Surveillance of Ug99 stem rust and the search for new resistance genes

Thomas Fetch, Jr. Cereal Research Centre, Winnipeg

Ug99 (race TTKS)

Origin and Spread of Race TTKS • In 1999, Pretorius et al. described Pgt-Ug99 from Uganda with

virulence on Sr31. Important since many CIMMYT-related wheat cultivars rely only on Sr31 gene for resistance.

• In 2000, race TTKSF reported in South Africa (Pretorius).

• In 2001, TTKSK (Ug99) spread to Kenya. In 2003 to Ethiopia.

• In 2006, race TTKSK detected in Sudan and Yemen. A new variant (TTKST) with virulence to gene Sr24 detected in Njoro.

• In 2007, a new race (TTTSK) with virulence to Sr36 detected in Njoro. Race TTKSK spreads to Iran. Races PTKSK and PTKST reported in Ethiopia. Race TTKSP (Sr24) reported in South Africa (Pretorius).

• In 2008, PTKST found in Kenya.

Origin and Spread of Race TTKS • In 2009, races TTKSK, TTKST, TTTSK reported in Tanzania.

Race TTKSF in Zimbabwe. Race PTKSK in Kenya and Yemen. Race PTKST in South Africa (Pretorius).

• In 2010, races TTKST and PTKST reported in Eritrea. Race TTTSK reported in Ethiopia. Race PTKST reported in Mozambique and Zimbabwe. Mutant race TTKSF+ (Matlabas) reported in Zimbabwe and South Africa (Pretorius).

• In 2012, race TTKSK found in Eritrea and races TTKSF, TTKST, and TTTSK reported in Uganda.

• In 2014, races TTKSK and TTTSK found in Rwanda.

Ug99 to South America?

Isard & Russo . An assessment of the risk of aerial transport of rust pathogens to the Western Hemisphere and within North America (BGRI 2011).

REGIONS OF POTENTIAL RISK

8 d per month, S. Africa to S. Amer.

Tracking movement of TTKS • Global Rust Initiative formed by Dr. Borlaug in 2004 in response to

Ug99 threat. In 2008, the Durable Rust Resistant Wheat project funded by Gates foundation. This is a multinational multidisciplinary effort by pathologists, breeders, geneticists, etc. to develop wheat with durable rust resistance. A key component is to track movement of TTKS.

• Trap plots with Sr31, 24+31, 36+31 are used to detect race TTKS or derivatives. Samples from trap plots and fields in the TTKS path are race-typed using sets of single-gene differential lines.

• Annual surveys conducted in Canada, USA, and Australia since 1919. Many countries now survey for new virulent races, including TTKS.

• Surveys and trap plots in Brazil, Uruguay, Argentina, Chile, etc. to get data on stem rust virulence and monitor for introduction of Ug99 into South America.

Map of 2013 surveys in Argentina and Uruguay using Survey Mapper on RustTracker website. http://rusttracker.cimmyt.org/?page_id=305

Tracking movement of TTKS • Plant trap plots of lines with Sr31 and highly susceptible

wheat like Morocco. Collect samples with rust and phenotype to race using international set of differential lines.

• Conduct survey of farm fields and collect samples of rusted wheat (if available) about every 20 km. Get data on location, incidence, severity, growth stage, etc. Pathotype to race as above.

• Input data on the Survey Tracker website. Can get access through David Hodson (D.Hodson@cgiar.org).

Searching for resistance to Ug99 • About 80-90% of the world wheat lines tested in Njoro,

Kenya since 2005 are susceptible to Ug99 • In 2004 when the alarm about Ug99 sounded, a large

proportion of the world wheat varieties relied on gene Sr31 alone, which is susceptible to TTKSK, TTKST, etc.

• In Canada and USA, about 85% of spring wheat are susceptible to TTKSK. Hard red winter (48%) and soft winter (27%) more resistant, due to Sr24 and Sr36.

• South America wheat with Sr24/Lr24 is susceptible to PTKST. Lines with Sr25/Lr19 will have intermediate resistance. Lr34 will provide some protection, and is complementary to other Sr genes.

Virulence of Ug99 • Ug99 is virulent on most major Sr genes presently used in

commercial wheat varieties. Virulent (Jin et al. 2007) to genes Sr5, 6, 7a/b, 8a/b, 9a/b/d/g, 10-12, 15-20, 23, 30, 31, 34, 38, McN, and Wld-1. Genes Sr9e, 14, 21, and 29 APR, not seedling.

• TTKSK avirulent to genes Sr13, 22, 24, 25, 26, 27, 28, 32, 33, 35, 36, 39, 40, 44, Tmp, and Tt-3. However, TTKST and PTKST are virulent to Sr24 impacting South American spring wheat and wheat cultivars in Africa and USA. TTTSK is virulent to Sr36 impacting USA winter wheat.

