2014 bgri ali

The worldwide Pst population structure and its temporal maintenance in Pakistan

Sajid Ali

The University of Agriculture, Peshawar, Pakistan &

Aarhus University, Denmark

#bgri2014

In the context of invasion Pst: Puccinia striiformis f.sp. tritici

PstS1 &

PstS2

2000

2003

Post-2000

Cases of recent invasions in Pst

Australia

1979

South American

Early 1900s

South African population

1996

“Warrior-Kranich” type strains in Europe

2011-present

North American

Early 1900s

Virulence to Yr9

1986

1998

(Milus et al., 2006, Hovmøller et al., 2008; Wellings et al., 2004; Singh et al., 2004)

Population subdivision for this long distance migrating

pathogen?

Worldwide Pst population structure

Worldwide representative set of 409 isolates, selected from INRA, France and AU, Denmark collection

Genotyped with 20 SSR markers

FST values for geographically spaced populations

NW

Europe

Mediterranean

Region

Central A

sia

East A

frica

Middle E

ast

Nepal

Pakistan

China

NW Europe - 0.420 0.380 0.500 0.380 0.370 0.410 0.390

Mediterranean Region 0.000 - 0.020 0.150 0.009 0.280 0.280 0.390

Central Asia 0.000 0.030 - 0.160 0.040 0.230 0.260 0.340

East Africa 0.000 0.000 0.000 - 0.140 0.380 0.280 0.540

Middle-East 0.000 0.020 0.000 0.000 - 0.260 0.250 0.360

Nepal 0.000 0.000 0.000 0.000 0.000 - 0.220 0.210

Pakistan 0.000 0.000 0.000 0.000 0.000 0.000 - 0.450

China 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -

Non-significant FST values (> 0.01) are shown in bold.

(Ali et al. 2014; PLOS Pathogens)

Worldwide population subdivision

Assignment with STRUCTURE at different K-values

K2

K3

K4

K5

K7

K6

K8

China

Nepal

Pakistan

Middle-‐East

Central Asia

Medite

rranean

region

NW Europe

East Africa



Discriminant analysis of principal components (ADEGENET) Identification six distinct genetic groups of Pst



NW Europe

ChinaNepal

Pakistan

Central Asia-‐Mediterranean

region

Eigen values’ contribution Number of clusters

BIC

CMiddle East-‐East Africa

A

200 300 400 500 600

2 4 6 8 10

B

France G1G2G3G4G5G6HUn

Azerbaijan G1G2G3G4G5G6HUn


Kyrgyzstan G1G2G3G4G5G6

Eritrea G1G2G3G4G5G6

Afghanistan G1G2G3G4G5G6

Cyprus G1G2G3G4G5G6

Iran

Israil G1G2G3G4G5G6

Lebanon G1G2G3G4G5G6

Turkey G1G2G3G4G5G6

Yemen G1G2G3G4G5G6

Yemen G1G2G3G4G5G6


Morocco

G1G2G3G4G5G6


Tunisia G1G2G3G4G5G6

Nepal G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Pakistan G1G2G3G4G5G6

China G1G2G3G4G5G6

-  Geographically spaced genetic groups identified


Worldwide population subdivision and source of recent invasions

Denmark G1G2G3G4G5G6HUn

Sources of these recent invasions?

Early 1900s

1979 1996

2003

2000

Early 1900s

FST Values

NW

Europe

North

Am

erica

South A

merica

Mediterrane

an Region

Central A

sia

South Africa

East A

frica

Middle E

ast

Nepal

Pakistan

China

NW Europe - 0.039 0.001 0.420 0.380 0.498 0.500 0.380 0.370 0.410 0.390 North America 0.100 - 0.046 0.409 0.368 0.485 0.490 0.378 0.364 0.400 0.398 South America 0.410 0.100 - 0.435 0.396 0.514 0.511 0.393 0.379 0.416 0.405 Mediterranean Region 0.000 0.000 0.000 - 0.020 0.109 0.150 0.009 0.280 0.280 0.390 Central Asia 0.000 0.000 0.000 0.030 - 0.044 0.160 0.040 0.230 0.260 0.340 South Africa 0.000 0.000 0.000 0.010 0.190 - 0.229 0.160 0.298 0.314 0.419 East Africa 0.000 0.000 0.000 0.000 0.000 0.006 - 0.140 0.380 0.280 0.540 Middle-East 0.000 0.000 0.000 0.020 0.000 0.000 0.000 - 0.260 0.250 0.360 Nepal 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.220 0.210 Pakistan 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.450 China 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - FST for aggressive strains 0.420 0.408 0.434 0.000 0.010 0.099 0.150 0.010 0.270 0.270 0.390

