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Population genetic analyses of plant pathogens: new challenges and opportunities
C.C. Linde{ XE "Linde, C.C." }
Botany and Zoology, Research School of Biology, College of Medicine, Biology and Environment, Bldg. 116, Daley Rd, Australian National
University, Canberra, ACT 0200, Australia
INTRODUCTION
The study of population genetics attempts to investigate
evolutionary forces such as mutation, migration, genetic drift,
selection and recombination, and how gene frequencies change
in populations to shape their genetic structure. These
evolutionary forces and the interaction amongst them are
particularly important in plant pathogens where, combined with
the pathogen’s life history characteristics, they determine the
evolutionary potential. The population genetics of plant
pathogens has been investigated for at least 30 years. Early
studies on population genetics of plant pathogens concentrated
on the effect sexual reproduction has on levels of genetic
diversity in populations (Burdon and Roelfs, 1985a, b) and what
impact that had on disease control. Similar studies have
continued with investigations of pathogen capacities to rapidly
adapt to new environments such as developing resistance
against a fungicide or overcoming a resistance gene in the plant
host (McDonald and Linde, 2002).
Although the questions we ask in the population genetics of
plant pathogens has not changed significantly, advances in DNA
sequencing and analytical approaches have significantly
improved the accuracy of parameter estimates. In particular,
coalescent based approaches are a powerful extension of
classical population genetics because it is a collection of
mathematical models that can accommodate biological
phenomena as reflected in molecular data. The emphasis in
coalescent thinking is to view populations backwards in time,
using the divergence observable in a population to estimate the
time to a most recent common ancestor. This ancestor is the
point where gene genealogies `coalesce’, in a single biological
organism.
The barley scald pathogen, Rhynchosporium secalis, will be used
as an example to illustrate the importance of some of these
evolutionary forces and how coalescent based methods
significantly improved our understanding of the pathogens’
biology.
MATERIALS AND METHODS
Populations of R. secalis were characterised with 14
microsatellite loci (Linde et al., 2009) and several sequence loci
(Zaffarano et al., 2009). Several population genetic parameters
were investigated, including migration among populations. This
was investigated with a coalescent method in the program IM
(Hey and Nielsen, 2004) and results were compared to estimates
derived from traditional F ST estimates (Weir and Cockerham,
1984).
pathogen populations are constantly influenced by the host
populations or human‐mediated migration.
With coalescent methods, the direction of migration is obtained.
This means the major source and sink populations for migration
can be determined which is useful in determining breaches of
quarantine or major migration routes due to eg prevailing wind
currents. In R. secalis, unusually high migration rates in both
directions between Australia and South Africa and Australia and
New Zealand cause particular concern for disease management.
A comparison of the results revealed that migration estimates
based on coalescent analyses were frequently non‐symmetric,
meaning one population contributed significantly more migrants
than the other. This contributed to migration estimates derived
from F st being over‐ or under‐estimated. Furthermore, F st derived
migration estimates were usually underestimated when the
migration was high, and/or when population sample sizes were
low.
Coalescent analyses provided population genetic parameter
estimates that are more reliable, are less dependent on
population sizes being stable and are affected less by
populations with small sample sizes. Improved analyses and
their usefulness in plant pathology are discussed.
REFERENCES
1. Burdon, J.J., Roelfs, A.P., 1985a. Isozyme and virulence variation in
asexually reproducing populations of Puccinia graminis and
Puccinia recondita on wheat. Phytopathology 75, 907–913.
2. Burdon, J.J., Roelfs, A.P., 1985b. The effect of sexual and asexual
reproduction on the isozyme structure of populations of Puccinia
graminis. Phytopathology 75, 1068–1073.
3. McDonald, B.A., Linde, C., 2002. Pathogen population genetics,
evolutionary potential, and durable resistance. Annu. Rev.
Phytopathol. 40, 349–379.
4. Linde, C.C., Zala, M., McDonald, B.A., 2009. Molecular evidence for
recent founder populations and human‐mediated migration in the
barley scald pathogen Rhynchosporium secalis. Molecular
Phylogenetics and Evolution 51, 454–464.
5. Zaffarano, P.L., McDonald, B.A., Linde, C.C., 2009.
Phylogeographical analyses reveal global migration patterns of the
barley scald pathogen Rhynchosporium secalis. Molecular Ecology,
279–293.
6. Hey, J., Nielsen, R., 2004. Multilocus methods for estimation
population sizes, migration rates and divergence times, with
application to the divergence of Drosophila pseudoobscura and D.
persimilis. Genetics 167, 747–760.
7. Weir, B.S., Cockerham, C.C., 1984. Estimating F‐statistics for the
analysis of population structure. Evolution 38, 1358–1370.
Keynote speaker
RESULTS AND DISCUSSION
The results of this comparison revealed that coalescent based
approaches offer several advantages over other analytical
methods to estimate parameters such as migration and genetic
drift. Traditional measures of the translation of F ST into gene
flow assume that subpopulations have the same size, population
sizes are constant, or that there are infinitely many populations,
and that migration rates are all symmetric. Due to these
underlying assumptions, migration estimates derived from F ST
are almost always flawed and incorrect estimates are achieved
when these assumptions are not met. This is often the case since
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