• Lines with gene Lr34 had reduced severity in the Kenya nursery. This gene gives multiple resistance to all rusts (Lr34/Yr18/Sr57).

Searching for resistance to Ug99 • In 2004, had 48 described Sr genes (up to Sr45). Only 15

(including Sr24 and Sr36) were resistant. Only Sr13, Sr24, Sr25, Sr26, Sr36, and SrTmp used extensively in breeding.

• Almost all effective genes are from wild species: Sr22 and 35 from T. monococcum, Sr24-26 and 43 from Thino ponticum, Sr32 and 39 from T. speltoides, Sr33 and 45 from T. tauchii, Sr36 and 40 T. timopheevi, Sr44 from Thino. intermedium. Sr13 is from Khapli emmer, and Sr27 is from rye.

• Sr33 and Sr35 recently cloned. No known virulence for Sr33, but virulence to Sr35 reported in Africa, China, Australia, and North and South America.

Searching for resistance to Ug99 • There are two strategies for rust resistance: major genes (all

stage resistance) and minor (adult plant resistance, APR). • Want to build a gene “stack” to combine several genes to

reduce the likelihood of developing new mutant rust strains • CIMMYT uses APR, genes Sr2, Lr34, Lr46, Lr67. • Durum wheat more resistant (Sr9e, Sr13, Sr14, lack of the D

genome suppressors). • Since Ug99 has defeated most major genes used in

common wheat, there has been a massive effort in the last decade to identify new sources of stem rust resistance.

Searching for resistance to Ug99 2014 BGRI Workshop Abstracts

Mining of new rust resistance genes from progenitor species of wheat, P. Chhuneja et al.* SrND643: a new gene effective against the Pgt race Ug99 group, B.R. Basnet et al. Mapping adult plant resistance to Pgt race Ug99 in Ecuadorian wheat cv. Morocho Blanco, J. Briggs et al.* Identification and genetic mapping of a putatively novel Ug99 stem rust resistance gene in hexaploid wheat, L. Gao et al. A search for new resistance to Pgt race TTKSK in wheat-intergeneric hybrids and their derivatives, J. C. Kielsmeier-Cook et al.* Fine-mapping SrCad on wheat chromosome 6DS, C. Hiebert et al. Field responses of wheat lines with resistance to African Pgt race PTKST introgressed from Aegilops sharonensis, Z.A. Pretorius et al. Evaluation of Kenyan and introduced wheat germplasm for seedling and adult plant resistance to Puccinia graminis f. sp.tritici race Ug99, Z. Kosgey et al.*

Searching for resistance to Ug99 2013 BGRI Workshop Abstracts

Wheat-alien chromosome addition lines for stem rust and yellow rust resistances, M. Rahmatov et al. Reaction of Turkish wild and landrace wheat and barley accessions to African Pgt race TTKSK, B. Steffenson et al. Introgression of resistance to African Pgt races from Sharon goatgrass (Aegilops sharonensis) into wheat, E. Millet et al. Identification of novel genes for resistance to African Pgt races in Aegilops spp. , J. Manisterski et al. Stem rust resistance in Aegilops spp., P.D. Olivera and Y. Jin Genetics of resistance to African Pgt races in Sharon goatgrass, B. Steffenson Stem rust and leaf rust resistances in wild relatives of wheat with D genomes, V.K. Vikas et al. Sources of resistance to stem rust in durum wheat, A.N. Mishra et al. Identification of new sources of resistance to wheat rusts, Satish-Kumar et al.

Searching for resistance to Ug99 2012 BGRI Workshop Abstracts

Screening of cytogenetic stocks for resistance to Pgt race Ug99. G. Fedak et al. Potentially new stem rust and leaf rust resistance genes derived from Aegilops speltoides and Thinopyrum ponticum. I. Dundas et al. Resistance to Pgt race TTKSK in Aegilops spp. P. D. Olivera and Y. Jin Reactions of Aegilops species to Pgt race TTKSK. J. C. Scott et al Moroccan durum wheat landraces harbor resistance to threatening races of Pgt and Pst. A. Ramdani et al. Stem rust resistance in durum wheat. P. D. Olivera et al. Identification of stem rust resistance genes in hexaploid wheat and their introgression using molecular markers* P. S. Yadav et al Identification of durum wheat germplasm from Iran, Italy, Argentina and Bulgaria putatively resistant to Puccinia graminis f. sp. tritici race Ug99* R. Kaviani et al Genome-wide search for novel sources of field resistance to Ug99 and other Ethiopian stem rust races in durum wheat* T. Letta et al.