P-value for aggressive strains 0.000 0.000 0.000 0.860 0.070 0.040 0.000 0.020 0.000 0.000 0.000

Non-significant FST values (> 0.01) are shown in bold.



STRUCTURE G1 G2 G3 G4 G5 G6

America

China

Nep

al

Pakistan

Middle-‐East

Central A

sia

Med

iterranean

region

NW Europ

e

South Africa

PstS1 and PstS2

PstS3

East Africa

G1 G2 G3 G4 G5 G6 DAPC

Recent invasions


Source of recent invasion







Cyprus G1G2G3G4G5G6

Iran

Israil G1G2G3G4G5G6


Turkey G1G2G3G4G5G6

Yemen G1G2G3G4G5G6

Yemen G1G2G3G4G5G6


Morocco

G1G2G3G4G5G6



Nepal G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6


China G1G2G3G4G5G6

-  Geographically spaced genetic groups identified -  Sources of recent invasions identified


Worldwide population subdivision and source of recent invasions

Diversity and recombinaIon in the

worldwide populaIons?

Recombination in Pakistan, Nepal and China


Diversity and recombination in worldwide populations

High genetic and genotypic diversity in Pakistan, Nepal

and China







Cyprus G1G2G3G4G5G6

Iran

Israil G1G2G3G4G5G6


Turkey G1G2G3G4G5G6

Yemen G1G2G3G4G5G6

Yemen G1G2G3G4G5G6


Morocco

G1G2G3G4G5G6



Nepal G1G2G3G4G5G6


Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6


China G1G2G3G4G5G6

-  Recombination and diversity in Himalayan and Near Himalayan regions

Diversity and recombination in PST worldwide populations


0.00

1.00

2.00

3.00

4.00

5.00

6.00

4 5 6 7

Telia

l pro

duct

ion

Weeks after inoculation

China

Nepal

Pakistan

Middle-East

Mediterranean

France

Telial progress curve for 56 PST isolates according to their geographical origin

Reduction in PST sexual reproduction ability in worldwide populations

(Ali et al. 2010; Fungal Genetics and Biology)







Cyprus G1G2G3G4G5G6

Iran

Israil G1G2G3G4G5G6


Turkey G1G2G3G4G5G6

Yemen G1G2G3G4G5G6

Yemen G1G2G3G4G5G6


Morocco

G1G2G3G4G5G6



Mexico G1G2G3G4G5G6

Nepal G1G2G3G4G5G6


Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6


China G1G2G3G4G5G6

Mexico G1G2G3G4G5G6


-  Centre of diversity in Himalayan and Near Himalayan -  Reduction in sexual reproduction ability during ancestral invasion


Ancestral relaIonship of worldwide PST populaIons

Reduction in PST sexual reproduction ability in worldwide populations

Ancestral relationship among worldwide populations

Ch Np Pk Ch Np Pk Ch Np Pk Ch Np Pk

Ch Np Pk


ABC analyses with DIYABC (Cornuet et al., 2008)

The six genetic groups together

Ancestral relationship among worldwide populations


Mexico G1G2G3G4G5G6

Nepal G1G2G3G4G5G6


Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6


China G1G2G3G4G5G6







Cyprus G1G2G3G4G5G6

Iran

Israil G1G2G3G4G5G6


Turkey G1G2G3G4G5G6

Yemen G1G2G3G4G5G6

Yemen G1G2G3G4G5G6


Morocco

G1G2G3G4G5G6



Mexico G1G2G3G4G5G6

Early 1900s

1979 1996


2000

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

Mexico G1G2G3G4G5G6

?

