Plant parasite coevolution

1
Pavan. R
Ph. D Scholar
Department of Genetics and Plant Breeding
University of Agricultural Sciences
Bengaluru-65

Warm Up ActivityWarm Up Activity
1.How do pathogen/plant populations respond to
deployment of host resistance?
2.Is development of 100% resistant variety is
better or a tolerant variety?
3.Can durability of R gene be predicated?
4.How does evolution of virulence affects
pathogen-is there a cost of virulence?
5.Why don't virulent strain dominate and wipe out
susceptible host population?
6.Do plants and pathogen coevolve in agriculture
system? 2

Evolution = CoevolutionEvolution = Coevolution≠≠
 Evolution is the change in the inherited
characteristics of biological populations over
successive generations
Species A has
some trait
unrelated to
species B
Species B evolves
in response to that
trait in species A
4

SymbiosisSymbiosis
 Many symbiotic relationships formed through
coevolution
 Relationship in which two species live closely
together
 Some types of symbiosis are; prey-predator,
mutuality, parasitic, commensalism and
mimicry
7

• One organism benefits from the interaction and
the other is not affected.
Example: Zebra (unaffected) and cattle egret
(benefits)
10

• A type of commensalism that exists in nature.
• One organism evolves to look like the other in
order to benefit itself.
• The mimic benefits from the situation while the
organism it mimics in unaffected.
Example: Orchid flowers
that mimic female
wasps as it invites
male wasps for mating
11

 One organism (parasite) lives on another
organism (host) harming it and possibly
causing death.
 The parasite lives on
or in the body of the
host.
Example:Example: Maize plant
(host) and Oospores
(parasite).
12

 Change in the gene (frequencies) in one
species determine the fitness of genotypes of the
other species, and leads to diversity in host
defences and parasite weaponry.
15

1. A wide variety of ecological and epidemiological
factors can maintain genetic diversity in
resistance and virulence.
2. Stochastic processes in population numberspopulation numbers
and gene frequenciesand gene frequencies can prolong the lifetime
of host and parasite alleles, sometimes greatly.
3. New methods offer the opportunity to test the
plethora of factors in whole population/s of
plants and parasites, not individual organisms.
Three main themes Brown and Tellier,
2011
16

Principles of plant immunity
17

Signal
Hypersensitive
response
Signal transduction
pathway
Avirulent
pathogen
Signal
transduction
pathway
Acquired
resistance
R-Avr recognition and
hypersensitive response
Systemic acquired
resistance
19

“For each resistance gene in
the host there is a
corresponding gene for
avirulence in the pathogen
conferring resistance and
vice versa”
Gene for gene (GFG) model
H.H. Flor, 1942
22

 It is a widely used model to understand the
population genetic processes driving coevolution for
three reasons.
1.It clearly differentiate between phenotypes in both the
host and the parasite, which lend themselves to
mathematical modeling and analysis.
2.By virtue of its clear phenotypes and generally simple
genetics, the GFG relationship is rapidly advancing in
area of research and discoveries in developing new
coevolutionary models.
3.This GFG system are widely and easily applicable to
other types of plant-parasite interaction. 25

26
c = cost of AVR on
RES plant
s = cost of disease
26

Lets implement this in R!!!
Resistant =RES or R
Susceptible = res or r
Avirulence = AVR or A
Virulence = avr or a 27

Brown and Tellier, Annual Review Phytopathology, 201128

In agriculture, alleles get fixed all the time in host and
parasite populations
Woolhouse et al. 2002 Nat Genet
29

Evolution of stripe rust virulence frequencies in wheat
Yr7
30

What do we observe in Nature?
Fixed alleles gradually in frequency (fitness)
That mean, “fixed alleles must remain fixed, but
not happening”
Reason proposed by Vanderplank (1863)
-There must be a cost of carrying the resistance allele
-There must be a cost of carrying the virulence allele
?
31

c = cost of AVR on
RES plant
s = cost of disease
b = cost of virulence
u = cost of resistance
32

Resistant =RES or R
Susceptible = res or r
Avirulence = AVR or A
Virulence = avr or a
33

Brown and Tellier, Annual Review Phytopathology, 2011
34

a) Increasing the cost of RES is to decrease the cost of avr
b) Increasing the cost of avr is to increase the cost of RES 35

Equilibrium points: Stability and instability
Frequency of resistance
Frequencyofvirulence
Unstable equilibrium
Stable equilibrium
36

