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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	
  
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.	
  	
  
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	
  
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	
  
	
  
DistribuIon	
  of	
  Pgt	
  isolates	
  genotyped	
  
1 to 5
6 to 10
Number of isolates
11-20
>20
Total	
  number	
  =	
  189	
  Pgt	
  isolates	
  
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	
  
	
  
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	
  
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	
  	
  
	
  
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	
  
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	
  
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)	
  
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	
  
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	
  
 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
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
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
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	
  
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	
  
ì	
  South	
  Africa	
  	
  
	
  Introduction	
  
Race 81 82,83 84 85 86S 86W 87S 87W 91 92 93 94 95 96 97 98 99 00 01 02 03 04 07 08 09 10
2SA002	
   1 3 1.7 9 14 2
2SA004 0.5 20.2 20.2 9 74 50 77 28 13 3 31 1 26 67 39 1 0.8
2SA006 31.6 2.8 55
2SA010 2 9.6 3.6 1
2SA018 1
2SA020 0.5
2SA032 4.5 8.2 8 7 1
2SA033 1
2SA036 8.5 1 1 10 2
2SA039 1.5
2SA043 0.5
2SA043 1.4 2
2SA045 31.1
2SA048 14.3 100 1.4 1
2SA049 2.5
2SA051 1
2SA052 1
2SA053 0.5
2SA054 1.5
2SA055 65 3.3 3.3 4.5
2SA088	
  (TTKSF) 35 68.8 81 85 69.7 26.1 38.4 39 78
2SA099 5 18.8 3 1 0.8
2SA100 58.2 55 27 15 29 16 1 5 13 5 2 1 0.8
2SA101 4.5 5.7 1 1
2SA102 70 54 36 59 37 53 53 12.4 10 12 23.8 1.1 8.9 12 1
2SA103 18 46 5 60 21 33 3 6 0.8 2
2SA104 14.1 9.8 8 3
2SA105 53.2 20.5 21 15
2SA106	
  (TTKSP) 2.2 17.9 14 2
2SA107	
  (PTKST) 4 1
2SA108	
  (TTKSF+)
100 100 100 100 100 100 100 100 100 100 100 100 100 100 0 100 100 100 100 100 100 100 100 100 100 100
Terefe	
  &	
  
Pretorius,	
  
2011a	
  ,	
  b
Le	
  Roux	
  and	
  Rijkenberg,	
  
1987 Le	
  Roux,	
  1989 Boshoff	
  et	
  al .,	
  2000 Komen,	
  2007
Terefe	
  et	
  al .,	
  
2010
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)	
  	
  
ì	
  South	
  Africa	
  	
  
	
  Hypothesis	
  
§  The	
  genotyping	
  of	
  South	
  African	
  Pgt	
  samples	
  collected	
  during	
  annual	
  
surveys	
  will	
  complement,	
  but	
  not	
  replace,	
  the	
  current	
  phenotyping	
  
strategy.	
  	
  
Materials	
  and	
  methods	
  
§  Pgt	
  collections	
  
§  Dr.	
  Tarakegn	
  Terefe	
  (ARC-­‐SGI,	
  Bethlehem,	
  SA)	
  
§  Surveys	
  
§  2010	
  –	
  84	
  collections	
  (country-­‐wide)	
  
§  2011	
  –	
  56	
  collections	
  (country-­‐wide)	
  
§  2012	
  –	
  102	
  collections	
  (Western	
  Cape	
  Province)	
  
§  CTAB	
  DNA	
  extraction	
  (Saghai-­‐Maroof	
  et	
  al.,	
  1984)	
  
§  Isolate	
  genotyping	
  
§  Ug99	
  vs	
  non-­‐Ug99	
  identification	
  –	
  Stage	
  1	
  qPCR	
  
§  Ug99	
  race	
  identification	
  –	
  Stage	
  2	
  qPCR	
  
§  Non-­‐Ug99	
  race	
  identification	
  –	
  SSR	
  analysis	
  (PgSUN7,	
  PgSUN20,	
  
PgSUN27,	
  PgSUN30,	
  PgSUN31,	
  PgSUN33,	
  PgSUN42,	
  PgSUN44	
  
(Karaoglu	
  et	
  al.,	
  2013)	
  
Materials	
  and	
  methods	
  
b
d
Ug99	
  positive	
  
P5111	
   P9406	
  
P13470	
   P18022	
  
Ug99	
  vs	
  non-­‐Ug99	
  identification	
  	
  
Materials	
  and	
  methods	
  
Ug99	
  negative	
  
b
d
P5111	
   P9406	
  
P13470	
   P18022	
  
Ug99	
  vs	
  non-­‐Ug99	
  identification	
  	
  
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%)
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)
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)	
  
Results	
  
2SA107	
  
2SA88	
  
2SA102	
  
2SA88	
  
2SA88/104	
  
Non-­‐Ug99	
  race	
  identification	
  
	
  
	
  -­‐	
  2010	
  survey	
  	
  
Results	
  
2SA105/88	
  
2SA105	
  
2SA105	
  
2SA88	
  
2SA105	
  
2SA106	
  
Non-­‐Ug99	
  race	
  identification	
  
	
  
	
  -­‐	
  2010	
  survey	
  	
  
Results	
  
2SA105/104
2SA105/88
2SA105
Non-­‐Ug99	
  race	
  identification	
  
	
  
	
  -­‐	
  2011	
  survey	
  	
  
Results	
  
Non-­‐Ug99	
  race	
  identification	
  
	
  
	
  -­‐	
  2012	
  survey	
  	
  
Results	
  
Non-­‐Ug99	
  race	
  identification	
  
	
  
