RESISTANCE IN POPULATIONS
B. PREDISPOSITION AND IMMUNISATION
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mechanism therefore had two components, (1) differences between plant stages in susceptibility to the pathogen (only susceptible in the flowering stage), and (2) differences between plant families (genotypes) in growth rate. A similar phenomenon was observed for the annual plant Senecio vulgaris and the rust fungus Puccinia lagenophorae (1. Frantzen and H. MUller-Scharer, unpublished). Plants at a young stage were less susceptible than plants at an older stage, probably because spores adhered less to the leaves of young plants. The plant families used in the experiments differed in rate of development and, therefore, the number of plants present in a susceptible state at the time of inoculation differed between families. Two plant families avoided disease compared to the third family. Again, this system showed the two components of the avoidance mechanism: the differences between plant stages in susceptibility, and the differences in rate of development.
The rate of development also may govern avoidance in crop pathosystems (Agrios, 1980).
For example, timing of blossoming and fruit set may vary between apple varieties and some of the varieties may blossom at a time when a pathogen is not infectious. The use of the mechanism of avoidance in agriculture may, however, be constrained by factors not related to crop protection, e.g. feasibility of harvest, and yield quality.
Avoidance is a disease defence mechanism that can be distinguished from resistance. It may be quite common. Its use in agriculture may be constrained by factors not related to crop protection.
The mechanism of immunisation was not investigated in detail, but probably involved development of the normal cascade of resistance responses following attack.
Immunisation may play a role in the concept of multilines or variety mixtures.
The spread of Erysiphe graminis f. sp. hordei Marchal was quantified for a barley population consisting of four varieties (Chin and Wolfe, 1984). The results suggested that spores of a non-virulent pathogen biotype landing on a resistant variety turned on defence mechanisms making the plants immune to the virulent pathogen biotypes.
The protection was not 100% as some reproduction of the virulent biotype occurred.
The epidemic was slowed down, but not stopped. In general, incomplete protection of the plants seems to be a characteristic of the mechanism of immunisation (Dean and Ku~, 1987).
Predisposition and immunisation are mechanisms likely to operate in populations, but it is difficult to estimate their significance in the development of epidemics in populations. A set of environmental conditions may be present in a population triggering both predisposition and immunisation. Which one will win? In the study by Chin and Wolfe (1984) is was likely that immunisation won. However, environmental conditions, biotic and abiotic, are dynamic and it might be difficult to predict the effects of predisposition and immunisation, respectively, on disease epidemics. Moreover, environmental conditions are not uniform in plant populations, especially in wild plant populations, and this makes predictions even more difficult.
The effects of the mechanisms of predisposition and immunisation on disease epidemics are hard to predict because of the stochastic nature of the environmental factors, biotic and abiotic, governing these mechanisms.
c.
RESISTANCEWe now arrive at the moment when a pathogen in an infectious state contacts a plant in a susceptible stage. It is assumed that the plant is predisposed to disease by the environmental conditions and the environmental conditions at the point of contact are suitable for the process of infection. In short, all is fine for development of disease.
Plal).t genotypes may, however, react in different ways to the pathogen. Some may inhibit its growth completely, others may inhibit growth incompletely, and some may not inhibit development of the pathogen at all, reflecting complete resistance, incomplete resistance and susceptibility, respectively. This subdivision of resistance is relevant to epidemics in plant populations. An epidemic does not progress in a population with only resistant plants, it is delayed in a population with plants having incomplete resistance, and progresses without any restriction in a population with only susceptible plants.
The genotypes of the pathogen may differ in their pathogenicity to plants. A genotype may develop on a plant without restriction, development may be limited or the genotype
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may not develop at all. This reflects virulence, the degree of aggressiveness, and avirulence, respectively.
If a host encompasses genotypes with reaction types in a continuous range of susceptibility to incomplete resistance the effect is called quantitative resistance.
The counterpart of quantitative resistance is aggressiveness of the pathogen. If the host reactions are either (close to) completely resistant or susceptible the effect is referred to as qualitative resistance. The pathogen is virulent or avirulent. As pointed out by Nelson (1978), this division into qualitative and quantitative resistance is relevant to understanding the development of epidemics. Qualitative resistance inhibits the infection process and prevents production of inoculum for progress of the epidemic.
Quantitative resistance does not inhibit the infection process completely and allows production of inoculum. The production may, however, be delayed (longer latent period) or may be reduced. The consequences are a delay of the epidemic and reduction of disease levels in a population.
