Understanding the Genetic Landscape of Puccinia graminis f.sp. tritici From a Global to a Country Perspective
1. ì
Understanding
the
genetic
landscape
of
Puccinia
graminis
f.
sp.
tritici
from
a
global
to
a
country
perspective
Les
J.
Szabo
USDA
ARS
Cereal
Disease
Laboratory
St.
Paul,
Minnesota,
USA
Botma
Visser
Department
Plant
Sciences
University
of
Free
State
Bloemfontein
9300,
South
Africa
Co-‐Authors:
ChrisIna
Cuomo
&
S.
Sakthikumar
Broad
InsItute
MIT
and
Harvard
Cambridge,
MA
USA
Jerry
L.
Johnson
USDA
ARS
Cereal
Disease
Laboratory
St.
Paul,
Minnesota,
USA
Robert
F.
Park
ACRCP,
Plant
Breeding
InsItute
University
of
Sydney
Eveleigh
New
South
Wales,
Australia
2. Pgt
genotyping
project
ì ObjecIves:
ì Characterize
the
global
geneIc
landscape.
ì Develop
molecular
diagnosIc
tools.
ì Track
regional
and
global
movement.
ì Elucidate
evoluIon
of
Pgt.
3. Pgt
genotyping
project:
Partners
Robert Park
Univ. of Syndey
USDA ARS CDL
Zak Pretorius & Botma Visser
Univ. of Free State
Tom Fetch
Agriculture & Agi - Food Sarah Hambleton
Agriculture & Agi - Food
Silvia German
Y. Anikster & H. Sela
Tel. Aviv University
Alexey Morgounov
CIMMYT
Funding:
DRRW
phase
II,
USDA
4. Pgt
genotyping
project:
Methods
ì Genome-‐wide
genotyping
ì Re-‐sequencing
ì Illumina
paired-‐end
reads
(101
bases,
20-‐30X)
ì 70
isolates
analyzed
ì ~
1
million
SNPs
ì Pgt
SNP
Chip
ì 1,536
SNP
loci
ì 153
isolates
analyzed
ì SNP
Panel
ì Ug99
Race
Group
(Ug99
RG)
ì 25
SNP
Loci
5. DistribuIon
of
Pgt
isolates
genotyped
1 to 5
6 to 10
Number of isolates
11-20
>20
Total
number
=
189
Pgt
isolates
6. Pgt
genetic
landscape
ì Genome-‐wide
genotyping
ì Re-‐sequencing
ì Pgt
SNP
Chip
ì Combined
data
sets.
ì 1,156
SNP
loci
ì Principle
coordinate
analysis
7. Africa
Asia
Australia
Europe
North
America
South
America
Coordinate
3
83ETH6_1
ETH2010_01a
(TRTTF)
83KEN_7a
Ug99
RG
96ZIM2a
84KEN8c
86MAR185c
2009KEN06b
(RTRJP)
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
AFRICA
8. Africa
Asia
Australia
Europe
North
America
South
America
Ug99
RG
96ZIM2a
84KEN8c
86MAR185c
09KEN06b
(RTRJP)
60IRN_10_b
83ETH6_1
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
ETH2010_01a
(TRTTF)
86PAK_1030_a
(RRRT)
06YEM34_1
(TRTTF)
ISR_2083_1
(TRRTF)
83KEN_7a
ISR_2147
(TTTTC)
ISR_2117
(TTJTC)
12TUR_6_c_1
12TUR_3_A_1
12TUR_6_B-‐2
Coordinate
3
AFRICA
ASIA
9. Africa
Asia
Australia
Europe
North
America
South
America
AFRICA
ASIA
AUSTRALIA
Ug99
RG
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
96ZIM2a
84KEN8c
86MAR185c
09KEN06b
(RTRJP)
60IRN_10_b
ISR_2147
(TTTTC)
ISR_2117
(TTJTC)
12TUR_6_c_1
83ETH6_1
ETH2010_01a
(TRTTF)
86PAK_1030_a
(RRRT)
06YEM34_1
(TRTTF)
ISR_2083_1
(TRRTF)
12TUR_3_A_1
