The document discusses the worldwide population structure of the wheat stripe rust pathogen Puccinia striiformis f.sp. tritici (Pst). Genetic analysis of 409 Pst isolates from around the world identified six distinct genetic groups. Pakistan, Nepal, and China showed high genetic diversity and evidence of recombination. The analysis also identified the likely sources of recent Pst invasions in different parts of the world, such as the Middle East, Europe, and Africa.

1. The worldwide Pst population structure and
its temporal maintenance in Pakistan
Sajid Ali
The University of Agriculture, Peshawar, Pakistan
&
Aarhus University, Denmark
#bgri2014

2. 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?

3. Worldwide
Pst
population
structure
Worldwide representative set of 409 isolates, selected from INRA, France and AU, Denmark collection
Genotyped with 20 SSR markers

4. FST values for geographically spaced populations
NWEurope
Mediterranean
Region
CentralAsia
EastAfrica
MiddleEast
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

5. Assignment with STRUCTURE at different K-values
K2
K3
K4
K5
K7
K6
K8
China
Nepal
Pakistan
Middle-­‐East
Central
Asia
Mediterranean
region
NW
Europe
East
Africa
(Ali et al. 2014; PLOS Pathogens)
Worldwide population subdivision

6. Discriminant analysis of
principal components
(ADEGENET)
Identification six distinct
genetic groups of Pst
(Ali et al. 2014; PLOS Pathogens)
Worldwide population subdivision
NW
Europe
China
Nepal
Pakistan
Central
Asia-­‐
Mediterranean
region
Eigen
values’
contribution Number
of
clusters
C
Middle
East-­‐
East
Africa
200
3
2
4
6
8
10

7. France G1
G2
G3
G4
G5
G6
H
Un
Azerbaijan G1
G2
G3
G4
G5
G6
H
Un
France G1
G2
G3
G4
G5
G6
H
Un
Kyrgyzstan G1
G2
G3
G4
G5
G6
Eritrea G1
G2
G3
G4
G5
G6
Afghanistan G1
G2
G3
G4
G5
G6
Cyprus G1
G2
G3
G4
G5
G6
Iran
Israil G1
G2
G3
G4
G5
G6
Lebanon G1
G2
G3
G4
G5
G6
Turkey G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
MoroccoG1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Tunisia G1
G2
G3
G4
G5
G6
Nepal G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Pakistan G1
G2
G3
G4
G5
G6
China G1
G2
G3
G4
G5
G6
- Geographically spaced genetic groups identified
(Ali et al. 2014; PLOS Pathogens)
Worldwide population subdivision and source of recent invasions
Denmark G1
G2
G3
G4
G5
G6
H
Un
Sources
of
these
recent
invasions?
Early 1900s
1979
1996
2003
2000
Early 1900s

8. FST Values
NWEurope
North
America
South
America
Mediterrane
anRegion
CentralAsia
SouthAfrica
EastAfrica
MiddleEast
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.
(Ali et al. 2014; PLOS Pathogens)
Worldwide population subdivision

9. STRUCTURE G1
G2
G3
G4
G5
G6
America
China
Nepal
Pakistan
Middle-­‐East
Central
Asia
Mediterranean
region
NW
Europe
South
Africa
PstS1
and
PstS2
PstS3
East
Africa
G1
G2
G3
G4
G5
G6
DAPC
Recent invasions
(Ali et al. 2014; PLOS Pathogens)
Source of recent invasion

10. France G1
G2
G3
G4
G5
G6
H
Un
Azerbaijan G1
G2
G3
G4
G5
G6
H
Un
France G1
G2
G3
G4
G5
G6
H
Un
Kyrgyzstan G1
G2
G3
G4
G5
G6
Eritrea G1
G2
G3
G4
G5
G6
Afghanistan G1
G2
G3
G4
G5
G6
Cyprus G1
G2
G3
G4
G5
G6
Iran
Israil G1
G2
G3
G4
G5
G6
Lebanon G1
G2
G3
G4
G5
G6
Turkey G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
MoroccoG1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Tunisia G1
G2
G3
G4
G5
G6
Nepal G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Pakistan G1
G2
G3
G4
G5
G6
China G1
G2
G3
G4
G5
G6
- Geographically spaced genetic groups identified
- Sources of recent invasions identified
(Ali et al. 2014; PLOS Pathogens)
Worldwide population subdivision and source of recent invasions
Diversity
and
recombinaIon
in
the
worldwide
populaIons?