Searching for resistance to Ug99 • SrCad: In Canadian wheat ‘AC Cadillac’ and ‘Peace’. Highly

resistant to Ug99 in Njoro since 2005. 2 genes, Lr34+SrCad. Linked to bunt gene Bt10 on chromosome 6DS (=Sr42?).

• SrWeb: In ‘Webster’ wheat, has Sr30 and SrWeb. SrWeb is intermediate resistant to Ug99, on 2BL and now Sr9h.

• SrTmp: In ‘Triumph 64’ winter wheat. Has 2 genes, Tmp resistance to Ug99 is at 6DS region near SrCad, but not SrCad. Have this gene in spring (LMPG, RL6071) backgrounds.

• SrTr129: In ‘Tr129’ spring wheat. Has 2 genes, SrTr129 maps to 6AS, pedigree and origin of gene uncertain.

TTKS on Cadillac

Searching for resistance to Ug99 • Since 2005 have 13 more numbered genes (up to Sr58).

Four (Sr55-58) are APR, and 7 of other 9 (Sr46-48, 50-53) are resistant to Ug99.

Published papers:

• Pretorius et al (2011) tested 65 SA bread wheat lines to TTKS+, TTTT, 3 SA races. Sr24 (12), Sr31(5), Sr2 (3). 8 lines resistant to all races (SrTmp?), Steenbras (Sr2+36).

• Rouse et al (2011) 700 USA spring wheat lines in Njoro. 88 had field R, screened these to TTKSK, TTKST, 8 NA races. Majority were R in field and seedling. Some Sr36, unknown.

Searching for resistance to Ug99 • Newcomb et al (2013) 2509 landraces in Njoro in 2007-08.

278 resistant, 36 had Sr2 or Sr36. Of 246, 78 landraces had R to MR field reactions, origins Fertile Crescent and Ethiopia.

• Zurn et al (2014) Iran landrace PI 626573 has new gene (SrWLR) on 2BL at Sr9 locus. Not SrWeb (9h) as is resistant to race RKQQ, maybe new Sr9 allele.

• Brazil wheat ‘Toropi’ has resistance to Ug99 (Dr. Rosa), not yet characterized to date.

Searching for resistance to Ug99 • Wild Species: Good sources of new rust resistance genes. • T. monococcum (A): Rouse and Jin (2011) 1061 lines, 79%

resistant to TTKSK, 6% R to TTTT, TRTT, QFCS, MCCF. Not Sr22 or 35, had 2 new genes. Also 205 T. urartu lines, 93% were R to TTKSK, but all were S to TTTT and TRTT.

• T. tauchii (D): Rouse et al (2011) 456 lines, 98 were R to TTKSK, and 12 lines to TTTT, TRTT, TPMK, RKQQ, QTHJ. Best one was SrTA10171 on 7DS near Sr57 (Lr34).

• Thinopyrum: Turner et al (2013) screened 17 amphiploid lines to TTKSK, TTTTF, TRTTF, TPMKC, MCCFC. All parents (13) resistant to all races, 3 lines novel resistance (Not Sr24, Sr25, or Sr26).

Searching for resistance to Ug99 • Xu et al (2009) screened 62 wheat-alien lines to TTKSK,

TTKST, TTTSK and 5 NA races. 12 amphiploids and 4 disomic lines may be novel resistance genes, mostly from Thinopyrum species (junceum, intermedium, ponticum, bessarabicum) and Aegilops (caudata and speltoides).

• T. turgidum: Olivera et al (2012) 359 lines USDA NSGC, 107 R to TTKSK, 123 R to TRTTF, 148 R to TTTTF; 90 were R to all. Sr2 in some lines, many lines had same IT pattern (same gene in multiple lines). Found 2 new genes in emmer.

Searching for resistance to Ug99 • Introgression of alien resistance genes has been problematic,

due to linkage drag and homologous pairing with common wheat

• Ph1 gene controls chromosome pairing (1958). Bhulllar et al (2014, PNAS) described C-Ph1 gene on 5A, 5B, and 5D. Silencing of C-PH1 using VIGS or RNA-i gave chromosome phenotypes like ph1 mutants, which could be useful to introgress alien genes.

• Lastly, recent report of ‘Eldo Ngano 1’ mutant wheat with Ug99 resistance derived by gamma irradiation (IAEA). Cultivar released in February 2014 in Kenya.

SUMMARY • Ug99 is mutating (8 variants are now known). • Ug99 is migrating (across east Africa, Yemen, Iran) and into

South Africa. Wind may carry spores to South America. • Desire your participation in BGRI global rust survey to provide

virulence information and detect arrival of Ug99. • Most of world wheat is susceptible to Ug99, includes S Amer. • There is a need to develop new wheat cultivars with new

pyramids of resistance genes. • Lots of genes available. Some from common wheat, few are

cloned (Sr33, Sr35), many from wild sources.