12TUR_6_B-‐2
AUS_126_6711
83KEN_7a
AUS_194_12356
AUS_326_12356
AUS_21_0
Coordinate
3
10. Africa
Asia
Australia
Europe
North
America
South
America
AFRICA
ASIA
AUSTRALIA
EUROPE
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
84CSK_764_3
(GHBS)
96ZIM2a
84KEN8c
86MAR185c
09KEN06b
(RTRJP)
60IRN_10_b
AUS_126_6711
ISR_2147
(TTTTC)
ISR_2117
(TTJTC)
12TUR_6_c_1
83ETH6_1
12TUR_3_A_1
12TUR_6_B-‐2
Ug99
RG
ETH2010_01a
(TRTTF)
86PAK_1030_a
(RRRT)
06YEM34_1
(TRTTF)
ISR_2083_1
(TRRTF)
INRA98_PGT0001
Coordinate
3
83KEN_7a
AUS_194_12356
AUS_326_12356
AUS_21_0
84CSK_75_9_C
11. Africa
Asia
Australia
Europe
North
America
South
America
AFRICA
ASIA
AUSTRALIA
EUROPE
NA
Coordinate
3
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
84CSK_764_3
(GHBS)
96ZIM2a
84KEN8c
86MAR185c
09KEN06b
(RTRJP)
60IRN_10_b
Ug99
RG
ISR_2147
(TTTTC)
ISR_2117
(TTJTC)
12TUR_6_c_1
AUS_126_6711
83ETH6_1
ETH2010_01a
(TRTTF)
86PAK_1030_a
(RRRT)
06YEM34_1
(TRTTF)
ISR_2083_1
(TRRTF)
INRA98_PGT0001
12TUR_3_A_1
12TUR_6_B-‐2
83KEN_7a
AUS_194_12356
AUS_326_12356
AUS_21_0
84CSK_75_9_C
01TX27_C
(TTTT)
01MN84A
(TTTT)
08WA130_1
74MN70_5C
(TCLK)
76MN1391
(TMLK)
56IN1970_2C
(RKRQ)
80MN518_3
(RKRQ)
91IA154_1
(QCCJ)
72MEX1370_C
(QFCQ)
59KS19
(MCCF)
75WA973B
(MCCD)
12. Africa
Asia
Australia
Europe
North
America
South
America
AFRICA
ASIA
AUSTRALIA
EUROPE
NA
SA
Coordinate
3
87KEN_3016_4
85MAR_42_2
84ETH_19_A
87KEN_11_4
80MAR_33_B
09ETH_8_3
(JRCQC)
84CSK_764_3
(GHBS)
96ZIM2a
84KEN8c
86MAR185c
09KEN06b
(RTRJP)
60IRN_10_b
Ug99
RG
ISR_2147
(TTTTC)
ISR_2117
(TTJTC)
12TUR_6_c_1
AUS_126_6711
83ETH6_1
ETH2010_01a
(TRTTF)
86PAK_1030_a
(RRRT)
06YEM34_1
(TRTTF)
ISR_2083_1
(TRRTF)
INRA98_PGT0001
12TUR_3_A_1
12TUR_6_B-‐2
83KEN_7a
AUS_194_12356
AUS_326_12356
AUS_21_0
84CSK_75_9_C
59KS19
(MCCF)
75WA973B
(MCCD)
91IA154_1
(QCCJ)
72MEX1370_C
(QFCQ)
74MN70_5C
(TCLK)
76MN1391
(TMLK)
56IN1970_2C
(RKRQ)
80MN518_3
(RKRQ)
01TX27_C
(TTTT)
01MN84A
(TTTT)
08WA130_1
13. Pgt
geneIc
landscape:
Ug99
RG
ì SNP
panel
ì Ug99
RG
ì 25
SNP
loci
Race
Sample
ID
Genotype
A003
A005
A007
A010
A012
A021
A022
A031
A013
A014
A017
A020
A023
A026
A030
A001
A004
A006
A011
A016
A018
A024
A029
A033
A034
TTKSK
98UgA_1
AF-‐001aa
CC
GG
GG
TT
TT
TT
CT
GG
CC
AA
CC
CC
AA
GG
AA
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSK
04Ken156/4
AF-‐001ab
CC
GG
GG
TG
TT
TT
CT
GG
CC
AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSK
07Ken34_1
AF-‐001ac
CC
GG
GG
TT
TT
TT
CT
GG
CC
AA
CC
CT
AA
GG
AA
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSK
07Ken11_2
AF-‐001ad
CC
GG
GG
TT
TT
TT
CT
GG
CC
AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSK
09Tan06_2
AF-‐001af
CC
GG
GG
TT
TT
TT
CT
GG
CC
AA
TT
