Wheat landrace PI 177906 has seedling resistance to stem rust caused by Puccinia graminis f. sp. tritici races TTKSK, TTKST, and BCCBC and field resistance to the Ug99 race group. Parents, 140 recombinant inbred lines, and 138 double haploid (DH) lines were evaluated for seedling resistance to races TTKSK and BCCBC. Parents and the DH population were evaluated for field resistance to Ug99 in Kenya. The 90K wheat single nucleotide polymorphism (SNP) genotyping platform was used to genotype the parents and populations. Goodness-of-fit tests indicated that two dominant genes in PI 177906 conditioned seedling resistance to TTKSK. Two major loci for seedling resistance were consistently mapped to the chromosome arms 2BL and 6DS. The BCCBC resistance was mapped to the same location on 2BL as the TTKSK resistance. Using field data from the three seasons, two major QTL were consistently detected at the same regions on 2BL and 6DS. Based on the mapping result, race specificity, and the infection type observed in PI 177906, the TTKSK resistance on 2BL is likely due to Sr28. One SNP marker (KASP_IWB1208) was found to be predictive for the presence of the TTKSK resistance locus on 2BL and Sr28.
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Two new races of the wheat (Triticum aestivum L.) stem rust pathogen, representing the fifth and sixth variants described within the Ug99 lineage, were detected in South Africa. Races TTKSP and PTKST (North American notation) were detected in 2007 and 2009, respectively. Except for Sr24 virulence, race TTKSP is phenotypically identical to TTKSF, a commonly detected race of Puccinia graminis f. sp. tritici (Pgt) in South Africa. PTKST is similar to TTKSP except that it produces a lower infection type on the Sr21 differential and has virulence for Sr31. Simple sequence repeat (SSR) analysis confirmed the genetic relationship amongst TTKSF, TTKSP, PTKST and TTKSK (Ug99). TTKSK, PTKST and TTKSF grouped together with 99% similarity, while sharing 88% genetic resemblance with TTKSP. These four races in turn shared only 31% similarity with other South African races. It is proposed that both TTKSP and PTKST represent exotic introductions of Pgt to South Africa.
Isolates of Puccinia graminis f. sp. tritici belonging to the Ug99 race group are virulent to a broad spectrum of resistance genes, rendering most of the world's wheat germplasm susceptible to stem rust (3). Following the initial detection of Ug99 (TTKSK, North American [NA] race notation) in Uganda, virulence to the widely used Sr31 resistance gene has been reported from Kenya, Ethiopia, Sudan, and Iran (2,3). In November 2009, a wheat genotype suspected to carry Sr31 showed a susceptible response to stem rust in a disease nursery (29°08′05.02′′S, 30°38′29.18′′E), inoculated with race TTKSP, near Greytown in KwaZulu-Natal, South Africa. Inoculation of urediniospores of the field collection (isolate UVPgt60) onto seedlings of line Federation4*/Kavkaz confirmed virulence for Sr31. In three independent, replicated, and comparative seedling tests, eight single-pustule isolates of UVPgt60 all typed to race PTKST following the NA race nomenclature. These isolates produced compatible infection types (ITs) (3+ to 4) on the Sr31 testers Gamtoos, Sr31/6*LMPG, Federation4*/Kavkaz, Kavkaz, and Clement, whereas isolate UVPgt59 (TTKSP) was avirulent (ITs ;1 to 1) on these genotypes. In addition to Sr31 virulence, the new race differed from TTKSP by producing a lower IT (2 to 2++) on Cns_T.mono_ deriv., the accepted entry for Sr21 in the NA differential set. The UVPgt60 isolates were clearly avirulent on Einkorn (Sr21) (IT ;1=), a response that also differed from those produced by BPGSC, TTKSF, and TTKSP (IT 2). With the exception of Sr21, UVPgt60 isolates had a virulence pattern similar to race TTKST (1), notably the virulence combination for Sr24 and Sr31. Isolate UVPgt60.6 was randomly selected for testing on additional Sr genes and South African wheat cultivars and breeding lines. Similar to the race identification experiments seedling tests were duplicated and compared with reactions produced by TTKSP and other races. Greenhouse temperatures for all seedling tests ranged between 18 and 25°C. On the basis of primary leaf responses, PTKST is avirulent (ITs 0; to 2++) for Sr13, 14, 21, 22, 25, 26, 27, 29, 32, 33, 35, 36, 37, 39, 42, 43, 44, Em, Tmp, and Satu and virulent (ITs 3 to 4) for Sr5, 6, 7b, 8a, 8b, 9a, 9b, 9d, 9e, 9g, 10, 11, 16, 17, 24, 30, 31, 34, 38, 41, and McN. From 103 South African wheat cultivars and lines tested as seedlings, 59 and 47 were susceptible (IT ≥ 3) to races PTKST and TTKSP, respectively. Simple-sequence repeat analysis (4) with selected primer pairs showed that PTKST clusters with isolates belonging to the Ug99 lineage. Subsequent to the collection made at Greytown, stem rust sampled in December 2009 from naturally infected breeders' lines at Cedara (29°32′19.59′′S, 30°16′03.50′′E), KwaZulu-Natal, revealed five isolates with a virulence profile similar to PTKST. On the basis of current evidence it appears that PTKST may be an introduction to South Africa rather than a single-step mutation from local stem rust races.