	
  -­‐	
  2012	
  survey	
  	
  
Results	
  
Race	
  data	
  summary	
  	
  
Race 98 99 00 01 02 03 04 07 08 09 10 10 11 12
2SA055 65 3.3 3.3 4.5
2SA088	
  (TTKSF) 35 68.8 81 85 69.7 26.1 38.4 39 78 53.7 35.9 37
2SA099 5 18.8 3 1 0.8
2SA100 1 0.8
2SA101
2SA102 53 12.4 10 12 23.8 1.1 8.9 12 1 1.9 1
2SA103 33 3 6 0.8 2
2SA104 14.1 9.8 8 3 1.2
2SA105 53.2 20.5 21 15 14.6 24.5 39
2SA106	
  (TTKSP) 2.2 17.9 14 2 1.2 1.9
2SA107	
  (PTKST) 4 1
2SA108	
  (TTKSF+) 22 30.1 14
2SA105	
  (?) 7.3 5.7 8
Unknown 1
100 100 100 100 100 100 100 100 100 100 100 100 100 100
Current	
  
genotyping	
  studyKomen,	
  2007
Terefe	
  et	
  
al .,	
  2010
Terefe	
  &	
  
Pretorius,	
  
2011a	
  ,	
  b
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	
  	
  
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)	
  
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.	
  	
  

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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  
  • 19. ì  South  Africa      Introduction   Race 81 82,83 84 85 86S 86W 87S 87W 91 92 93 94 95 96 97 98 99 00 01 02 03 04 07 08 09 10 2SA002   1 3 1.7 9 14 2 2SA004 0.5 20.2 20.2 9 74 50 77 28 13 3 31 1 26 67 39 1 0.8 2SA006 31.6 2.8 55 2SA010 2 9.6 3.6 1 2SA018 1 2SA020 0.5 2SA032 4.5 8.2 8 7 1 2SA033 1 2SA036 8.5 1 1 10 2 2SA039 1.5 2SA043 0.5 2SA043 1.4 2 2SA045 31.1 2SA048 14.3 100 1.4 1 2SA049 2.5 2SA051 1 2SA052 1 2SA053 0.5 2SA054 1.5 2SA055 65 3.3 3.3 4.5 2SA088  (TTKSF) 35 68.8 81 85 69.7 26.1 38.4 39 78 2SA099 5 18.8 3 1 0.8 2SA100 58.2 55 27 15 29 16 1 5 13 5 2 1 0.8 2SA101 4.5 5.7 1 1 2SA102 70 54 36 59 37 53 53 12.4 10 12 23.8 1.1 8.9 12 1 2SA103 18 46 5 60 21 33 3 6 0.8 2 2SA104 14.1 9.8 8 3 2SA105 53.2 20.5 21 15 2SA106  (TTKSP) 2.2 17.9 14 2 2SA107  (PTKST) 4 1 2SA108  (TTKSF+) 100 100 100 100 100 100 100 100 100 100 100 100 100 100 0 100 100 100 100 100 100 100 100 100 100 100 Terefe  &   Pretorius,   2011a  ,  b Le  Roux  and  Rijkenberg,   1987 Le  Roux,  1989 Boshoff  et  al .,  2000 Komen,  2007 Terefe  et  al .,   2010
  • 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.    
  • 22. Materials  and  methods   §  Pgt  collections   §  Dr.  Tarakegn  Terefe  (ARC-­‐SGI,  Bethlehem,  SA)   §  Surveys   §  2010  –  84  collections  (country-­‐wide)   §  2011  –  56  collections  (country-­‐wide)   §  2012  –  102  collections  (Western  Cape  Province)   §  CTAB  DNA  extraction  (Saghai-­‐Maroof  et  al.,  1984)   §  Isolate  genotyping   §  Ug99  vs  non-­‐Ug99  identification  –  Stage  1  qPCR   §  Ug99  race  identification  –  Stage  2  qPCR   §  Non-­‐Ug99  race  identification  –  SSR  analysis  (PgSUN7,  PgSUN20,   PgSUN27,  PgSUN30,  PgSUN31,  PgSUN33,  PgSUN42,  PgSUN44   (Karaoglu  et  al.,  2013)  
  • 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)  
  • 28. Results   2SA107   2SA88   2SA102   2SA88   2SA88/104   Non-­‐Ug99  race  identification      -­‐  2010  survey    
  • 29. Results   2SA105/88   2SA105   2SA105   2SA88   2SA105   2SA106   Non-­‐Ug99  race  identification      -­‐  2010  survey    
  • 30. Results   2SA105/104 2SA105/88 2SA105 Non-­‐Ug99  race  identification      -­‐  2011  survey    
  • 31. Results   Non-­‐Ug99  race  identification      -­‐  2012  survey    
  • 32. Results   Non-­‐Ug99  race  identification      -­‐  2012  survey    
  • 33. Results   Race  data  summary     Race 98 99 00 01 02 03 04 07 08 09 10 10 11 12 2SA055 65 3.3 3.3 4.5 2SA088  (TTKSF) 35 68.8 81 85 69.7 26.1 38.4 39 78 53.7 35.9 37 2SA099 5 18.8 3 1 0.8 2SA100 1 0.8 2SA101 2SA102 53 12.4 10 12 23.8 1.1 8.9 12 1 1.9 1 2SA103 33 3 6 0.8 2 2SA104 14.1 9.8 8 3 1.2 2SA105 53.2 20.5 21 15 14.6 24.5 39 2SA106  (TTKSP) 2.2 17.9 14 2 1.2 1.9 2SA107  (PTKST) 4 1 2SA108  (TTKSF+) 22 30.1 14 2SA105  (?) 7.3 5.7 8 Unknown 1 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Current   genotyping  studyKomen,  2007 Terefe  et   al .,  2010 Terefe  &   Pretorius,   2011a  ,  b
  • 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)  
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