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 01AL21CW 04MN485CW 04TX32CW 04TX67CW 99NCCW 99NC LBBCW ARG512 1CW AZB1 2CW AZB6 1CW BRA19 3CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2CW EGY154A

CW EGY195ACW NZ97 13 3CW SF98 1 2

CW EGY195BCW ES9 1CW GBR15 3 09CW GBR1 1 09CW HG95 10 1CW HG95 3 2CW ISR L 2CW ITA14 1CW MI91 2CW NZ97 8 1CW PER87 4107 2CW PER95 82CW Race1CW SF96 4 1CW SKAZ16BCW SKAZ44 3

CW TJK7 1CW UZB5 2

CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG4 1CW URG6 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2ED ETH4114 7ED ETH4 1

AG ISR1400AG ISR850

0.1 changes

Ctg10-3

CW 01AL21CW 04MN485CW 04TX32CW 04TX67CW 99NCCW 99NC LBBCW ARG512 1CW AZB1 2CW AZB6 1CW BRA19 3CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2CW EGY154ACW EGY195ACW EGY195BCW ES9 1CW GBR15 3 09CW GBR1 1 09CW HG95 10 1CW HG95 3 2CW ITA14 1CW MI91 2CW NKAZ51 2CW NZ97 8 1CW PER87 4107 2CW PER95 82CW Race1CW Race9CW SF96 4 1

CW SF98 1 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW ITA1 1DW M11 1DW M14 3DW ETH26 2

OG ISR850AG ISR1400

ED ETH4114 7ED ETH4 1

CW SKAZ16BCW SKAZ44 3CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG4 1CW URG6 2CW UZB5 20.1 changes

Ctg12-2

CW 01AL21CW 04MN485CW 04TX32CW 04TX67CW CAN71 2 96CW EGY195B

CW 99NCCW AZB6 1CW EGY154ACW HG95 10 1CW NKAZ51 2CW NZ97 8 1CW Race1CW SKAZ16BCW URG17 3CW URG4 1ED ETH4114 7

CW 99NC LBBCW ARG512 1

CW AZB1 2CW BRA19 3CW CZ18 09CW EGY195ACW ES9 1CW ISR L 2CW ITA14 1CW NZ97 13 3CW PER95 82CW Race9CW SF98 1 2CW TUR29 1 09CW URG6 2DW CH14 21DW F2 2DW F5 3CW CZSK95 9 2CW GBR15 3 09CW PER87 4107 2CW TUR1 1 09CW AZB5 1CW GBR1 1 09CW MI91 2CW CZ10 9DW M14 3DW M11 1ED ETH4 1CW CZ4 09DW CA1 2DW ES27DW ETH26 2DW ARG9 3

CW CHL08 3 3CW CZ11 09CW CZ20 09CW HG95 3 2CW TJK7 1DW ES1 1DW ITA1 1

AG ISR1400AG ISR850

0.05 changes

Ctg34-1

CW 01AL21CW 04MN485CW 04TX32

CW 04TX67CW CAN71 2 96CW ARG512 1

CW CHL08 3 3CW TUR29 1 09

ED ETH4114 7CW CZ10 9CW TUR1 1 09CW URG17 3CW AZB1 2CW AZB5 1

CW CZ20 09CW EGY154ACW EGY195ACW GBR15 3 09CW HG95 10 1CW HG95 3 2CW ITA14 1CW Race9CW 99NC

CW BRA19 3CW CZ18 09

CW ES9 1DW CH14 21CW SF98 1 2

CW UZB5 2DW ARG9 3DW CA1 2DW ES1 1DW ES27DW F2 2DW ITA1 1DW M11 1DW M14 3ED ETH26 2

DW F5 3CW Race1

CW TJK7 1CW CZSK95 9 2CW GBR1 1 09CW NKAZ51 2

CW NZ97 8 1CW CZ11 09CW NZ97 13 3

CW 99NC LBBCW EGY195BCW URG6 2

CW PER95 820.5 changes Ctg47-1

CW 01AL21CW 04MN485

CW 04TX32CW ARG512 1

CW AZB5 1CW CZ18 09

CW CZSK95 9 2CW ES9 1CW ISR L 2DW ES1 1DW ES27DW ITA1 1

CW Race1CW TJK7 1DW F2 2

CW NZ97 13 3DW ARG9 3DW CA1 2DW CH14 21DW F5 3DW M11 1DW M14 3DW ETH26 2

ED ETH4114 7ED ETH4 1

AG ISR1400OG ISR850

CW SKAZ16BCW 04TX67CW 99NCCW 99NC LBBCW AZB1 2CW AZB6 1

CW BRA19 3CW GBR15 3 09

CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ20 09CW CZ4 09CW EGY154ACW EGY195ACW EGY195BCW GBR1 1 09CW HG95 10 1CW HG95 3 2CW ITA14 1CW MI91 2CW NKAZ51 2CW NZ97 8 1

