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The worldwide Pst population structure and
its temporal maintenance in Pakistan
Sajid Ali
The University of Agriculture, P...
In	
  the	
  context	
  of	
  invasion	
   	
   	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
...
Worldwide	
  Pst	
  population	
  structure 	
   	
   	
  	
  
Worldwide representative set of 409 isolates, selected from...
FST values for geographically spaced populations
NWEurope
Mediterranean
Region
CentralAsia
EastAfrica
MiddleEast
Nepal
Pak...
Assignment with STRUCTURE at different K-values
K2
K3
K4
K5
K7
K6
K8
China
Nepal
Pakistan
Middle-­‐East
Central	
  Asia
Me...
Discriminant analysis of
principal components
(ADEGENET)
Identification six distinct
genetic groups of Pst
(Ali et al. 201...
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...
FST Values
NWEurope
North
America
South
America
Mediterrane
anRegion
CentralAsia
SouthAfrica
EastAfrica
MiddleEast
Nepal
P...
STRUCTURE G1	
   G2	
   G3	
   G4	
   G5	
   G6	
  
America	
  
China	
  
Nepal	
  
Pakistan	
  
Middle-­‐East	
  
Central...
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...
Recombination in Pakistan,
Nepal and China
(Ali et al. 2014; PLOS Pathogens)
Diversity and recombination in worldwide popu...
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...
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
Medit...
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...
Ancestral relationship among worldwide populations 	
   	
  	
  
ChNpPkChNp Pk Ch Np PkCh NpPk
Ch Np Pk
(Ali et al. 2014; ...
The six genetic groups together
Ancestral relationship among worldwide populations 	
   	
  	
  
(Ali et al. 2014; PLOS Pa...
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...
Khyber Peshawar
Nowshera
Haripur
Abbottabad
Tanawal
Mansehra
Attarshisha
Balakot
Siran
Battal
Oghi
Skardu
Battagram
Islama...
Development of rapid genotyping DNA extraction à Directly from infected lesion
(Ali et al. 2011; BMC Research Notes)
Paki...
ns	
  
ns	
  
ns	
  
ns	
  
ns	
  
ns	
  
ns	
  
ns	
   ns	
   ns	
   ns	
  
ns	
  
ns	
  
ns	
  
0	
  
0.1	
  
0.2	
  
0....
A high pathotypic diversity à 53 pathotypes out of 127 isolates tested
With varying virulence frequencies across location...
Comparison of eight temporally sampled populations
Locations
Sample size FST
between
2010 and 2011
Number of resampled MLG...
-  Resistance genes deployment considering the information on worldwide
population subdivision and diversity
- Worldwide v...
Current work:
- Wheat sampling in 2013 in all
major PST regions
- To be SSR genotyped
- Berberis sampling from the
Berberi...
Thanks to
all those who contributed to the
worldwide yellow rust collection
French project: EMERFUNDIS, ANR 07-BDIV-003
Eu...
Thank	
  you
Picture provided by Tarnab Agricultural Research Station, Peshawar, Pakistan
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2014 bgri ali

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2014 bgri ali

  1. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 16. The six genetic groups together Ancestral relationship among worldwide populations       (Ali et al. 2014; PLOS Pathogens)
  17. 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. 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. 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. 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. 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. 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. 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. 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. 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. 26. Thank  you Picture provided by Tarnab Agricultural Research Station, Peshawar, Pakistan

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