Unstable equilibrium Stable equilibrium
37

38
Tellier and Brown, Proc. Roy. Soc. B, 2007
38

 Avirulence selects for increased resistance
 Resistance selects for increased virulence
= indirect frequency-dependent selection
→ graph of alleles frequencies (R,a) spirals
 Selection for RES weaker as RES more common
 Or selection for avr weaker as avr more common
= direct frequency-dependent selection
→ graph spirals to a stable equilibrium point
• Tellier and Brown, Proc. Roy. Soc. B, 2007
• Brown and Tellier, Ann Rev Phytopat 2011
41

 The cost of being diseased must be greater than the
cost of RES; otherwise, there would be no net benefit
to a plant in being resistant, and susceptibility would
become fixed in the plant population, followed by
fixation of virulence in the parasite.
 The cost to a parasite of being unable to reproduce on a
host to which it is avirulent is usually very high; in
many cases, mathematical models are simplified by
assuming that AVR parasites cannot reproduce on
RES hosts at all.
43

 Natural selection in which the fitness of an allele’s
depends on its own frequency or that of other alleles
 Two types:
1.Indirect frequency dependent selection (iFDS):
gene frequency in one species affects the fitness of
the other species.
Frequency Dependent Selection (FDS)
 iFDS acts together with the costs of resistance and
virulence to drive the cyclical dynamics of the mode
i.e., Unstable equilibrium
44

2. Direct frequency dependent selection (dFDS):
gene frequency of a species affects its own
contribution to fitness.
 Negative direct frequency dependent
selection(ndFDS): dFDS in which the contribution of
an allele to fitness declines as its frequency
increases
 ndFDS, stabilizes polymorphism in RES and AVR
genes spirals inwards to fixation at the interior
equilibrium point.
45

Processes maintaining polymorphism
in coevolutionary models
 In host-parasite coevolution, all processes that
generate ndFDS in theoretical models involve
uncoupling cycles of gene frequencies in time
or space.
All the models of GFG coevolution assumes that,
both host and parasite are haploid, each in a single
population.
46

 Due to the continuous efforts of theoreticians from
several disciplines, they have shown some factors
that promote stable or quasi-stable polymorphism
falls into one of two categories:
(a) those that lead to stable/balanced polymorphism
by generating ndFDS at RES or AVR loci or
both or, in one case, by overdominance.
(b) those that promote statistical polymorphism, by an
increase in the time to allele fixation reflected
in polymorphism.
47

 The high frequency of autoinfection generates ndFDS
by decreasing selection for avr parasites when the
frequency of avr is high.
Time factor
49

 If a parasite completes its life cycle before its
host plant?
 This results in delayed genetic feedback between
host and parasite populations.
 Such a delay causes changes in allele
frequencies from natural selection to occur
sequentially in host and pathogen populations,
uncoupling the dynamics of allele cycles in the two
species and thus promoting stable equilibrium.
51

Spatial factors
 Two aspects
1.Environmental conditions may not be
homogeneous, so selection pressures may vary
from place to place.
2.Spatial separation may restrict gene flow
between populations by reducing dispersal of
seeds and spores.
52

• dFDS is generated by the migration between
two or more populations that exhibit
asynchronous coevolutionary cycles, in
accordance with models of migration-selection
balance in which they have different
environmental characteristics.
(Levene, 1953)
53

Genetic factors
 Mutations in RES and AVR genes promote
dFDS, although this effect is weaker than
ecological and epidemiological processes.
High mutation rates prevent alleles from going
extinct and promote diversity at loci that might
not be under selection in the current
population.
Salathe et.al., 2005
54

Epidemiological factors
 Density dependent disease transmission create dFDS
Density-dependent disease transmission is assumed
to describe life cycles of parasites following the
off-season (e.g., overwintering or over summering),
when the inoculum load at the start of the next host
season determines the severity of the epidemic.
Gandon et.al.,2002
55

Over dominance factor
 It is a property of diploid organisms in which
heterozygotes have higher mean fitness than
either class of homozygote.
 It arises when a host has two resistance alleles
at a locus and is thus resistant to a greater
proportion of the parasite population than either
class of homozygote, with only one resistance allele
at that locus.
56

 In diploid hosts, however, alleles can be masked
from negative selection and thus prevented from
becoming extinct.
 i.e., Polymorphic equilibria can exist and be
stable, when there is no cost to the parasite of
virulence
57

