Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution
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Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution

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Jim Kolmer, University of Minnesota

Jim Kolmer, University of Minnesota

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    Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution Presentation Transcript

    • Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution M. Liu - J. A. Kolmer USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108 N. Rodrigue University of Calgary Heredity 2013: published online
    • Puccinia triticina host differentiation Aegilops speltoides (B genome) type Found only in few sites in Israel Durum wheat (AB genome) type Found in Mexico, S. America, Europe, Middle East, little SSR- virulence variation Common wheat (ABD genome) type Worldwide – highly variable
    • World-wide P. triticina SSR groups North America South America Central Asia Middle East Europe New Zealand South Africa Durum isolates (EU, SA, ME, NA) Aegilops speltoides 587 isolates FST = 0.331 Two major clades of common wheat isolates Durum groups distinct from common wheat groups Ethiopian durum types – distinct from other durum isolates
    • Objective: To further infer the evolutionary relationships among P. triticina host specific types with coalescence theory and DNA single nucleotide polymorphism (SNP) markers Initial hypothesis: A.speltoides original form – followed by common wheat form and then durum form Coalescence theory – trace all alleles of a gene back to a most recent common ancestor
    • 2 2 3 2 2 2 2 2 2 3 2 2 1 2 2 2 2 1 3 2 2 1 2 2 2 11 8 2 In total 70 P. triticina samples • 48 on Triticum aestivum • 20 on T. turgidum •  2 on Aegilops speltoides 239 SNPs in 15 loci •  1 house keeping gene (RPB2) •  4 SSR flanking regions •  10 anonymous regions selected by IGV (Integrative Genomics Viewer, Robinson et al. 2011) Isolate sampling
    • Inference of haplotypes based on diploid (dikaryotic) data PHASE 2.1 Stephens, M et al 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68:978—989 Confirmed by sequencing selected loci
    • Phylogenetic analyses CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW AZB1 2 CW AZB6 1 CW BRA19 3 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY154A CW EGY195A CW NZ97 13 3 CW SF98 1 2 CW EGY195B CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW ISR L 2 CW ITA14 1 CW MI91 2 CW NZ97 8 1 CW PER87 4107 2 CW PER95 82 CW Race1 CW SF96 4 1 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW UZB5 2 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG4 1 CW URG6 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 EDETH41 AG ISR1400 AG ISR850 0.1changes Ctg10-3 CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW AZB1 2 CW AZB6 1 CW BRA19 3 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY154A CW EGY195A CW EGY195B CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW ITA14 1 CW MI91 2 CW NKAZ51 2 CW NZ97 8 1 CW PER87 4107 2 CW PER95 82 CW Race1 CW Race9 CW SF96 4 1 CW SF98 1 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 OG ISR850 AG ISR1400 ED ETH4114 7 EDETH41 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG4 1 CW URG6 2 CW UZB5 2 0.1changes Ctg12-2 CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW CAN71 2 96 CW EGY195B CW 99NC CW AZB6 1 CW EGY154A CW HG95 10 1 CW NKAZ51 2 CW NZ97 8 1 CW Race1 CW SKAZ16B CW URG17 3 CW URG4 1 ED ETH4114 7 CW 99NC LBB CW ARG512 1 CW AZB1 2 CW BRA19 3 CW CZ18 09 CW EGY195A CW ES9 1 CW ISR L 2 CW ITA14 1 CW NZ97 13 3 CW PER95 82 CW Race9 CW SF98 1 2 CW TUR29 1 09 CW URG6 2 DW CH14 21 DW F2 2 DW F5 3 CW CZSK95 9 2 CW GBR15 3 09 CW PER87 4107 2 CW TUR1 1 09 CW AZB5 1 CW GBR1 1 09 CW MI91 2 CW CZ10 9 DW M14 3 DW M11 1 EDETH41 CW CZ4 09 DW CA1 2 DW ES27 DW ETH26 2 DW ARG9 3 CW CHL08 3 3 CW CZ11 09 CW CZ20 09 CW HG95 3 2 CW TJK7 1 DW ES1 1 DW ITA1 1 AG ISR1400 AG ISR850 0.05changes Ctg34-1 CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW CAN71 2 96 CW ARG512 1 CW CHL08 3 3 CW TUR29 1 09 EDETH41147 CW CZ10 9 CW TUR1 1 09 CW URG17 3 CW AZB1 2 CW AZB5 1 CW CZ20 09 CW EGY154A CW EGY195A CW GBR15 3 09 CW HG95 10 1 CW HG95 3 2 CW ITA14 1 CW Race9 CW 99NC CW BRA19 3 CW CZ18 09 CW ES9 1 DW CH14 21 CW SF98 1 2 CW UZB5 2 DW ARG9 3 DW CA1 2 DW ES1 1 DW ES27 DW F2 2 DW ITA1 1 DW M11 1 DW M14 3 EDETH262 DW F5 3 CW Race1 CW TJK7 1 CW CZSK95 9 2 CW GBR1 1 09 CW NKAZ51 2 CW NZ97 8 1 CW CZ11 09 CW NZ97 13 3 CW 99NC LBB CW EGY195B CW URG6 2 CW PER95 82 0.5changes Ctg47-1 CW 01AL21 CW 04MN485 CW 04TX32 CW ARG512 1 CW AZB5 1 CW CZ18 09 CW CZSK95 9 2 CW ES9 1 CW ISR L 2 DW ES1 1 DW ES27 DW ITA1 1 CW Race1 CW TJK7 1 DWF22 CW NZ97 13 3 DW ARG9 3 DW CA1 2 DW CH14 21 DWF53 DW M11 1 DW M14 3 DW ETH26 2 EDETH41147 EDETH41 AG ISR1400 OG ISR850 CW SKAZ16B CW 04TX67 CW 99NC CW 99NC LBB CW AZB1 2 CW AZB6 1 CW BRA19 3 CW GBR15 3 09 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ20 09 CW CZ4 09 CW EGY154A CW EGY195A CW EGY195B CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW ITA14 1 CW MI91 2 CW NKAZ51 2 CW NZ97 8 1 CW PER95 82 CW URG6 2 CW Race9 CW SF98 1 2 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG4 1 CW UZB5 2 0.1changes Ctg67-1 CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW EGY154A CW URG4 1 CW AZB1 2 CW AZB5 1 CW AZB6 1 CW CHL08 3 3 CW CZ10 9 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY195A CW ISR L 2 CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW NZ97 13 3 CW SF98 1 2 CW SKAZ16B CW TJK7 1 CW TUR29 1 09 CW UZB5 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 ED ETH26 2 ED ETH4114 7 ED ETH4 1 CW BRA19 3 CW CAN71 2 96 CW HG95 10 1 CW HG95 3 2 CW PER87 4107 2 CW PER95 82 CW SF96 4 1 CW SKAZ44 3 CW URG6 2 CW CZ11 09 CW EGY195B CW MI91 2 CW NZ97 8 1 CW Race1 CW TUR1 1 09 CW URG17 3 0.05changes Ctg84-1 CW 01AL21 CW 04TX32 CW Race1 CW BRA19 3 CW ITA14 1 CW SF96 4 1 CW TUR1 1 09 CW 04TX67 CW 99NC CW EGY195A CW TJK7 1 CW CZ18 09 DW ARG9 3 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 ED ETH4 1 CW SKAZ44 3 CW TUR29 1 09 CW ARG512 1 CW AZB5 1 CW CAN71 2 96 CW CHL08 3 3 CW CZ11 09 CW CZ20 09 CW CZSK95 9 2 CW EGY154A CW GBR15 3 09 CW HG95 10 1 CW HG95 3 2 CW NKAZ51 2 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW URG17 3 CW URG4 1 CW URG6 2 CW UZB5 2 DW F5 3 AG ISR1400 AG ISR850 0.1changes RPB2 CW 01AL21 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW AZB1 2 CW AZB5 1 CW BRA19 3 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW EGY154A CW EGY195A CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW ISR L 2 CW ITA14 1 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW Race1 CW SF96 4 1 CW SF98 1 2 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG4 1 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 DW F5 3 ED ETH4114 7 ED ETH4 1 0.05 changes 161D CW AZB1 2 CW AZB5 1 CW AZB6 1 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY154A CW ES9 1 CW ISR L 2 CW NZ97 13 3 CW PER87 4107 2 CW SF96 4 1 CW SF98 1 2 CW SKAZ16B DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 AG ISR1400 AG ISR850 CW EGY195A CW GBR15 3 09 CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW NKAZ51 2 CW PER95 82 CW Race9 CW SKAZ44 3 CW TJK7 1 CW TUR29 1 09 CW URG6 2 CW UZB5 2 ED ETH4114 7 ED ETH4 1 0.1 changes Ctg9-2 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW AZB1 2 CW TUR29 1 09 CW CZ11 09 CW AZB6 1 CW CZ18 09 CW CZ4 09 CW CZSK95 9 2 CW HG95 10 1 CW HG95 3 2 CW Race1 CW TJK7 1 CW AZB5 1 CW BRA19 3 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ20 09 CW EGY195A CW EGY195B CW ES9 1 CW GBR11 3 09 CW GBR15 3 09 CW GBR1 1 09 CW ISR L 2 CW ITA14 1 CW NKAZ51 2 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW PER95 82 CW SF98 1 2 CW TUR1 1 09 CW URG17 3 CW URG6 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 ED ETH4 1 0.05 changes 91U CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW AZB1 2 CW AZB6 1 CW BRA19 3 CW CAN71 2 96 CW SF98 1 2 CW CZ11 09 CW CZ18 09 CW CZ4 09 CW CZSK95 9 2 CW EGY154A CW EGY195B CW HG95 10 1 CW HG95 3 2 CW NKAZ51 2 CW NZ97 8 1 CW PER95 82 CW Race1 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG6 2 CW AZB5 1 CW CHL08 3 3 CW CZ10 9 CW CZ20 09 CW EGY195A CW ES9 1 CW GBR11 3 09 DW ARG9 3 DW F2 2 CW GBR15 3 09 CW GBR1 1 09 CW ISR L 2 CW ITA14 1 CW MI91 2 CW NZ97 13 3 CW PER87 4107 2 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 ED ETH4 1 0.05 changes 91D CW 01AL21 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW AZB1 2 CW AZB5 1 CW BRA19 3 CW CHL08 3 3 CW CHL08 5 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW EGY154A CW EGY195A CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW HG95 3 2 CW ISR L 2 CW ITA14 1 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW Race1 CW SF96 4 1 CW SF98 1 2 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG4 1 DW 09AZ103A DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 ED ETH4 1 AG ISR1400 0.05changes 161U CW 01AL21 CW 04MN485 CW 04TX67 CW ARG512 1 CW BRA19 3 CW CAN71 2 96 CW EGY154A CW Race9 CW 04TX32 CW 99NC CW 99NC LBB CW AZB1 2 CW AZB5 1 CW AZB6 1 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY195A CW EGY195B CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW ISR L 2 CW ITA14 1 CW MI91 2 CW NKAZ51 2 CW Race1 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW PER95 82 CW SF96 4 1 CW SF98 1 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 ED ETH4 1 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG4 1 CW URG6 2 CW UZB5 2 DW F5 3 AG ISR1400 0.1 changes Ctg5-1 CW 01AL21 CW 04MN485 CW 99NC LBB CW ARG512 1 CW AZB5 1 CW AZB6 1 CW BRA19 3 CW CAN71 2 96 CW CHL08 3 3 CW CZ11 09 CW EGY154A CW EGY195B CW HG95 10 1 CW HG95 3 2 CW NKAZ51 2 CW NZ97 8 1 CW PER95 82 CW Race1 CW Race9 CW URG17 3 CW URG4 1 CW URG6 2 CW TUR1 1 09 CW CZ10 9 CW MI91 2 CW PER87 4107 2 CW CZSK95 9 2 CW 04TX32 CW 04TX67 CW 99NC CW CZ18 09 CW CZ4 09 CW EGY195A CW ES9 1 CW ITA14 1 CW NZ97 13 3 CW SF98 1 2 CW SKAZ16B CW SKAZ44 