CW PER95 82CW URG6 2

CW Race9CW SF98 1 2CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG4 1CW UZB5 20.1 changes

Ctg67-1

CW 01AL21CW 04MN485CW 04TX32CW 04TX67CW 99NC

CW 99NC LBBCW ARG512 1CW EGY154ACW URG4 1CW AZB1 2CW AZB5 1CW AZB6 1CW CHL08 3 3CW CZ10 9CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2

CW EGY195ACW ISR L 2

CW ES9 1CW GBR15 3 09CW GBR1 1 09CW NZ97 13 3CW SF98 1 2CW SKAZ16BCW TJK7 1CW TUR29 1 09CW UZB5 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3ED ETH26 2ED ETH4114 7ED ETH4 1

CW BRA19 3CW CAN71 2 96CW HG95 10 1CW HG95 3 2CW PER87 4107 2CW PER95 82CW SF96 4 1CW SKAZ44 3CW URG6 2

CW CZ11 09CW EGY195BCW MI91 2CW NZ97 8 1CW Race1CW TUR1 1 09CW URG17 3

0.05 changesCtg84-1

CW 01AL21CW 04TX32CW Race1

CW BRA19 3CW ITA14 1CW SF96 4 1CW TUR1 1 09

CW 04TX67CW 99NCCW EGY195ACW TJK7 1CW CZ18 09DW ARG9 3DW CH14 21DW ES1 1DW ES27DW F2 2DW ITA1 1DW M11 1DW M14 3DW ETH26 2ED ETH4114 7ED ETH4 1

CW SKAZ44 3CW TUR29 1 09

CW ARG512 1CW AZB5 1CW CAN71 2 96CW CHL08 3 3CW CZ11 09CW CZ20 09CW CZSK95 9 2CW EGY154ACW GBR15 3 09CW HG95 10 1CW HG95 3 2CW NKAZ51 2CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW URG17 3CW URG4 1CW URG6 2CW UZB5 2DW F5 3

AG ISR1400AG ISR850

0.1 changes

RPB2

CW 01AL21CW 04TX32CW 04TX67CW 99NC

CW 99NC LBBCW ARG512 1CW AZB1 2CW AZB5 1CW BRA19 3CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW EGY154ACW EGY195ACW ES9 1CW GBR15 3 09CW GBR1 1 09CW ISR L 2CW ITA14 1CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW Race1CW SF96 4 1CW SF98 1 2CW SKAZ16BCW SKAZ44 3CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG4 1

DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW ITA1 1DW M11 1DW M14 3DW ETH26 2DW F5 3

ED ETH4114 7ED ETH4 1

0.05 changes

161D

CW AZB1 2CW AZB5 1CW AZB6 1CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2

CW EGY154ACW ES9 1CW ISR L 2CW NZ97 13 3CW PER87 4107 2CW SF96 4 1CW SF98 1 2CW SKAZ16BDW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2

AG ISR1400AG ISR850

CW EGY195ACW GBR15 3 09CW GBR1 1 09CW HG95 10 1CW HG95 3 2CW NKAZ51 2CW PER95 82CW Race9CW SKAZ44 3CW TJK7 1CW TUR29 1 09CW URG6 2CW UZB5 2ED ETH4114 7ED ETH4 1

0.1 changes

Ctg9-2

CW 04MN485CW 04TX32CW 04TX67CW 99NCCW 99NC LBB

CW AZB1 2CW TUR29 1 09CW CZ11 09

CW AZB6 1CW CZ18 09CW CZ4 09CW CZSK95 9 2CW HG95 10 1CW HG95 3 2CW Race1CW TJK7 1

CW AZB5 1CW BRA19 3CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ20 09CW EGY195ACW EGY195BCW ES9 1CW GBR11 3 09CW GBR15 3 09CW GBR1 1 09CW ISR L 2CW ITA14 1CW NKAZ51 2CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW PER95 82CW SF98 1 2CW TUR1 1 09CW URG17 3CW URG6 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2ED ETH4114 7ED ETH4 1

0.05 changes 91U

CW 01AL21CW 04MN485CW 04TX32CW 04TX67CW 99NCCW 99NC LBBCW AZB1 2CW AZB6 1CW BRA19 3

CW CAN71 2 96CW SF98 1 2

CW CZ11 09CW CZ18 09CW CZ4 09CW CZSK95 9 2CW EGY154ACW EGY195BCW HG95 10 1CW HG95 3 2CW NKAZ51 2CW NZ97 8 1CW PER95 82CW Race1CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG6 2