Genetic factors
Multi-locus GFG systems can display complex
changes in allele frequencies.
When mutation rates are low and the population size
is finite, genotypes with many virulent alleles may
be fixed in the parasite population.
The combination of multi-locus interactions and
meta-population structure promotes a very high
level of random genetic drift and contributes to long-
term statistical polymorphism.
59

Ecological factors
Spatial models can generate complex patterns in the
distribution of genotypes.
In a metapopulation, a few populations can become
desynchronized from the remainder and act as
pacemakers to spread regularly over the whole
metapopulation.
This occurs with several RES and AVR gene pairs, in
a two-dimensional space with limited migration.
60

Geographic mosaic theory of coevolution
 It describes spatially structured heterogeneous
populations, is widely applicable to plants and their
parasites.
 It suggests that variation in selection across
coevolutionary hot and cold spots is of crucial
importance to evolving interactions.
 Forms and strength of natural selection on
interacting species vary among populations.
 Geographic structure and heterogeneous
habitats are thought to promote dFDS and thus,
stable polymorphism. 61

Bore holes Drilling with rostrum Geographic
variation in
rostrum length
(9-19 mm)
Matching
variation in
pericarp
thickness
(6-20 mm)
Toju, 2009. BMC Evolutionary Biology
Japanese camellia
63

Predictions of geographic mosaic theory
of co-evolution
• Co-evolving traits vary among populations
• Traits are well-matched in some local communities
and not in others
• There may routinely be local transient mixtures of
traits.
• Few co-evolving traits will be widespread across
geographic ranges or fixed within interacting spp.
64

Coevolution in agriculture
In agriculture, by contrast, it has been recognized
for almost a century that, with rare exceptions, GFG
resistances only control crop diseases for a few
years.
Brown, 1995
The rates of evolution of RES and AVR genes is
rapid.
Plant-parasite coevolutionary dynamics, nature
follow the trench warfare model, whereas in
agriculture, they take the form of an arms race.
65

• Many of the factors that generate ndFDS and
stabilize genetic diversity in nature are excluded
from farming systems.
• Volunteer plants growing from seed banks are not
encouraged and are often destroyed as weeds.
• Most major crops are annuals, rather than
perennials or biennials.
• The life cycles of crops and their pathogens are
highly synchronized because large fields contain
genetically uniform crop varieties.
66

 Farmers seek to achieve a uniform environment
capable of predictable crop production, rather than
a heterogeneous environment.
 Over the last century, many new RES genes have
been introduced, which is equivalent to a high rate
of mutation in the host.
 Large areas of uniform crops and parasite dispersal
over large distances, mean that host and parasite
life cycles are closely coupled, weakening
epidemiological feedbacks.
67

• Aim of agriculture is to produce large amounts of
food of acceptable quality at affordable prices.
• Problem is
1.Unpredictable outbreaks of disease.
2.The climate is becoming less predictable
3.The number of pesticides available to farmers is
declining
68

• Increasing the genetic diversity of crops, which
can slow the development of epidemics and
reduce the severity of disease.
• Breeding for quantitative resistance, which is
often more durable than GFG resistance because
pathogens often adapt more slowly.
• Using resistance genes for which the
corresponding parasite virulence has a high cost.
Approaches for crop management
(Aim to reduce the speed with which
pathogens adapt to crops)
69

Arms race model
The unstable case with repeated fixation of alleles
has been called an arms race, as the two species
acquire new weapons and defenses.
 Evolution of new R genes relatively young, nearly
identical in sequence to susceptible alleles 70

Trench warfare model
 The stable case with balanced polymorphism has
been described as trench warfare, as allele
frequencies advance and retreat but change little
over time.
 Resistance and susceptibility alleles would be old,
differ greatly in DNA sequence
71

Natural plant
systems
• Yes  No
 Reciprocal
selection (co-
evolution
Agriculture
systems
Characteristic
 Host mobility
 Spatial extent of
particular
resistance genes
 Host fitness (e.g.,
seed production)
 Durability of
resistance alleles
 Battle model
 Influenced by host
dispersal capabilities
 Confined to
relatively small
areas; patchy
 Outcome of co-
evolutionary
processes
 Resistance genes
expected to be
ancient and durable
 Trench warfare?
Epidemics alternate
with period of low
pathogen population
 Not influenced by host
dispersal capabilities
 Presented over large
contiguous areas
 Ensured with
pesticides
 R genes often
obsolete within a few
years
 Arms race?
 Diversity of vir-avir
polymorphisms
 Often highly diverse  Often very limited
72

73
“Running as fast as
possible just to stay in the
same place”
Van Valen

Plant parasite coevolution

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