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKST
06Ken19v3
AF-‐001ba
CT
GG
GA
TT
TT
TT
CT
GT
TT
AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKST
07Ken18
AF-‐001bb
CC
GG
GG
TT
TT
TT
CT
GT
TT
AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTTSK
07Ken24_4
AF-‐001ca
CC
GA
GG
TT
TT
TT
CT
GG
CC AA
TT
CT
AC
GG
AC
AG
GG
TC
CC
GG
GG
CC
AA
GA
AA
TTTSK
09Tan07_1
AF-‐001cc
CC
GG
GG
GG
TT
TT
CT
GG
CC AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTTSK
09Tan08_2
AF-001cd CC
GG
GG
GG
TT
AT
CT
GG
CC AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSF
UvPgt55
AF-‐001da
CC
GG
GG
TT
TT
AA
TT GG
CC AG
CC
CC
AA
GA
AA
AA
GA
TT
CC
GG
AG
AC
AT
GG
AG
TTKSF
09Zim01_1
AF-‐001db
CC
GG
GG
TT
TT
AA
CT
GG
CC AA
CC
CC
AA
GG
AA
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSF
UvPgt61.2
AF-‐001dd
CC
GG
GG
TT
TT
AA
CT
GG
CC AA
CC
CC
AA
GA
AA
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
PTKST
UvPgt60
AF-‐001fa
CT
GG
GG
TT
TT
TT
CT
GT
TT
AA
CC
CT
AC
GG
AC
AA
GG
TT
CC
GG
GG
CC
AA
GG
AA
TTKSP
UvPgt59
AF-‐001ea
CC
GG
GG
TT
TG
AA
TT GG
CC AA
CC
CC
AA
GA
AA
AA
GG
TT
CT
AG
AG
AC
AT
GG
AA
14. Pgt
genetic
landscape:
Ug99
RG
KENYA
ETHIOPIA
ZIMBABWE
UGANDA
SOUTH AFRICA
TANZANIA
ERITREA
Pgt
race
TTKSK
Kenya
Uganda
1998 2007 2008 20102004 20122009
AF-001aa
AF-001ad
AF-001ac
AF-001ab
AF-001aa
AF-001af
AF-001ad
AF-001ac
AF-001ab
AF-001da
AF-001cd
AF-001cc
AF-001ca
AF-001bb
AF-001ba
AF-001ea
AF-001dd
AF-001db
AF-001fa
Genotype
TTKSK
PTKST
TTTSK
TTKSF
TTKST
TTKSP
15. Pgt
genetic
landscape:
Summary
ì Ug99
RG
is
an
unique
geneIc
group.
ì Individual
races
of
Ug99
RG
consist
of
mulIple
genotypes.
ì Genotyping
results
clearly
demonstrates
that
Pgt
has
spread
globally.
1 to 5
6 to 10
Number of isolates
11-20
>20
16. Pgt
genetic
landscape:
Summary
ì This
represents
the
first
step
in
characterizing
the
Pgt
global
populaIon.
ì It
will
take
parIcipaIon
by
the
global
rust
community
to
complete
this
project.
Robert Park
Univ. of Syndey
USDA ARS CDL
Zak Pretorius & Botma Visser
Univ. of Free State
Tom Fetch
Agriculture & Agi - Food Sarah Hambleton
Agriculture & Agi - Food
Silvia German
Y. Anikster & H. Sela
Tel. Aviv University
Alexey Morgounov
CIMMYT
17. ì
South
Africa
Pgt
genotyping
partnership
USDA-‐ARS
Prof.
Szabo
UFS
Dr.
Visser,
Prof.
Pretorius
ARC-‐SGI
Dr.
Terefe
Pgt
DNA
SNP
technology
CollecIons
Selected
collecIons
18. ì
South
Africa
Introduction
§ South
Africa
(http://www.indexmundi.com/agriculture/?country=za&commodity=wheat&graph=production)
§ 29th
ranked
wheat
producer
in
the
world
§ 2013
production
reached
1700
MT
§ Annual
Pgt
surveys
started
in
South
Africa
in
1980
(Le
Roux
and
Rijkenberg,
1987)
§ Currently
conducted
by
Dr.