11. Recombination in Pakistan,
Nepal and China
(Ali et al. 2014; PLOS Pathogens)
Diversity and recombination in worldwide populations
High genetic and genotypic
diversity in Pakistan, Nepal
and China

12. France G1
G2
G3
G4
G5
G6
H
Un
Azerbaijan G1
G2
G3
G4
G5
G6
H
Un
France G1
G2
G3
G4
G5
G6
H
Un
Kyrgyzstan G1
G2
G3
G4
G5
G6
Eritrea G1
G2
G3
G4
G5
G6
Afghanistan G1
G2
G3
G4
G5
G6
Cyprus G1
G2
G3
G4
G5
G6
Iran
Israil G1
G2
G3
G4
G5
G6
Lebanon G1
G2
G3
G4
G5
G6
Turkey G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
MoroccoG1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Tunisia G1
G2
G3
G4
G5
G6
Nepal G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Pakistan G1
G2
G3
G4
G5
G6
China G1
G2
G3
G4
G5
G6
- Recombination and diversity in Himalayan and Near Himalayan regions
Diversity and recombination in PST worldwide populations
(Ali et al. 2014; PLOS Pathogens)

13. 0.00
1.00
2.00
3.00
4.00
5.00
6.00
4 5 6 7
Telialproduction
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)

14. France G1
G2
G3
G4
G5
G6
H
Un
Azerbaijan G1
G2
G3
G4
G5
G6
H
Un
France G1
G2
G3
G4
G5
G6
H
Un
Kyrgyzstan G1
G2
G3
G4
G5
G6
Eritrea G1
G2
G3
G4
G5
G6
Afghanistan G1
G2
G3
G4
G5
G6
Cyprus G1
G2
G3
G4
G5
G6
Iran
Israil G1
G2
G3
G4
G5
G6
Lebanon G1
G2
G3
G4
G5
G6
Turkey G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
MoroccoG1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Tunisia G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Nepal G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Pakistan G1
G2
G3
G4
G5
G6
China G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Denmark G1
G2
G3
G4
G5
G6
H
Un
- Centre of diversity in Himalayan and Near Himalayan
- Reduction in sexual reproduction ability during ancestral invasion
(Ali et al. 2014; PLOS Pathogens)
Ancestral
relaIonship
of
worldwide
PST
populaIons
Reduction in PST sexual reproduction ability in worldwide populations

15. Ancestral relationship among worldwide populations
ChNpPkChNp Pk Ch Np PkCh NpPk
Ch Np Pk
(Ali et al. 2014; PLOS Pathogens)
ABC analyses with DIYABC (Cornuet et al., 2008)

16. The six genetic groups together
Ancestral relationship among worldwide populations
(Ali et al. 2014; PLOS Pathogens)

17. Mexico G1
G2
G3
G4
G5
G6
Nepal G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Pakistan G1
G2
G3
G4
G5
G6
China G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Azerbaijan G1
G2
G3
G4
G5
G6
H
Un
France G1
G2
G3
G4
G5
G6
H
Un
Kyrgyzstan G1
G2
G3
G4
G5
G6
Eritrea G1
G2
G3
G4
G5
G6
Afghanistan G1
G2
G3
G4
G5
G6
Cyprus G1
G2
G3
G4
G5
G6
Iran
Israil G1
G2
G3
G4
G5
G6
Lebanon G1
G2
G3
G4
G5
G6
Turkey G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
Yemen G1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
MoroccoG1
G2
G3
G4
G5
G6
France G1
G2
G3
G4
G5
G6
H
Un
Tunisia G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Early 1900s
1979
1996
Denmark G1
G2
G3
G4
G5
G6
H
Un
2000
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
Mexico G1
G2
G3
G4
G5
G6
?
- 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
(Ali et al. 2014; PLOS Pathogens)

18. Khyber Peshawar
Nowshera
Haripur
Abbottabad
Tanawal
Mansehra
Attarshisha
Balakot
Siran
Battal
Oghi
Skardu
Battagram
Islamabad
KASHMIR
PAKISTAN
Berberis zone
Non-Berberis
zone
Sampled
in
2010
Sampled
in
2011
Off-season
Berberis zone
200
km
Pakistani
PST
population;
a
high
genetic
diversity
Temporal
maintenance
of
Pakistani
PST
populaIons

19. Development of rapid genotyping DNA extraction à Directly from infected lesion
(Ali et al. 2011; BMC Research Notes)
Pakistani
PST
population;
a
high
genetic
diversity

20. 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)
Pakistani
PST
population;
a
high
genetic
diversity

21. 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
Pakistani
PST
population;
a
high
genetic
diversity

22. 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)
Pakistani
PST
population;
a
high
genetic
diversity

23. - 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.?

24. 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

25. 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

26. Thank
you
Picture provided by Tarnab Agricultural Research Station, Peshawar, Pakistan