Puccinia graminis
Scientific classification
P. graminis
P. graminis tritici

Ug99 is a lineage of wheat stem rust (Puccinia graminis f. sp. tritici), which is present in wheat fields in several countries in Africa and the Middle East and is predicted to spread rapidly through these regions and possibly further afield, potentially causing a wheat production disaster that would affect food security worldwide.[1] It can cause up to 100% crop losses and is virulent against many resistance genes which have previously protected wheat against stem rust.

Although Ug99-resistant varieties of wheat do exist, a screen of 200,000 wheat varieties used in 22 African and Asian countries found that only 5-10% of the area of wheat grown in these countries consisted of varieties with adequate resistance.[1]

The original race of Ug99, which is designated as 'TTKSK' under the North American nomenclature system, was first detected in Uganda in 1998[2] and first characterised in 1999[2] (hence the name Ug99) and has since been detected in Kenya, Ethiopia, Eritrea, Sudan, Yemen, Iran, Tanzania, Mozambique, Zimbabwe, South Africa,[3] and Egypt. There are now 13 known races of Ug99.[4] They are all closely related and are believed to have evolved from a common ancestor, but differ in their virulence/avirulence profiles and the countries in which they have been detected.[1]


Ug99 is the product of a type of somatic nuclear exchange event which has not been observed in other stem rust races.[5] During this event and thereafter the nuclei have not experienced recombination.[5]

Gene resistance

Ug99 and its variants differ from other strains of the Black Stem Rust (BSR) pathogen due to their ability to overcome resistance genes in wheat that have been durable against the BSR pathogen for decades.[6] These resistant Sr genes, of which 50 are known, give wheat different resistances to stem rust.[2] The virulence in Uganda was virulent against Sr31 and is specific to Ug99.[2] The massive losses of wheat that have occurred have been devastating, but in recent years the wheat rust epidemic has been effectively controlled through selection and breeding for additional Sr' genes.[2] United States Department of Agriculture (USDA) researchers are testing genes to determine their Ug99 resistance, which will ultimately aid in the development of wheat varieties that will be able to fight off the rust. Resistance has been identified in a small number of spring wheat land races from North America - 23 out of 250 races with adult plant resistance, 27 out of 23,976 SNPs conveying APR, and only 9 races having seedling resistance.[7] This resistance is present prior to Ug99 pathogen challenge being present in NA to drive selection.[7] USDA has stated that they are now studying winter wheat land races where resistance is more probable.[citation needed] Due to the fact that the screening of the winter races is more challenging, results from the studies are not expected for another five to seven years.[when?] In addition to the research being conducted by the USDA, The United Kingdom’s Department for International Development (DFID), along with Bill & Melinda Gates Foundation, announced in February 2011 that they will be granting $40 million to a global project led by Cornell University to combat virulent strains of Ug99.[8] The five-year grant to the Durable Rust Resistance in Wheat (DRRW) project will support attempts to identify new resistance genes as well as reproduce and distribute rust resistant wheat seeds to farmers.[8]

Sr33 is an introgression from a wild wheat Aegilops tauschii. This gene is an ortholog to Mla in barley. Confers resistance, and also various other resistances to other stem rust races.[9]

There has been a continuous process of development of new resistant cultivars and failure of those cultivars. This demonstrates the need for continuous improvement.[10]


There are 13 races of Ug99, which (under the North American nomenclature system) have the designations TTKSK, TTKSF, TTKST, TTTSK, TTKSP, PTKSK, PTKST, TTKSF+,[3] TTKTT, TTKTK, TTHSK, PTKTK, and TTHST.[4] They are all closely related and are believed to have evolved from a common ancestor.[1]


Also known as PTKS.[11] The first Ug99 race to be characterised.[12][11] Like most Ug99 races, and unlike other stem rust varieties, it is virulent against the Sr gene Sr31;[12][11] also virulent against Sr38.[11] Avirulent against Sr24.[12][11] It was found in Uganda[11] in 1999, Kenya[12] in 2001,[4] Ethiopia in 2003,[4] Sudan and Yemen in 2006,[4] Iran in 2007,[4] and Tanzania[1] in 2009,[4] Eritrea in 2012,[4] and Rwanda and Egypt in 2014.[4]

Sr14 does not protect seedlings against TTKSK[13] but does provide moderate resistance at later stages.[13]


First detected in South Africa in 2000,[4] Zimbabwe 2009,[4] and Uganda in 2012.[4]


Discovered in Kenya in 2006[12] was the first Ug99 race found to be virulent against Sr gene Sr24.[1][12] TTKST is now the predominant stem rust race in Kenya.[1]

Sr14 is effective against TTKST.[13]


First detected in Kenya in 2007,[4] Tanzania in 2009,[4] Ethiopia in 2010,[4] Uganda in 2012,[4] and Rwanda in 2014.[4]


First detected in South Africa in 2007.[4]


First detected in Ethiopia in 2007,[4] Kenya in 2009,[4] Yemen in 2009,[4] and South Africa in 2017.[4][14]


First detected in Ethiopia in 2007,[4] Kenya in 2008,[4] South Africa in 2009,[4] Eritrea and Mozambique and Zimbabwe in 2010.[4]


First detected in both South Africa and Zimbabwe in 2010.[4] Virulent against Sr9h.[15][16][17]


First detected in Kenya in 2014.[4]


First detected in Kenya,[4][18] Rwanda,[4][18] Uganda,[4][18] Eritrea,[4] and Egypt[4][18] in 2014.


