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 CoAuthors: 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
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Understanding the Genetic Landscape of Puccinia graminis f.sp. tritici From a Global to a Country Perspective
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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.
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-001afAF-001adAF-001acAF-001ab
AF-001da
AF-001cdAF-001ccAF-001ca
AF-001bbAF-001ba
AF-001ea
AF-001ddAF-001db
AF-001fa
GenotypeTTKSK
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 56 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 - FoodSarah Hambleton
Agriculture & Agi - Food
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Silvia German
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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
Ug99 race A003 A005 A007 A010 A012 A021 A022 A031TTKSF 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 A031Phenotype TTKSF CC GG GG TT TT AA TT GG
TTKSP CC GG GG TT TG AA TT GGPTKST CT GG GG TT TT TT CT GTTTKSF+ 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 TTKSPS017-‐11 CC GG GG TT TT AA TT GG TTKSFS019-‐11 CC GG GG TT TT AA TT GG TTKSFS021-‐11 CC GG GG TT TT AA TT GG TTKSFS027-‐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 TTKSFS032-‐11 CC GG GG TT TT AA TC GG TTKSF+S033-‐11 CC GG GG TT TT AA TT GG TTKSFS034-‐11 CC GG GG TT TT AA TT GG TTKSFS035-‐11 CC GG GG TT TT AA TT GG TTKSFS036-‐11 CC GG GG TT TT AA TT GG TTKSFS037-‐11 CC GG GG TT TT AA TC GG TTKSF+S038-‐11 CC GG GG TT TT AA TT GG TTKSFS039-‐11 CC GG GG TT TT AA TT GG TTKSFS041-‐11 CC GG GG TT TT AA TC GG TTKSF+S042-‐11 CC GG GG TT TT AA TT GG TTKSFS044-‐11 CC GG GG TT TT AA TT GG TTKSFS045-‐11 CC GG GG TT TT AA TT GG TTKSFS046-‐11 CC GG GG TT TT AA TC GG TTKSF+S047-‐11 CC GG GG TT TT AA TT GG TTKSFS048-‐11 CC GG GG TT TT AA TT GG TTKSFS049-‐11 CC GG GG TT TT AA TT GG TTKSFS052-‐11 CC GG GG TT TT AA TT GG TTKSFS053-‐11 CC GG GG TT TT AA TT GG TTKSFS054-‐11 CC GG GG TT TT AA TT GG TTKSFS056-‐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+
-‐ 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.