Download Combining genotypic and phenotypic predictions of invasive

Emerging plant diseases:
combining
bi i genotypic
t i and
d phenotypic
h
t i
data to improve our predictions of
i
invasive
i pathogens
th
Matteo Garbelotto, U.C. Berkeley, with funding from NSF,
USDA and the Gordon and Betty Moore Foundation
USDA,
Croucher P., Danti R., Della Rocca G.,
Dodd R.,
R Kasuga T
T., Gonthier P.,
P Huberli
D., Mascheretti S., Pautasso M, Rizzo D.
Genotype
Genotype-----Phenotype
Phenotype
(Inheritance-----------------Selection)
•
•
•
•
Genetic code: mendelian inheritance
Genetic code: uniparental
Epigenetic: cytoplasmic, gene expression
E i
Environmental
t l ffactors
t
Understanding phenotype is very complex and
requires extensive experimentation (common
gardens, reciprocal plantings, crosses and
progeny, segregation analysis)
• Can we genetically identify causal agents
and differentiate it from closely related
microbes?
– Synonymy
S
often
ft due
d to
t our ignorance
i
and
d
inability to compare microbes side by side
(time and space issues)
– Genetics (and hard work) have helped:
Ophiostoma ulmi- O. novo-ulmi; Ceratocystis fimbriata and other
C. spp, Seiridium cardinale and other S. spp, Fusarium
subglutinans and relatives, Heterobasidion annosum and H.
irregulare, among others
– Let’s assume we can (wishful thinking….)
Genetic structure of an
invasive microbial species
• Species has ancient
lineages evolved in
isolation (drift, selection,
etc.)
• Introduced population only
partial representation of
source
• Specific genotypes
associated
i t d with
ith specific
ifi
phenotypes
= introduced
Species has ancient lineages evolved
in isolation (e.g.
(
P. ramorum))
• Genetic
G
ti divergence
di
• Phenotypic diversity:
– Mating type
– Growth rate
– Pathogenicity
Mating type
• Because of long isolation (drift without migration) P.
ramorum lineages have different mating types: NA1
and
d NA2 are A2 while
hil EU1 iis A1
A1. A
Approximately
i t l
66% of P. ramorum pairings (12 A2 by 1 A1) will
produce oospores
• Loci under selection may be linked to mating type
• Recombination will accelerate evolutionary rate (see
Prediction section)
• Sexual structures mayy confer advantage
g
Sexual structures may confer
advantage
• Sexually produced oospores allow for
survival in harsher climatic conditions
.
• Homothallic species such as P. nemorosa and P.
pseudosyringae are less virulent than P. ramorum but
are also introduced in California (Linzer et al. 2008)
and have a much broader distribution
distribution, why?
– History (introduced earlier ?)
– Because homothallic they produce oospores
Growth rate…
Radial growth in vittro
15
NA2 vs. NA1
10
5
0
NA1
NA2
12C
NA1
NA2
20C
NA1
NA2
24C
Lineage across temperatures
NA 1 < NA2 , P < 0
0.0001
0001
Pathogenicity among lineages
Interaction of lineage and host: beware of
growth rates…
80
3.5
300
70
3.0
Mean(Lesion area mm2)
60
Mean(Lesion area m
mm2)
250
200
150
100
50
0
(Mean(Lesion area cm2)
350
NA1
NA2
12
NA1
NA2
20
NA1
NA2
24
Rhododendron sp.
Across temperatures
p
NA1 < NA2, P = 0.05
2.5
50
2.0
40
1.5
30
1.0
20
0.5
10
0
NA1
NA2
12
NA1
NA2
20
NA1
NA2
0.0
NA1
NA2
24
Umbellularia californica
Across temperatures
p
NA1 < NA2 , P = 0.008
Camellia setsugeken
At 20C ((others not tested))
NA1 > NA2 , P < 0.0001
Introduced population only partially
represents phenotypes and genotypes
of source
• One or more mating types?
• How low is genetic diversity?
• If introduced population has fixed alleles at any locus,
what is the consequence?
• Genotypic/Phenotypic diversity low
• If Host genotype x Pathogen genotype interaction
exists genotypic diversity will affect breeding
exists,
programs
Seiridium cardinale and cypress
canker
k (i
(in review
i
Phytopathology)
Ph t
th l
)
•
•
•
•
Mortality in Mediterranean up to 95% locally
Introduced in mid 1900s
No sex observed in Mediterranean
Little variability observed in Mediterranean
• PERFORMED A GENETIC ANALYSIS OF
PATHOGEN COMPARING MEDITERRANEAN AND
CALIFORNIA POPULATIONS AND A FEW OTHER
PROVENANCES USING SEQUENCE DATA AND
MICROSATELLITES
Result of comparison
p
• All indices of diversity much higher in
CA than in MED
• LD (linkage disequilibrium) present only
in MED,
MED sex in CA?
• Two haplotypes (link to mating types?)
b
based
d on sequence d
data
t only
l iin CA
CA,
one in the rest of the world
• Microsateliite data indicate two
introductions in MED both from CA: one
genotype only introduced in each
instance
Consequences of strong
bottleneck: no sex
Consequences of bottleneck (2)
All genotypes closely related:
easier to breed host for resistance
S. cardinale p
present in both
CA and MED but…
• Both mating types probably present in
CA
• Greater genic diversity in CA
• Introducing different genotypes from CA
may accelerate evolution if different
mating type introduced and may (even
without sex) nullify resistant cypress
lines (only disease management option)
Specific genotypes associated
with specific phenotypes
• Some specific genotypes carry specific
phenotypes
h
t
• Phytopthora cinnamomi: different
genotypes associated with different
commodities and transported around
the world: are genotypes equivalent?