First detected in Kenya in 2014.[19] Differs from the original (TTKSK) by avirulence against Sr30.[19] Similar to TTHST.[19]


First detected in Kenya in 2014.[19] Differs from PTKSK by virulence against SrTmp.[19] Differs from TTKTK by avirulence against Sr21.[19]


First detected in Kenya in 2013.[4]



There is some evidence that race TTKSK may have been present in Kenya.[20]


Severe stem rust infections observed in Uganda. Ug99 identified, characterised as having virulence on Sr31 and named.[20]


TTKSF detected in South Africa.[1]


TTKSK detected in Kenya.[1]


TTKSK detected in Ethiopia.[1]


TTKSK detected in Sudan and Yemen.[20]
TTKST, a new variant of Ug99 with virulence to Sr24, detected in Kenya.[20]


TTTSK detected in Kenya.[1]
TTKSP detected in South Africa.[1]
PTKSK detected in Ethiopia.[1]
PTKST detected in Ethiopia.[1]


FAO announced the presence of Ug99 in Iran.[1]
PTKST detected in Kenya.[1]


TTKSK detected in Tanzania.[1]
TTKST detected in Tanzania.[1]
TTTSK detected in Tanzania.[1]
TTKSF detected in Zimbabwe.[1]
PTKSK detected in Kenya.[1]
PTKST detected in South Africa.[1]


TTKST detected in Eritrea.[3]
PTKST detected in Eritrea.[3]
PTKST detected in Mozambique.[3]
PTKST detected in Zimbabwe.[3]
TTKSF+ detected in South Africa.[3]
TTKSF+ detected in Zimbabwe.[3]


TTHST confirmed in Kenya[4]


TTKTK confirmed in Egypt,[21] Kenya, Eritrea, Rwanda, and Uganda.[4]
TTHSK confirmed in Kenya[4][19]
PTKTK confirmed in Kenya[4][19]
TTKTT confirmed in Kenya.[19]
TTKST detected in Egypt.[21]
TTKSK detected in Egypt.[21]

Geographic spread

This section needs expansion. You can help by adding to it. (November 2020)


Although Ug99 has not yet reached China,[22] other stem rust races already have,[22] and an effort is under way to marry resistance against present races with future needs for resistance against Ug99 whenever it arrives.[22]


Although Sr5, Sr21, Sr9e, Sr7b, Sr11, Sr6, Sr8a, Sr9g, Sr9b, Sr30, Sr17, Sr9a, Sr9d, Sr10, SrTmp, Sr38, and SrMcN are no longer effective in Lebanon, Sr11, Sr24, and Sr31 still are which is diagnostic for the absence of Ug99 from Lebanon.[23]