-  The worldwide spread with population subdivision and loss of sexual reproduction - PST possibly originated in the Himalayan and Near Himalayan region

-  Re-emergence linked with the recent invasions

Overall conclusions on worldwide populations


Khyber PeshawarNowshera

HaripurAbbottabad

TanawalMansehra

Attarshisha

BalakotSiran

Battal

Oghi

Skardu

Battagram

Islamabad

KASHMIR

PAKISTAN

Berberis zone

Non-Berberis zone

Sampled in 2010

Sampled in 2011

Off-seasonBerberis zone

200 km

Pakistani PST population; a high genetic diversity

Temporal maintenance of Pakistani PST populaIons

Development of rapid genotyping DNA extraction à Directly from infected lesion

(Ali et al. 2011; BMC Research Notes)


ns

ns

ns ns

ns ns

ns ns ns ns ns ns

ns

ns

0

0.1

0.2

0.3

0.4

0.5

Heterozygosity

Geographical region

He Ho

Year Location Sample

size MLGs

Genotypic diversity

2010

Khyber 35 25 0.971 Peshawar 12 9 0.939 Nowshera 19 8 0.673 Haripur 42 20 0.864 Abbottabad 34 31 0.993 Mansehra 28 27 0.997 Battal 46 33 0.967 Battagram 9 9 1 Attarshisha 30 22 0.966 Balakot 24 18 0.975 Skardu 63 54 0.991

2011

Peshawar 33 23 0.973 Nowshera 16 10 0.825 Abbottabad 18 9 0.706 Mansehra 61 54 0.991 Tanawal 22 19 0.983 Siran 51 33 0.939 Oghi 19 16 0.977 Battal 35 30 0.99 Battagram 20 17 0.984 Attarshisha 40 31 0.953 Balakot 27 21 0.977

A high genotypic diversity and non-significant FIS

across all locations

(Ali et al. 2014; Molecular Ecology)


A high pathotypic diversity à 53 pathotypes out of 127 isolates tested With varying virulence frequencies across locations

Location Number of isolates

pathotyped No. of different

pathotypes detected No. of different

virulences detected Khyber 18 14 16 Peshawar 4 2 13 Nowshera 5 3 15 Haripur 20 13 15 Abbottabad 14 10 15 Mansehra 5 5 15 Battal 24 18 17 Battagram 6 6 15 Attarshisha 16 11 12 Balakot 11 11 16 Skardu 4 4 17

Maximum no. of virulences tested - 26 Maximum no. of pathotypes observed 53 -

- Vr2, Vr6, Vr7, Vr8, Vr9 and VrSu in a high frequency - Vr5, Vr15 detected - AvrVicto detected


Comparison of eight temporally sampled populations

Locations

Sample size FST between

2010 and 2011 Number of resampled MLGs and their frequency over two years*

Peshawar 45 0.0719 1 (5:3)

Nowshera 35 0.0863 1 (13:1)

Abbottabad 52 0.2375 1 (1:11)

Mansehra 89 0.0522 2 (2:2) (1:6)

Battal 81 0.0740 0

Battagram 29 0.0661 0

Attarshisha 70 0.1359 0

Balakot 51 0.0609 1 (1:5)

(Ali et al. 2014; Molecular Ecology)


-  Resistance genes deployment considering the information on worldwide population subdivision and diversity

- Worldwide virulence structure to be re-analyzed

Overall conclusions and perspectives

-  Future invasion risks assessment and management

-  Broader perspective for breeders, considering invasions

-  Role of sexual reproduction in PST biology in Pakistan and China

- What strategy to adapt while considering the Berberis spp.?

Current work: - Wheat sampling in 2013 in all

major PST regions

- To be SSR genotyped

-  Berberis sampling from the Berberis zone

-  Sequence characterization to identify the species (and f.sp.)

HEC-Start-up Research Grant

Rust-Fight Danish Council for Strategic Research

The University of Agriculture, Peshawar, Pakistan

Pakistani PST population; a high genetic diversity Current work

Thanks to all those who contributed to the

worldwide yellow rust collection

French project: EMERFUNDIS, ANR 07-BDIV-003 European Integrated Project: BIOEXPLOIT, FOOD-CT-2005-513959 Higher Education Commission, Pakistan

Thank you

Picture provided by Tarnab Agricultural Research Station, Peshawar, Pakistan