CW AZB5 1CW CHL08 3 3CW CZ10 9CW CZ20 09CW EGY195ACW ES9 1

CW GBR11 3 09DW ARG9 3DW F2 2

CW GBR15 3 09CW GBR1 1 09CW ISR L 2CW ITA14 1CW MI91 2CW NZ97 13 3CW PER87 4107 2DW CA1 2DW CH14 21DW ES1 1DW ES27DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2ED ETH4114 7ED ETH4 1

0.05 changes 91D

CW 01AL21CW 04TX32CW 04TX67CW 99NCCW 99NC LBBCW ARG512 1CW AZB1 2CW AZB5 1CW BRA19 3CW CHL08 3 3CW CHL08 5 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW EGY154ACW EGY195ACW ES9 1CW GBR15 3 09CW GBR1 1 09CW HG95 3 2CW ISR L 2CW ITA14 1CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW Race1CW SF96 4 1CW SF98 1 2CW SKAZ16BCW SKAZ44 3CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG4 1DW 09AZ103ADW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2ED ETH4114 7ED ETH4 1

AG ISR14000.05 changes

161U

CW 01AL21CW 04MN485CW 04TX67CW ARG512 1CW BRA19 3CW CAN71 2 96CW EGY154ACW Race9

CW 04TX32CW 99NCCW 99NC LBBCW AZB1 2CW AZB5 1CW AZB6 1CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2CW EGY195ACW EGY195BCW ES9 1CW GBR15 3 09CW GBR1 1 09CW HG95 10 1CW HG95 3 2CW ISR L 2CW ITA14 1CW MI91 2

CW NKAZ51 2CW Race1

CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW PER95 82CW SF96 4 1

CW SF98 1 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW ITA1 1DW M11 1DW M14 3DW ETH26 2

ED ETH4114 7ED ETH4 1

CW SKAZ16BCW SKAZ44 3CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG4 1CW URG6 2CW UZB5 2DW F5 3

AG ISR14000.1 changes

Ctg5-1

CW 01AL21CW 04MN485CW 99NC LBBCW ARG512 1CW AZB5 1

CW AZB6 1CW BRA19 3CW CAN71 2 96CW CHL08 3 3CW CZ11 09CW EGY154ACW EGY195BCW HG95 10 1CW HG95 3 2CW NKAZ51 2CW NZ97 8 1CW PER95 82CW Race1CW Race9CW URG17 3

CW URG4 1CW URG6 2

CW TUR1 1 09CW CZ10 9CW MI91 2

CW PER87 4107 2CW CZSK95 9 2

CW 04TX32CW 04TX67CW 99NCCW CZ18 09CW CZ4 09CW EGY195ACW ES9 1

CW ITA14 1CW NZ97 13 3CW SF98 1 2CW SKAZ16BCW SKAZ44 3CW UZB5 2DW ARG9 3DW CA1 2DW CH14 21DW ES1 1DW ES27DW F2 2DW F5 3DW ITA1 1DW M11 1DW M14 3DW ETH26 2CW TJK7 1

CW AZB1 2CW TUR29 1 09ED ETH4114 7ED ETH4 1

CW CZ20 09CW GBR15 3 09CW GBR1 1 09

0.5 changes

Ctg1-3

CW 01AL21CW 04MN485CW 04TX32CW 04TX67CW 99NCCW 99NC LBBCW ARG512 1CW AZB1 2CW AZB5 1CW AZB6 1CW BRA19 3CW CAN71 2 96CW CHL08 3 3CW CZ10 9CW CZ11 09CW CZ18 09CW CZ20 09CW CZ4 09CW CZSK95 9 2CW EGY154ACW EGY195A

CW EGY195BDW ARG9 3DW CA1 2DW CH14 21DW ES27DW F2 2DW F5 3DW M11 1DW M14 3DW ETH26 2

ED ETH4114 7CW ES9 1CW GBR15 3 09CW GBR1 1 09CW HG95 10 1CW HG95 3 2CW ISR L 2CW ITA14 1CW MI91 2CW NKAZ51 2CW NZ97 13 3CW NZ97 8 1CW PER87 4107 2CW PER95 82CW Race1CW Race9CW SF96 4 1CW SF98 1 2CW SKAZ16BCW SKAZ44 3CW TJK7 1CW TUR1 1 09CW TUR29 1 09CW URG17 3CW URG4 1CW URG6 2CW UZB5 2DW ES1 1DW ITA1 1ED ETH4 1

AG ISR1400AG ISR850

0.05 changes

Ctg10-2

Durum type

Aegilops type

Ethiopia durum

Legends

Common wheat

01AL21_1PER87_4_1

F5_3_2

SF98_1__2NZ97_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_2ISR850_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

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4647

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72 73747576

77 7879 8081

82

83848586

8788

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 1AB C DE FGH I J K L MN O P QR S T U VW XY Z [ Present

Past

Durum wheat Common wheat Aegilops

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?

Coo

rd. 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.