics of the resistance reactions and data available from detailed genetical analysis of various race/cultivar combinations. Cultivars are classified with respect to ten postulated resistance genes and B. lactucae races are defined by the virulence genes present. The practical significance of these studies is discussed in relation to both future lettuce breeding programmes and to the choice of cultivars available to counteract any given local race situation.     

Acclimation of Plasmopara halstedii (sunflower downy mildew) in relationship with trade-off between virulence and aggressiveness in a local pathogen population

The acclimation in relationship with virulence cost was analysed for seven Plasmopara halstedii (sunflower downy mildew) isolates including five progeny isolates of several races descending from two parental isolates of races 100 and 710. Aggressiveness criteria were analysed in one sunflower inbred line showing a high level of quantitative resistance. Isolates of races 100 and 3xx were characterised with shorter latent period and higher sporulation density than isolates of races 7xx. All isolates showed high percentage infection values and caused a large reduction in seedling size except for one isolate involved in dwarfing. The seven isolates were divided, according to their virulence and aggressiveness, into two main groups as more aggressive isolates of the 100 and 3xx races which do not overcome the sunflower differential host D3, and less aggressive isolates of 7xx races which can overcome D3. Consequently, the 100 and 3xx avirulent races had a virulence cost measured by differences in aggressiveness (from 45.5 to 76.3%) compared to 7xx virulent races carrying unnecessary virulence gene.