Landscape genetics and gene flow in the banana pathogenic fungus

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Landscape genetics and gene flow in the banana

pathogenic fungus

Mycosphaerella fijiensis

Fabien Halkett, Adrien Rieux, Sonia Cogneau-Perineau, Luc de Lapeyre de Bellaire, Virginie Ravigné, Marie-Françoise

Zapater, Luc Pignolet and Jean Carlier

CIRAD, Montpellier CARBAP, Cameroon

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Mutation

Recombinaison

Genetic drift Gene flow

Selection _{Reproductive strategy}

Dispersal processes Population size Demographic fluctuations Plant resistances Fungicides Adaptation of pathogen populations

Efficient and durable strategies of disease management should be define in time and space taking into account epidemiology

and evolutionary potential of pathogens

Objective: To infer gene flow and dispersal processes in M. fijiensis

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Mycosphaerella fijiensis

• panmictic populations

• Relative demographic stability

Recent epidemic 3 dispersal modes:

- Infected plant material - Ascospores (sexual cycle) - Conidia (asexual cycle)

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Population structure at different geographic scales ofMycosphaerella fijiensis

plant/plantation locality country continent Globe

Fst= 0.28 -0.52 Fst= 0.19 Fst= 0.30 Fst= 0.11 Fst= 0.13 Fst= 0.0 COSTA RICA CAMEROON

 High level of genetic diversity  Panmixia

 Founder effects

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Populations structure and dispersal modes of

Mycosphaerella fijiensis

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Population

analysis in

M. fijiensis

within a production

area (few 100 km long)

Cameroon Transect of 270 km 10 sites (26.8 km) 287 isolats / 15 microsatellites markers Costa Rica Transect of 297 km 15 sites (26.4 km) 347 isolats / 7 PCR-RFLP and 9 microsatellites markers

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Population analysis in

M. fijiensis

within a

production area (few 100 km long)

0.012 to 0.17 0.014 to 0.26 Differentiation between populations, F_st < 0.04 NS < 0.02, NS linkage disequilibrium, r_D ~ 1.00 ~ 1.00 Genotypic diverstiy, D_G 0.41 to 0.59 0.31 to 0.46 Gene diversity, H_E Costa Rica Cameroon

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Population analysis in

M. fijiensis

within a

production area (few 100 km long)

0 0.2 0.4 0.6 0.8 1

1-Lim 2-Agr 3-Yo 4-BaK 5-Fo 6-KoB 7-Man 8-Ey 9-AMb 10-AMa

Differentiation between populations:

Costa Rica: F_st = 0.012 to 0.17 (Costa Rica) Cameroon: F_st = 0.014 to 0.26 (Cameroon) Clustering analysis

Costa Rica: no structure detected Cameroon: number of cluster K = 3

Transect of 270 km

Cluster 1 Cluster 2 Cluster 3

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Population analysis in

M. fijiensis

within a

production area (few 100 km long)

1

4 π D σ ²

b ≈

d_m = mean dispersal distance of ascospores d_m<< 300 km 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0 1 2 3 4 5 6 F_ST/(1 - F_ST) Log distance (km) 0 0.05 0.1 0.15 0.2 0.25 0 1 2 3 4 5 6 F_ST/(1 - F_ST) Log distance (km)

Cameroon Costa Rica

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Population analysis in

M. fijiensis

within a

production area (few 100 km long)

• IBD Analysis on a distance too long in regard

with dispersal capacity of the pathogen

• No realistic genetic model

- Effects of barriers

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10 Km

• 105 sites – 6 isolats / sites (bananas)

• Assignation Bayesian method

GENELAND (Guillot et al., 2005): spatial method

Population analysis at a local scale ( few 10 km long)

1- Landscape genetics analysis

-To deliminate pathogen populations -To detect barriers to gene flow

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10 Km

Population analysis at a local scale ( few 10 km long)

Transect of 33km

2- Isolation by distance analysis -To assess dispersal pattern within continuous population

• 90 sites separated by 1Km, 250 m or 50 m • 2 to 6 isolat / sites

Isolation by distance analysis in continuous population (Rousset, 2000)

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Population analysis in

M. fijiensis

at a local scale

( few 10 km long)

10 km ● Number of population K=2 ● F_ST = 0,111 between Populations 1 and 2 ● Discontinuity observed in 2001 F_ST = 0,14 between samples 5-Fo and 6-KoB from

previous analysis

1 2

5-Fo 6- KoB

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Population analysis in

M. fijiensis

at a local scale

( few 10 km long)

●No physical barrier between pop 1 and 2

●Effects of potential physical barriers not detected

10 Km

Carte des probabilités d’appartenance à la population n° 1

L A T I T U D E LONGITUDE F O R E T M O N T A G N E 1 2 Lanscape genetic analysis

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Population analysis at a local scale ( few 10 km long)

-0.5 -0.3 -0.1 0.1 0.3 0.5 0.7 0.9 1.1 1.3 1.5 -7 -6 -5 -4 -3 -2 -1 0 Ln(d) en degrés F /( 1 -F )

Isolation by distance analysis

- On the transect of 33km: No significant isolation by distance - On the whole sample:

No significant isolation by distance in Pop 1 Significant isolation by distance in Pop 1 + 2

10 km

1 2

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Hypothetical population structure in

M. fijiensis

No IBD on short transects IBD on Long transects 2D sampling in Cameroon

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Conclusions

• IBD model might be not adapted to described dispersal processes and gene flow in M. fijiensis

• Local population structure of M. fijiensis might be a mosaic of distinct patches initiated from single long-distance dispersal evens

Simulation-based approach to test effects on IBD of high densities and demographic scenarios

Landscape genetic study on larger geographical scale Development of new inference models

Description of dispersal processes:

- Stochastic versus gradual dispersal in space - Man mediated versus natural dispersal