3 CW UZB5 2 DW ARG9 3 DW CA1 2 DW CH14 21 DW ES1 1 DW ES27 DW F2 2 DW F5 3 DW ITA1 1 DW M11 1 DW M14 3 DW ETH26 2 CW TJK7 1 CW AZB1 2 CW TUR29 1 09 ED ETH4114 7 ED ETH4 1 CW CZ20 09 CW GBR15 3 09 CW GBR1 1 09 0.5changes Ctg1-3 CW 01AL21 CW 04MN485 CW 04TX32 CW 04TX67 CW 99NC CW 99NC LBB CW ARG512 1 CW AZB1 2 CW AZB5 1 CW AZB6 1 CW BRA19 3 CW CAN71 2 96 CW CHL08 3 3 CW CZ10 9 CW CZ11 09 CW CZ18 09 CW CZ20 09 CW CZ4 09 CW CZSK95 9 2 CW EGY154A CW EGY195A CW EGY195B DW ARG9 3 DW CA1 2 DW CH14 21 DW ES27 DW F2 2 DW F5 3 DW M11 1 DW M14 3 DW ETH26 2 ED ETH4114 7 CW ES9 1 CW GBR15 3 09 CW GBR1 1 09 CW HG95 10 1 CW HG95 3 2 CW ISR L 2 CW ITA14 1 CW MI91 2 CW NKAZ51 2 CW NZ97 13 3 CW NZ97 8 1 CW PER87 4107 2 CW PER95 82 CW Race1 CW Race9 CW SF96 4 1 CW SF98 1 2 CW SKAZ16B CW SKAZ44 3 CW TJK7 1 CW TUR1 1 09 CW TUR29 1 09 CW URG17 3 CW URG4 1 CW URG6 2 CW UZB5 2 DW ES1 1 DW ITA1 1 ED ETH4 1 AG ISR1400 AG ISR850 0.05changes Ctg10-2 Durum type Aegilops type Ethiopia durum Legends Common wheat
    • 01AL21_1 PER87_4_1 F5_3_2 SF98_1__2 NZ97_13_2 ITA14_1_2 SKAZ16B_2 ES9_1_2 ISR_L_2_2 EGY195A_2 UZB5_2_2 CZ18_09_2 TJK7_1_2 CHL08_3_1 NZ97_13_1 M14_3_2 F2_2_1 CA1_2_2 M11_1_2 CH14_21_1 ARG9_3_2 ETH26_2_2 F2_2_2 M14_3_1 ITA1_1_2 CA1_2_1 CH14_21_2 ES1_1_1 ETH26_2_1 ARG9_3_1 ES27_2 ITA1_1_1 ES1_1_2 SF98_1__1 ES9_1_1 CZ18_09_1 UZB5_2_1 SKAZ16B_1 ITA14_1_1 CZSK95__2 AZB5_1_2 04TX32_1 ARG512__2 URG17_3_1 CZ11_09_1 TUR29_1_2 ETH4_1_2 E1_1_1 E4090_3_1 ETH4114_1 ETH4_1_1 E10_4_2 E16_4_2 E16_1_2 E6_1_2 E4090_3_2 E16_1_1 E16_4_1 E10_4_1 ETH4114_2 ISR1400_1 ISR1400_2 MI91_2_1 NKAZ51__1 CAN71_2_1 Race9_1 04MN485_1 URG17_3_2 BRA19_3_2 CAN71_2_2 PER95_8_2 URG6_2_1 Race9_2 99NC_LB_1 EGY195B_1 EGY154A_1 NZ97_8__2 URG4_1_2 04MN485_2 MI91_2_2 CZ10_9_2 CHL08_3_2 URG4_1_1 EGY195B_2 EGY154A_2 NZ97_8__1 NKAZ51__2 PER95_8_1 CZ11_09_2 HG95_10_1 ARG512__1 CZSK95__1 PER87_4_2 CZ10_9_1 AZB6_1_1 Race1_1 04TX67_1 AZB1_2_1 AZB6_1_2 TJK7_1_1 TUR29_1_1 HG95_3__1 URG6_2_2 99NC_1 04TX32_2 SKAZ44__1 04TX67_2 AZB1_2_2 CZ4_09_1 CZ4_09_2 EGY195A_1 01AL21_2 GBR1_1__1 GBR15_3_1 CZ20_09_2CZ20_09_1 GBR15_3_2 GBR1_1__2 99NC_LB_2 BRA19_3_1 99NC_2 TUR1_1__1 SF96_4__1 HG95_3__2 M11_1_1 E11_1_2 F5_3_1 ES27_1 E6_1_1 E1_1_2 ISR850_2 ISR850_1 Race1_2 E11_1_1 HG95_10_2 TUR1_1__2 ISR_L_2_1 AZB5_1_1 SKAZ44__2 SF96_4__2 0.01 Splitstree analysis indicated significant tree like branching – no recombination detected – phylogenetic study allowed PHIW test between and within loci – no recombination Loci are selectively neutral
    • Grouping of P. triticina populations based on 239 SNPs from one house keeping gene, four SSR flanking regions and ten anonymous loci. L=340 CI=0.791 RI=0.927 Outgroup: P. persistens P. triticina on A. speltoides appears as sister clade to all others. Most P. triticina on durum wheat formed a clade nested in common wheat group. P.triticina on durum from Ethiopia formed a unique clade. Phylogenetic analyses Bootstrap/Posterior Prob. outgroup 01AL21 GBR15 3 09 GBR1 1 09 CZ20 09 04MN485 04TX32 TUR1 1 09 ITA14 1 04TX67 CAN71 2 96 ARG512 1 EGY195B 99NC 99NC LBB AZB1 2 AZB6 1 BRA19 3 CHL08 3 3 CZ10 9 MI91 2 CZ11 09 CZ4 09 EGY154A HG95 10 1 HG95 3 2 NKAZ51 2 Race1 URG4 1 NZ97 8 1 PER87 4107 2 PER95 82 URG6 2 Race9 SF96 4 1 SKAZ44 3 TUR29 1 09 URG17 3 E11 1 AZB5 1 CZ18 09 CZSK95 9 2 EGY195A ES9 1 ISR L 2 ARG9 3 CA1 2 CH14 21 ES1 1 ES27 