Terefe
at
the
Small
Grain
Institute
(ARC-‐SGI)
in
Bethlehem
(see
poster
89
for
2011
and
2012
data)
§ Relies
on
phenotyping
viable
collections
on
standard
differentials
20. ì
South
Africa
Introduction
§ SSR
analyses
identified
two
unrelated
Pgt
lineages
within
South
Africa
(Visser
et
al.,
2011)
§ Lineage
1
–
non-‐Ug99
races
§ Lineage
2
–
Ug99
race
group
members
(see
poster
88)
§ Why
is
the
South
African
situation
relevant
at
a
global
level?
§ Half
of
the
Ug99
race
group
members
occur
in
South
Africa
§ Possible
movement
of
races
from
Africa
to
Australia
was
suggested
(Watson
and
de
Sousa,
1982)
21. ì
South
Africa
Hypothesis
§ The
genotyping
of
South
African
Pgt
samples
collected
during
annual
surveys
will
complement,
but
not
replace,
the
current
phenotyping
strategy.
23. Materials
and
methods
b
d
Ug99
positive
P5111
P9406
P13470
P18022
Ug99
vs
non-‐Ug99
identification
24. Materials
and
methods
Ug99
negative
b
d
P5111
P9406
P13470
P18022
Ug99
vs
non-‐Ug99
identification
25. Results
Ug99
vs
non-‐Ug99
identification
Year Number
of
isolates Ug99
positive Ug99
negative Failed
DNA
extraction
2010 84 64
(76%) 19
(23%) 1
(1%)
2011 56 36
(64%) 17
(30%) 3
(6%)
2012 102 51
(50%) 49
(48%) 2
(2%)
26. Materials
and
methods
Ug99
race
identification
Ug99
race A003 A005 A007 A010 A012 A021 A022 A031
TTKSF C
(H) G
(H) G
(H) T
(H) T
(H) A
(H) T
(F) G
(H)
C
(H) G
(H) G
(H) T
(H) T
(H) A
(H) T
(F) G
(H)
TTKSP C
(H) G
(H) G
(H) T
(H) T
(H) A
(H) T
(F) G
(H)
C
(H) G
(H) G
(H) T
(H) G
(F) A
(H) T
(F) G
(H)
PTKST C
(H) G
(H) G
(H) T
(H) T
(H) T
(F) C
(H) G
(H)
T
(F) G
(H) G
(H) T
(H) T
(H) T
(F) T
(F) T
(F)
TTKSF+ C
(H) G
(H) G
(H) T
(H) T
(H) A
(H) C
(H) G
(H)
C
(H) G
(H) G
(H) T
(H) T
(H) A
(H) T
(F) G
(H)
27. Results
Ug99
race
identification
-‐
2011
survey
A003 A005 A007 A010 A012 A021 A022 A031
Phenotype TTKSF CC GG GG TT TT AA TT GG
TTKSP CC GG GG TT TG AA TT GG
PTKST CT GG GG TT TT TT CT GT
TTKSF+ CC GG GG TT TT AA CT GG
Isolates S004-‐11 CC GG GG TT TT AA TC GG TTKSF+
S005-‐11 CC GG GG TT TT AA TC GG TTKSF+
S006-‐11 CC GG GG TT TT AA TC GG TTKSF+
S009-‐11 CC GG GG TT TT AA TC GG TTKSF+
S015-‐11 CC GG GG TT TG AA TT GG TTKSP
S017-‐11 CC GG GG TT TT AA TT GG TTKSF
S019-‐11 CC GG GG TT TT AA TT GG TTKSF
S021-‐11 CC GG GG TT TT AA TT GG TTKSF
S027-‐11 CC GG GG TT TT AA TC GG TTKSF+
S030-‐11 CC GG GG TT TT AA TC GG TTKSF+
S031-‐11 CC GG GG TT TT AA TT GG TTKSF
S032-‐11 CC GG GG TT TT AA TC GG TTKSF+
S033-‐11 CC GG GG TT TT AA TT GG TTKSF
S034-‐11 CC GG GG TT TT AA TT GG TTKSF
S035-‐11 CC GG GG TT TT AA TT GG TTKSF
S036-‐11 CC GG GG TT TT AA TT GG TTKSF
S037-‐11 CC GG GG TT TT AA TC GG TTKSF+
S038-‐11 CC GG GG TT TT AA TT GG TTKSF
S039-‐11 CC GG GG TT TT AA TT GG TTKSF
S041-‐11 CC GG GG TT TT AA TC GG TTKSF+
S042-‐11 CC GG GG TT TT AA TT GG TTKSF