There may be specific interactions between genotypes of the host and genotypes of the pathogen. Using agricultural terms, we are talking about race-specific resistance and cultivar-specific pathogenicity, respectively. Specific interactions between genotypes of host and pathogen may be determined in both qualitative and quantitative resistance.
Qualitative resistance inhibits development of an epidemic. Quantitative resistance reduces the rate of development of an epidemic. The counterpart of qualitative resistance is virulence of the pathogen. The counterpart of quantitative resistance is aggressiveness of the pathogen. Specific interactions between genotypes of the host and genotypes of the pathogen are possible.
The reader should be aware of the confusion in the literature concerning the term resistance and the types of resistance. The terminology adopted here is basically that of Parlevliet (1989) because it is suitable for describing processes at the population level, in which resistance is involved. Additionally, the term qualitative is used here as a logical counterpart of quantitative resistance. The definitions of virulence and avirulence deviate from the terminology of Parlevliet (1989), but seem logical and fit the common use of these terms (Ennos, 1992).
After this consideration of terminology, we now examine disease development in wild pathosystems. The perennial plant Plantago lanceolata is infected by the necrotrophic fungus Phomopsis subordinaria (teleomorph Diaporthe adunca). An insect vector is involved in the transmission of the fungus (de Nooij, 1988). Transmission is also possible by splash dispersal (Linders et aI., 1996). Variation of resistance in host populations was investigated (de Nooij and van Damme, 1988a). The study is summarised in the box below.
Resistance of Plantago Ianceolata to Phomopsis subordilUlria - Plants sampled in 3 populations
- Sampling along a transect at distances of 5 m - Clones inoculated with P. subordinaria - Lesion size was between 193 mm and 246 mm - Significant differences between populations - No significant differences within populations - Survival decreased with increasing lesion size
Differences in resistance to P. subordinaria were detected between populations and not within populations. The differences in resistance were relevant to survival of plants.
More resistant plants had a higher probability of survival.
Variation in pathogenicity was also investigated using the same plant populations (de Nooij and van Damme, 1988b). Differences in pathogenicity were detected between and within populations (see box below). The differences within populations were detected on a rather small scale. The differences determined were relevant to survival of the host plant.
Pathogenicity of P. subordinaria - Isolates collected in 3 populations
- Isolates collected from 12 plants in a population - Three clones inoculated with isolates
- Lesion size was between 176 mm and 314 mm - Significant differences between populations - Significant differences within populations - Differences on a scale of 1.5 m
The work of de Nooij and van Damme (l988b) is a notable exception (Ennos, 1992) among studies on wild and weed pathosystems for measuring the distribution of pathogenicity in the pathogen population on such a small scale. The studies of the wild pathosystem P. lanceolata -P. subordinaria illustrate some phenomena of interest.
• The presence of quantitative resistance of the host and the corresponding aggressiveness of the pathogen.
• The relevance of quantitative resistance to plant survival.
• Variation of quantitative resistance and aggressiveness on a rather small spatial scale.
• Specific interactions between host plants and isolates were present suggesting a gene-for-gene interaction.
• The variation in aggressiveness of the pathogen seemed to be larger than that of quantitative resistance of the host. This suggested that the variation in aggressiveness was not only the result of a reaction to the variation in quantitative resistance, but
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also the result of isolation phenomena in the pathogen population. Isolation might be explained by the limitations of the transmission of the fungus by way of an insect vector and by way of splash dispersal.
The genetic basis of quantitative resistance and aggressiveness was not unravelled for the pathosystem P. lanceolata - P. subordinaria. This is a general drawback of studies on wild and weed pathosystems. Experimental crosses are a prerequisite for a classical genetic analysis, but are often not feasible. One of the few exceptions is work by Burdon (1987b). Plants of the perennial Glycine canescens were sampled in two populations and tested for resistance to nine races of the rust fungus Phakopsora pachyrhizi. Both quantitative and qualitative resistance were determined and resistance was race-specific. Subsequent crosses between plant lines indicated the presence of one, two or three resistance genes (factors) in the plant lines. The identity of the resistance genes in the plant lines remained unknown. Application of the principles of the gene-for-gene theory suggested the presence of at least 10-12 resistance genes in each of the G. canescens populations.
The major point of interest in the study by Burdon (1987b) was that race-specific resistance may be present in wild pathosystems and the gene-for-gene theory, more recently called allele-for-allele hypothesis (e.g. Newton and Andrivon, 1995), may apply.