See also


  1. ^ a b c d e f g h i j k l m n o p q r s t u v Singh, Ravi P.; Hodson, David P.; Huerta-Espino, Julio; Jin, Yue; Bhavani, Sridhar; Njau, Peter; Herrera-Foessel, Sybil; Singh, Pawan K.; Singh, Sukhwinder; Govindan, Velu (8 September 2011). "The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production" (PDF). Annual Review of Phytopathology. 49 (1): 465–481. doi:10.1146/annurev-phyto-072910-095423. PMID 21568701. S2CID 24770327. Archived from the original (PDF) on 16 February 2020.
  2. ^ a b c d e Pretorius, Z. A.; Singh, R. P.; Wagoire, W. W.; Payne, T. S. (2000). "Detection of Virulence to Wheat Stem Rust Resistance Gene Sr31 in Puccinia graminis. f. sp. tritici in Uganda". Plant Disease. American Phytopathological Society. 84 (2): 203. doi:10.1094/pdis.2000.84.2.203b. ISSN 0191-2917. PMID 30841334.
  3. ^ a b c d e f g h Hodson, D. P.; Grønbech-Hansen, J.; Lassen, P.; Alemayehu, Y.; Arista, J.; Sonder, K.; Kosina, P.; Moncada, P.; Nazari, K.; Park, R. F.; Pretorius, Z. A.; Szabo, L. J.; Fetch, T.; Jin, Y. "Tracking the Wheat Rust Pathogens" (PDF). 2012 Borlaug Global Rust Initiative Technical Workshop Proceedings. Borlaug Global Rust Initiative. Archived (PDF) from the original on October 5, 2019. Retrieved 28 November 2012.
  4. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag ah ai aj ak al "Pathotype Tracker – Where is Ug99?". CIMMYT.
  5. ^ a b Li, Feng; Upadhyaya, Narayana M.; Sperschneider, Jana; Matny, Oadi; Nguyen-Phuc, Hoa; Mago, Rohit; Raley, Castle; Miller, Marisa E.; Silverstein, Kevin A. T.; Henningsen, Eva; Hirsch, Cory D.; Visser, Botma; Pretorius, Zacharias A.; Steffenson, Brian J.; Schwessinger, Benjamin; Dodds, Peter N.; Figueroa, Melania (2019-11-07). "Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation". Nature Communications. Springer Science and Business Media LLC. 10 (1): 5068. Bibcode:2019NatCo..10.5068L. doi:10.1038/s41467-019-12927-7. ISSN 2041-1723. PMC 6838127. PMID 31699975. S2CID 207916981.
  6. ^ "USDA Coordinated Approach to Address Pgt-Ug99". ARS. September 20, 2017.
  7. ^ a b Bajgain, P.; Rouse, MN; Bulli, P.; Bhavani, S.; Gordon, T.; Wanyera, R.; Njau, PN; Legesse, W.; Anderson, JA; Pumphrey, MO (2015-10-14). "Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races". BMC Plant Biology. BioMed Central/Springer Science and Business Media LLC. 15 (1): 249. doi:10.1186/s12870-015-0628-9. ISSN 1471-2229. PMC 4606553. PMID 26467989. S2CID 54521938.
  8. ^ a b McCandless, Linda (February 27, 2011). "$40M grant to fight wheat pathogen that threatens global food security". Cornell Chronicle. Retrieved October 5, 2019.
  9. ^ Periyannan, Sambasivam; Moore, John; Ayliffe, Michael; Bansal, Urmil; Wang, Xiaojing; Huang, Li; Deal, Karin; Luo, Mingcheng; Kong, Xiuying; Bariana, Harbans; Mago, Rohit; McIntosh, Robert; Dodds, Peter; Dvorak, Jan; Lagudah, Evans (2013-06-27). "The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99". Science. American Association for the Advancement of Science. 341 (6147): 786–788. doi:10.1126/science.1239028. ISSN 0036-8075. PMID 23811228. S2CID 206549297.
  10. ^ Wessels, Elsabet; Prins, Renée; Boshoff, Willem H. P.; Zurn, Jason D.; Acevedo, Maricelis; Pretorius, Zacharias A. (2019). "Mapping a Resistance Gene to Puccinia graminis f. sp. tritici in the Bread Wheat Cultivar 'Matlabas'". Plant Disease. American Phytopathological Society. 103 (9): 2337–2344. doi:10.1094/pdis-10-18-1731-re. ISSN 0191-2917. PMID 31306087.
  11. ^ a b c d e f Nagarajan, Subrahmaniam; Kogel, Hans J.; Zadoks, Jan C. (2012). "Epidemiology of Puccinia graminis f.sp. tritici-Ug99 in the Rift Valley "Flyway" from Uganda-Kenya to Yemen". Plant Health Progress. American Phytopathological Society. 13 (1): 31. doi:10.1094/php-2012-1114-01-rv. ISSN 1535-1025.
  12. ^ a b c d e f Jin, Y.; Szabo, L. J.; Pretorius, Z. A.; Singh, R. P.; Ward, R.; Fetch, T. (2008). "Detection of Virulence to Resistance Gene Sr24 Within Race TTKS of Puccinia graminis f. sp. tritici". Plant Disease. American Phytopathological Society. 92 (6): 923–926. doi:10.1094/pdis-92-6-0923. ISSN 0191-2917. PMID 30769714.