S044-‐11 CC GG GG TT TT AA TT GG TTKSF
S045-‐11 CC GG GG TT TT AA TT GG TTKSF
S046-‐11 CC GG GG TT TT AA TC GG TTKSF+
S047-‐11 CC GG GG TT TT AA TT GG TTKSF
S048-‐11 CC GG GG TT TT AA TT GG TTKSF
S049-‐11 CC GG GG TT TT AA TT GG TTKSF
S052-‐11 CC GG GG TT TT AA TT GG TTKSF
S053-‐11 CC GG GG TT TT AA TT GG TTKSF
S054-‐11 CC GG GG TT TT AA TT GG TTKSF
S056-‐11 CC GG GG TT TT AA TC GG TTKSF+
S057-‐11 CC GG GG TT TT AA TC GG TTKSF+
S058-‐11 CC GG GG TT TT AA TC GG TTKSF+
S059-‐11 CC GG GG TT TT AA TC GG TTKSF+
S061-‐11 CC GG GG TT TT AA TC GG TTKSF+
S062-‐11 CC GG GG TT TT AA TC GG TTKSF+
TTKSF
TTKSF+
(see
poster
45)
34. ì
South
Africa
Discussion
-‐ Genotyping
of
Pgt
collections
-‐ Indicated
significant
genetic
variation
within
the
population
-‐ Forced
changes
in
the
survey
protocol
-‐ Confirmed
the
wide
distribution
of
TTKSF+
before
it
was
detected
on
phenotype
level
-‐ Confirmed
possible
multiple
genotypes
for
a
single
phenotype
(2SA105)
-‐ Indicated
the
presence
of
an
unknown
genotype
-‐ Help
with
planning
of
future
surveys
-‐ Confirmed
the
continued
need
for
phenotyping
-‐ Partnership
led
to
the
establishment
of
Pgt
genotyping
capacity
at
UFS
with
the
hope
of
expanding
both
in
the
future
35. Acknowledgements
§ Prof.
Les
Szabo
(USDA-‐ARS,
St
Paul,
USA)
for
genotyping
partnership
§ BGRI
for
invitation
and
financial
support
to
report
on
partnership
§ Dr.
Tarakegn
Terefe
(ARC-‐SGI,
Bethlehem,
SA)
for
Pgt
collections
§ Mr.
Tonny
Selinga
(UFS)
for
technical
assistance
§ Prof.
Liezel
Herselman
(UFS)
§ Prof.
Zakkie
Pretorius
(UFS)
36. Literature
cited
-‐ Boshoff
WHP,
van
Niekerk
BD
and
Pretorius
ZA,
2000.
Suid
Afrikaanse
Tydskrif
vir
Plant
en
Grond
17:
60-‐62.
-‐ Karaoglu
H,
Lee
CMY
and
Park
R,
2013.
Australasian
Plant
Pathology
42:
271-‐281.
-‐ Komen
JS,
2007.
Studies
on
chemical
control
of
wheat
stem
rust.
M.Sc.
Dissertation,
University
of
the
Free
State,
Bloemfontein,
South
Africa.
-‐ Le
Roux,
1989.
Phytophylactica
21:
255-‐258.
-‐ Le
Roux
J
and
Rijkenberg,
1987.
Phytophylactica
19:
467-‐472.
-‐ Saghai-‐Maroof
MA,
Soliman
KM,
Jorgensen
RA
and
Allard
RW,
1984.
Proceedings
of
the
National
Academy
of
Sciences
USA
81:
8014–8018.
-‐ Terefe
T
and
Pretorius
ZA,
2011a.
47th
Congress
of
the
South
African
Society
for
Plant
Pathology,
23-‐26
January,
Kruger
National
Park,
South
Africa.
-‐ Terefe
T
and
Pretorius
ZA,
2011b.
BGRI
Technical
Workshop,
13-‐16
June,
St
Paul,
Minnesota,
USA.
-‐ Terefe
T,
Pretorius
ZA,
Paul
I,
Mebalo
J,
Meyer
L
and
Naicker
K,
2010.
South
African
Journal
of
Plant
and
Soil
27:
163-‐167.
-‐ Visser
B,
Herselman
L,
Park
RF,
Karaoglu
H,
Bender
CM
and
Pretorius
ZA,
2011.
Euphytica
179:
119-‐127.
-‐ Watson
IA
and
de
Sousa
CNA,
1982.
Proceedings
of
the
Linnaean
Society
NSW
106:
311-‐321.