1- Huge oak mortality in Colima,
M i (T
Mexico
(Tainter
i t ett al.l 2000)
2- Problems in CA Christmas tree
n rseries (2002)
nurseries
(2002).
3- Quasi-extinction of rare manzanita in
CA (Swiecki et al.
al 2004)
• All th
three recently
tl reported
t d (10 years))
• All three associated with P. cinnamomi
• All three associated with the same novel
genotype
g
yp of the p
pathogen
g
Widespread mortality of Ione manzanita
caused by P. cinnamomi
Newly
described
genotype
associated with
all three recent
emergent
problems:
should all
genotypes be
considered the
same?
Genotype
Genotype-----Phenotype
Phenotype
(How will they change in exotic populations?)
• B
Bottleneck
ttl
k and
d founder
f
d effects
ff t
• Purifying selection
• Novel selection pressures: evolutionary
p
leaps
• Hybridization
Understanding linkages between genotype and
phenotype is complex. Predicting how
phenotype
p
yp will change
g in invasive p
populations
p
even more challenging
Genotypic and phenotypic diversity do not
necessarily
y correlate: S. cardinale g
growth rate
• Mean always lower for MED (founder effect)
g ) much higher
g
for MED
• Variance ((range)
population even if much narrower genetically:
IN NOVEL PATHOSYSTEMS
MALAPTATION MAY LEAD TO GREATER
VARIABILITY OF PHENOTYPE ?
Circles represent genotypes:
red shade indicates those that
were introduced, are common
in all infested sites, and are the
progenitors of all other
genotypes. Relatedness is
indicated by connecting lines
From 3 related genotypes to
about 100 related genotypes
in absence of sex and in
about
b t 20 years. IIn S
S.
cardinale 1 genotype gave
rise to about 24 in 60 years
Predicting the future
• Diversification directly dependent on:
- number and relatedness of introduced
genotypes
- type (sex
(sex. vs
vs. asex
asex.)) and rate of
reproduction
- population
l ti size
i
- transmission rate
(pathogenicity/saprobic ability/ecological
adaptation)
Predicting the future
• While diversification is not needed: a
single
g g
genotype
yp of a p
pathogen
g could
cause havoc…
• transmission rate is key: pathologists
have overemphasized pathogenicity
aspect while neglecting ecology
Introduction by US troops of H. irregulare
from North America into Italy shows
ecology may be more important
North
N
th American
A
i
H
Heterobasidion
b idi
irregulare and pine mortality associated with it
• Pathogenicity same as native sp.
• Sporulation much more significant in exotic
p
ability
y more significant
g
in exotic
• Saprobic
3
volum
me colonized
d (cm )
500
450
400
b
350
300
250
200
150
a
100
50
0
H. annosum
H. irregulare
25% of genotypes had
admixed genomes
All loci potentially
g
in first pphase of
introgressed
sympatry
20% of cases were
recombinant novel alleles
Introduced Forest Pathogens
Chestnut Blight
Cryphonectria parasitica
Dutch Elm Disease
Ophiostoma umli & O. novo-ulmi
White Pine Blister Rust
Cronartium ribicola
Phytophthora root rot
Phytophthora cinnamomi
Predicting impacts of invasions (I)
I = k * ithcps / v
- k = constant depending on the pathosystem
- i = number of introduction events
- t = transmission rate
- h = density of sporulating hosts
- c = permeability of landscape
- p = favorability of climatic conditions
- s = synchronicity between host susceptibility and
pathogen life cycle
- v = spatial variation in susceptible hosts
There is no simple calculation of some
of these variables (e.g. “t”) because of
complex
p
interactions and trade-offs
• Spore size, reproductive rate, density of
hosts etc
hosts,
etc. may counterbalance one another
• To use an old terminology probably familiar to
most here:
- r selected pathogens (P. ramorum: huge
reproductive potential in short time)
- K selected pathogens (S. cardinale or F.
circinatum: prolonged sporulation)
CONCLUSIONS
• Genetic structure of exotic microbe species is
extremely relevant: lineages and even genotypes
within species may deserve our full attention
• Comparison of source and introduced population is
important in assessing risk and improving predictions
• Most linkages
g between p
phenotype
yp and g
genotype
yp are
based on circumstantial evidence. Direct
experimentation needed. Malaptation in exotic
systems may result in great phenotypic variability
• Genetic structure can be used to determine whether
sex is occurring in source and in introduced pops.
Sex can directly affect adaptation
CONCLUSIONS
• Sex can lead to greater range because of production
of sexual spores
• Plant pathologist need to emphasize role of ecology
besides pathogenicity
• Estimation of essential variables is alternative to
predictions based on simple biological and climatic
traits
• Hybridization will complicate predictions and
accelerate adaptation (basic unpredictable nature of
outcome when hybridization is ongoing)
Finally…
• New evidence from P. ramorum suggests
significant role of epigenetic control. That
means individual
i di id l genotypes
t
with
ith a diff
differentt
history will behave differently permanently.
Genetic information may need to be matched
up by knowledge of history of where
genotypes
g
yp have been