Race-specific resistance and the suitability of the gene-for-gene theory was also demonstrated for the weed pathosystem Senecio vulgaris - Erysiphe fischeri (Harry and Clarke, 1986, 1987). Neither Harry and Clarke (1986, 1987) nor Burdon (1987b) distinguished qualitative and quantitative resistance in their analysis, although the data presented indicated both types of resistance.
Both qualitative and quantitative resistance are present in wild and weed pathosystems. The variation of resistance in the host populations and the variation of pathogenicity in the pathogen populations may be relatively large. The underlying genetics are rather poorly understood.
The vanatIOn of resistance and pathogenicity in host and pathogen populations, respectively, may be dynamic. This was demonstrated for the pathogenicity of the rust fungus Melampsora lini infecting plants of Linum marginale (Burdon and Jarosz, 1992).
Nine populations of the rust were sampled during 2, 3, or 4 years. The date of sampling and the number of dates of sampling differed between years and populations. The data were, however, analysed on a year to year base. The isolates sampled were tested on a differential set of host lines and classified to five categories. The distribution of isolates over these five categories changed significantly from year to year for each rust population indicating relatively strong dynamics. The authors explained the temporal changes by metapopulation dynamics (genetic drift, extinction / recolonisation events) rather than by considering the changes as a response to the variation of resistance in the host populations.
We tum now to crop pathosystems and the picture becomes simpler with respect to variation of resistance in the host population. The variation is nearly absent, or at least low compared to wild and weed pathosystems. In so far as it is present, variation is nearly completely managed by man. The reason for this low variation is well understood and of long standing (see e.g. Zadoks and Schein, 1979). Crops should be high yielding and as uniform as possible to ease the harvest. The selection force exerted by man during centuries of plant breeding has resulted in rather uniform crops with few resistances to diseases. The frequency of resultant epidemics, like those of yellow rust, then stimulated breeding for disease resistance (Johnson, 1992). As pointed out by Johnson, breeding for resistance to a number of diseases affecting crops is a difficult task given the constraints of agronomic demands (e.g. yield quality). Moreover, resistance should be durable.
Durability is, however, the exception rather than the rule in crops. This may be explained by the "flexibility" of the pathogens as outlined next.
The dynamics of the population of Phytophthora infestans was studied in The Netherlands (Drenth et aI., 1994), using isolates collected before and after 1980 (see Box).
Dutch population of P. infestans - Isolates collected before 1980 ("old") - Isolates collected after 1980 ("new") - Differential set to test for pathogenicity - DNA fingerprinting using the probe RG-S7 - 148 "old" isolates belonged to 8 races - "old" isolates were same fingerprint genotype - 253 "new" isolates belonged to 73 races - "new" isolates were 134 distinct genotypes
Two explanations for the change of genetic variation around 1980 were presented by the authors: a new population was introduced into The Netherlands from Mexico consisting of a large number of heterogeneous isolates, and the introduction of the A2 mating type, also from Mexico, into the former Al mating type Dutch population allowed sexual reproduction and an increase in genetic diversity. In common to both explanations is that gene flow from Mexico to The Netherlands had a tremendous effect on the genetic constitution of the Dutch population, which might have severe consequences for the protection of potatoes against late blight. As pointed out by Fry et al. (1992) the devastating potato late blight outbreak in Europe in 1845 might have been caused by a previous gene flow of P. infestans from Mexico to Europe and, following Andrivon (1996), that gene flow may have passed from Mexico via South America to Europe.
The relevant point in the potato late blight story is that a reservoir exists from which races disperse to vacant sites, which are crops not yet occupied by the pathogen due to resistance or any other adequate control measure. It is a matter of trial and error for the pathogen to "send out" the right race to break the control measure.
Looking at the size of the metapopulation of P. infestans, or the European population of E. graminis f.sp. hordei, it is clear that one or more reservoirs exist. These reservoirs
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may exist as (sub)populations on crop populations not protected against the pathogen, as (sub) populations on populations of alternate hosts, or as survival units outside a host.
Migration of races is assured by various vectors. Even pathogens like soil-borne fungi and viruses may be transported over large distances by man acting as a vector.
The sizes of (meta)populations of pathogens are large compared to crop populations and provide enough reservoirs to develop new races to confront crop populations frequently with races never encountered before.
We may assume that a crop population is confronted frequently with races of a pathogen not encountered before. This triggers the question how often? This question will be returned to in a later section (IV. Selection and Fitness).
