2014 bgri ali

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