F2 2 F5 3 ITA1 1 M11 1 M14 3 ETH26 2 NZ97 13 3 SF98 1 2 TJK7 1 UZB5 2 SKAZ16B ETH4114 7 E1 1 E6 1 E10 4 E16 1 E16 4 E4090 3 ETH4 1 AG ISR1400 AG ISR850 Pp HSZ0689 Pp HSZ0695 100/100/100/100 100/95/97/<50 100/66/100/60 73/<50/69/<50 75/<50/99/<50 100/<50/<50/73 77/53/98/<50 57/<50/<50/<50 76/<50/<50/<50 55/<50/<50/<50 51/<50/<50/<50 100/57/98/57 100/92/100/<50 89/<50/75/<50 100/<50/90/<50 63/<50/59/62 72/<50/<50/<50 72/<50 /<50/<50 56/<50 /<50/<50 63/<50/99/71 73/<50/52/<50 78/<50/66/<50 52/<50/61/<50 52/<50/54/<50 73/<50/82/70 100/100/100/95
    • Carbone Lab Coalescence – Estimation of TMRCA Genetree software Version 9.0 by R. C. Griffiths ü Under infinite sites model ü DNA sequences from non-recombining loci ü Construct maximum likelihood coalescence genealogies ü  Estimate relative mutation ages and time of most recent common ancestors (TMRCA)
    • CarboneLab Coalescence – Estimation of TMRCA Genetree software Version 9.0 by R. C. Griffiths 0.0 0.2 0.4 0.6 0.8 1.0 12 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 303132 33 34 35 3637 38 39 40 41 42 43 44 45 4647 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62636465 66 67 68 69 70 71 72 737475 76 77 7879 8081 82 83 84 85 86 87 88 11 1 11 111 1 1 3 8 13 1 1 143 1 1 1 11 12 2 1 1 42 3 1 2 1 1 AB C DE FGH I J K L MN O P QR S T U VW XY Z [ Present Past Durum wheat Common wheatAegilops 35 isolates 35 haplotypes 88 compatible segregating sites order of coalescence: durum wheat common wheat A. speltoides
    • Coalescence – BEAST Analysis 72 isolates P. persistens outgroup 10,395 sites order of divergence: A. speltoides Eth durum common wheat cultivated durum cultivated durum nested in common wheat type
    • Low levels of genetic divergence among population due to: ü Recent divergence? ü Recurrent gene flow? Nielson, R and Wakeley, J. 2001. Distinguishing migration from isolation: a markov chain Monte Carlo approach. Genetics 158:885 - 896 Coalescence – Isolation with migration
    • Isolation with Migration Reciprocal gene flow common wheat form durum wheat form Unidirectional gene flow common wheat form Ethiopia durum form Ethiopia durum form cultivated durum form (1/3 runs) No gene flow with A. speltoides form
    • Ethiopia P. triticina 2011-2013 180 isolates – collected by M. Acevedo 60% common wheat type MCDSS – MBDSS TCBSQ -Kenya 15% cultivated durum type BBBQJ 15% avirulent Thatcher type on durum landraces – EEEEE Ethiopia – emmer and durum landraces still grown maintain EEEEE types? Coord.2 Coord. 1 Principal Coordinates (PCoA) Durum Eth-durum common wheat SSR genotypes
    • Conclusion Puccinia triticina on Aegilops speltoides diverged initially. There is no recurrent gene flow between P. triticina populations on Aegilops spetoides and Triticum spp.. P. triticina Ethiopia durum type – oldest form on wheat? The divergence between populations on common wheat and cultivated durum wheat is most recent. Total sequence data now available – conduct analysis with >80,000 SNPs – A. speltoides type most divergent
    • ACKNOWLEDGEMENTS We thank Drs. Les Szabo, John Fellers and Christina Cuomo for facilitating ML to access IGV and Pt whole genome database; Kun Xiao, Jerry Johnson and Kim Phuong Nguyen for technical help; Mark Hughes for IT supports; all the labs in CDL providing computers for doing coalescence analyses.