If crops are confronted frequently with new races of a pathogen, a reaction is required to minimise crop losses due to disease. Until now, the reaction of man has been primarily in breeding crops for resistance based on the gene-for-gene hypothesis, that is in deploying race-specific resistance. To summarise a long story, a plant variety has a factor enabling recognition of a corresponding factor in a pathogen race. These factors are called commonly R gene and Avr gene, respectively. More details are given elsewhere in this book (chapter 2). The quintessence is to have the right R-genes in the crop plants to recognise the pathogenic races arriving at the population. And, as outlined above, the race arriving at the crop may change with time. Some varieties may resist for quite a long time and are called durably resistant (Johnson, 1992), other varieties do not resist for long.
Three strategies may be followed to increase the chance of durability of resistance.
The first strategy is "pyramiding" of R-genes in one variety, reducing the R-gene homogeneity to which the pathogen population is exposed, and integrated control (Crute and Pink, 1996). The strategy of "pyramiding" has, in general, not resulted in more durability. This might be a result of the constraints set by using traditional breeding methods. Consequently, R genes were used for which the matching virulence- genes were already present in the pathogen (meta)population. The second strategy may be based on rotating cultivars with different R-genes over seasons, planting cultivars with different R-gene complements in adjacent fields, or using the concept of variety mixtures / multi lines, as described in previous sections (III. A and B). An example of the third strategy is the integration of race-specific resistance in chemical control.
This strategy was, for example, forced on lettuce growers as races of Bremia lactucae in the UK became insensitive to fungicides (Crute and Pink, 1996).
A whole cascade of defence reactions may be turned on after recognition of the pathogen race by (the product of) one R-gene as outlined above. These genes are often called major genes (but see comments by Nelson, 1978). The type of resistance triggered is often complete, qualitative resistance, but may also be incomplete, quantitative resistance. In the case of quantitative resistance, several genes may be involved in the start of the defence reaction of the host: each such minor gene contributes a part to the reaction. If minor genes are involved, the type of resistance is called partial
(Parlevliet, 1989). As pointed out by Parlevliet, partial resistance might be more durable than resistance based on major genes: he referred to the durability of partial resistance of corn to Puccinia sorghi and of barley to Puccinia hordei as examples. He also pointed to the problems involved in breeding for partial resistance, which are primarily based on the difficulties of separating the effects of major genes and minor genes as both often go hand in hand. Also, the protection achieved by partial resistance may depend on the severity of an epidemic, which in turn may depend on environmental conditions. This indicates a point relevant to employing partial resistance and the multiline I variety mixture concept to protect crops from diseases. Epidemics will still occur although at a relatively low level. This might be acceptable from the point of view of durability, but what about the damage caused to the crops by the low level of epidemics? This question will be central to the next section.
D. COMPENSATION AND TOLERANCE
This section deals with the mechanisms of compensation and tolerance. Compensation may operate at the individual plant level and at the population level. Compensation at the individual plant level might be the basis for the mechanism of tolerance. First, compensation at the individual plant level will be described for the weed pathosystem Senecio vulgaris - Puccinia lagenophorae.
The effects of the rust P. lagenophorae on plants of the annual weed S. vulgaris were quantified by Paul and Ayres (1984). The sixth leaf (third leaf pair on the stem) of plants was inoculated with the fungus, or the leaf was not inoculated and plants served as control. After establishment of the rust, the net photosynthesis was measured in the eighth leaf (fourth leaf pair on the stem). Net photosynthesis of leaf eight on plants with an infected sixth leaf was significantly higher than the net photosynthesis of leaf eight on the control plants, compensating partially for the losses in net photosynthesis of the infected sixth leaf. Compensation of losses by increased photosynthesis rate was also demonstrated for crops such as broad beans (Murray and Walters, 1992, and references therein).
If the capacity for compensation differs between two plant genotypes, compensation is an underlying mechanism of tolerance and tolerance is defined as "that capacity of a cultivar resulting in less yield or quality loss relative to disease severity or pathogen development when compared with other cultivars" (Schafer, 1971). Later on, Clarke (1986) argued that demonstration of tolerance is impossible because disease severity can not be measured precisely. A theoretical exercise may, however, make it clear that tolerance is measurable.
Consider the case of two crop varieties. The difference between the two varieties in crop yield is determined if disease is absent (8y). Subsequently, we estimate the disease severity - crop yield relation for each cultivar. The absolute difference between the curves of the varieties is constant, i.e. independent of the disease severity, and equals:
where 8Ytol is the crop yield difference caused by the difference in tolerance between