  13. ^ a b c Kumar, Sachin; Fetch, Tom G.; Knox, Ron E.; Singh, Asheesh K.; Clarke, John M.; Depauw, Ron M.; Cuthbert, Richard D.; Campbell, Heather L.; Singh, Davinder; Bhavani, Sridhar; Pozniak, Curtis J.; Meyer, Brad; Clarke, Fran R. (2020-11-19). "Mapping of Ug99 stem rust resistance in Canadian durum wheat". Canadian Journal of Plant Pathology. Informa UK Limited: 1–13. doi:10.1080/07060661.2020.1843073. ISSN 0706-0661.
  14. ^ Terefe, T.; Pretorius, Z. A.; Visser, B.; Boshoff, W. H. P. (2019). "First Report of Puccinia graminis f. sp. tritici Race PTKSK, a Variant of Wheat Stem Rust Race Ug99, in South Africa". Plant Disease. American Phytopathological Society. 103 (6): 1421. doi:10.1094/pdis-11-18-1911-pdn. ISSN 0191-2917.
  15. ^ Randhawa, Mandeep S.; Singh, Ravi P.; Dreisigacker, Susanne; Bhavani, Sridhar; Huerta-Espino, Julio; Rouse, Matthew N.; Nirmala, Jayaveeramuthu; Sandoval-Sanchez, Maricarmen (2018-11-30). "Identification and Validation of a Common Stem Rust Resistance Locus in Two Bi-parental Populations". Frontiers in Plant Science. Frontiers Media SA. 9: 1788. doi:10.3389/fpls.2018.01788. ISSN 1664-462X. PMC 6283910. PMID 30555507.
  16. ^ Pretorius, Z. A.; Szabo, L. J.; Boshoff, W. H. P.; Herselman, L.; Visser, B. (2012). "First Report of a New TTKSF Race of Wheat Stem Rust (Puccinia graminis f. sp. tritici) in South Africa and Zimbabwe". Plant Disease. American Phytopathological Society. 96 (4): 590. doi:10.1094/pdis-12-11-1027-pdn. ISSN 0191-2917. PMID 30727416.
  17. ^ Rouse, Matthew N.; Nirmala, Jayaveeramuthu; Jin, Yue; Chao, Shiaoman; Fetch, Thomas G.; Pretorius, Zacharias A.; Hiebert, Colin W. (2014-06-10). "Characterization of Sr9h, a wheat stem rust resistance allele effective to Ug99". Theoretical and Applied Genetics. Springer Science and Business Media LLC. 127 (8): 1681–1688. doi:10.1007/s00122-014-2330-y. ISSN 0040-5752. PMID 24913360. S2CID 2598581.
  18. ^ a b c d Patpour, M.; Hovmøller, M. S.; Justesen, A. F.; Newcomb, M.; Olivera, P.; Jin, Y.; Szabo, L. J.; Hodson, D.; Shahin, A. A.; Wanyera, R.; Habarurema, I.; Wobibi, S. (2016). "Emergence of Virulence to SrTmp in the Ug99 Race Group of Wheat Stem Rust, Puccinia graminis f. sp. tritici, in Africa". Plant Disease. American Phytopathological Society. 100 (2): 522. doi:10.1094/pdis-06-15-0668-pdn. ISSN 0191-2917.
  19. ^ a b c d e f g h i Fetch, T.; Zegeye, T.; Park, R. F.; Hodson, D.; Wanyera, R. (2016). "Detection of Wheat Stem Rust Races TTHSK and PTKTK in the Ug99 Race Group in Kenya in 2014". Plant Disease. American Phytopathological Society. 100 (7): 1495. doi:10.1094/pdis-11-15-1356-pdn. ISSN 0191-2917.
  20. ^ a b c d Singh, Ravi P.; Hodson, David; Huerta-Espino, Julio; Jin, Yue; Njau, Peter; Wanyera, Ruth; Herrera-Foessel, Sybil; Ward, Richard W. (2008). "Will Stem Rust Destroy The World's Wheat Crop?". Advances in Agronomy. 98: 272–309. doi:10.1016/S0065-2113(08)00205-8. ISBN 9780123743558.
  21. ^ a b c Patpour, M.; Hovmøller, M. S.; Shahin, A. A.; Newcomb, M.; Olivera, P.; Jin, Y.; Luster, D.; Hodson, D.; Nazari, K.; Azab, M. (2016). "First Report of the Ug99 Race Group of Wheat Stem Rust, Puccinia graminis f. sp. tritici, in Egypt in 2014". Plant Disease. American Phytopathological Society. 100 (4): 863. doi:10.1094/pdis-08-15-0938-pdn. ISSN 0191-2917.
  22. ^ a b c Wu, Xian Xin; Lin, Qiu Jun; Ni, Xin Yu; Sun, Qian; Chen, Rong Zhen; Xu, Xiao Feng; Qiu, Yong Chun; Li, Tian Ya (2020). "Characterization of Wheat Monogenic Lines with Known Sr Genes and Wheat Lines with Resistance to the Ug99 Race Group for Resistance to Prevalent Races of Puccinia graminis f. sp. tritici in China". Plant Disease. American Phytopathological Society. 104 (7): 1939–1943. doi:10.1094/pdis-12-19-2736-re. ISSN 0191-2917. PMID 32396054.
  23. ^ Rola El Amil (Lebanese Agricultural Research Institute, Lebanon) (2020-11-09). (DAY 2) - Phytosanitary Safety for Transboundary pest prevention - Yellow and Black rust population variability. CGIAR Germplasm Health Webinar series. Phytosanitary Awareness Week. International Institute of Tropical Agriculture / CGIAR. Slide at 00:44:37.