During the 2000 to 2001 season, 27 stem rust samples were collected from wheat (Triticum aestivum), barley (Hordeum vulgare), and triticale (× Triticosecale) cultivars and lines in the Western Cape, South Africa. Following inoculation and multiplication on McNair 701 seedlings, 40 single pustule isolates of P. graminis f. sp. tritici were established. Twenty-six isolates obtained from wheat, barley, or triticale that produced a similar reaction pattern on a set of differentiating host lines, were designated as pathotype Pgt-2SA55. Pgt-2SA55 is avirulent to Sr5, -6, -7b, -8b, -9b, -9e, -9g, -23, -24, -27, -30, -38, and -Gt, and virulent to Sr11, and -Agi. The remaining 14 isolates, all from wheat and designated as pathotype Pgt-2SA88, were avirulent to Sr24, -27, and -Agi, and virulent to Sr5, -6, -7b, -8b, -9b, -9e, -9g, -11, -23, -30, -38, and -Gt. On an expanded differential set, representative isolates of each pathotype were all avirulent to Sr13, -15, -21, -22, -25, -26, -29, -31, -32, -33, -35, -39, -43, and -Em, and virulent to Sr7a, -8a, -9a, -9d, -9f, -10, -12, -14, -16, -19, -20, -34, and Lc. Pgt-2SA55 was avirulent on cv. Renown (Sr2, -7b, -9d, and -17), whereas Pgt-2SA88 was virulent on this cultivar and Line R Sel carrying only Sr17. Both pathotypes differ from those identified previously in South Africa (1) and to our knowledge, Pgt-2SA88 is the first local isolate to have virulence towards Sr8b and the T. ventricosum-derived gene Sr38. Virulence to Sr38 has been reported in a P. graminis f. sp. tritici isolate collected in Uganda (2). Pathotype Pgt-2SA88 is virulent to seedlings of the previously resistant South African cvs. SST 57 (heterogeneous), Tugela, Tugela DN, and PAN 3377. Furthermore, 20% of the elite breeding lines in the spring and winter wheat breeding program of the Small Grain Institute expressed susceptible seedling reactions to Pgt-2SA88. Triticale cvs. Rex and Kiewiet were heterogeneous in their seedling reaction towards Pgt-2SA55. Seedling and field reactions recorded for the barley cvs. Sterling and SSG 532 and the experimental varieties Puma and Jaguar, showed an increase in stem rust susceptibility to Pgt-2SA55 when compared with existing South African pathotypes. The higher incidence of stem rust in commercial fields and experimental plots of wheat and barley in the Western Cape may be attributed to a recent increase in the cultivation of stem rust-susceptible cultivars in the region. The detection of two new pathotypes of P. graminis f. sp. tritici is of concern to the local small grain industry and requires continued resistance breeding.
Frequent emergence of new variants in the Puccinia graminis f. sp. tritici Ug99 race group in Kenya has made pathogen survey a priority. We analyzed 140 isolates from 78 P. graminis f. sp. tritici samples collected in Kenya between 2008 and 2014 and identified six races, including three not detected prior to 2013. Genotypic analysis of 20 isolates from 2013 and 2014 collections showed that the new races TTHST, TTKTK, and TTKTT belong to the Ug99 race group. International advanced breeding lines were evaluated against an isolate of TTKTT (Sr31, Sr24, and SrTmp virulence) at the seedling stage. From 169 advanced lines from Kenya, 23% of lines with resistance to races TTKSK and TTKST were susceptible to TTKTT and, from two North American regional nurseries, 44 and 91% of resistant lines were susceptible. Three lines with combined resistance genes were developed to facilitate pathogen monitoring and race identification. These results indicate the increasing virulence and variability in the Kenyan P. graminis f. sp. tritici population and reveal vulnerabilities of elite germplasm to new races.
The Ug99 race (TTKSK) of wheat stem rust was first detected in Uganda in 1998 (Pretorius et al. 2000) and since then, seven additional variants have been reported: TTKSF, TTKST, TTTSK, TTKSP, PTKSK, PTKST, and TTKSF+ (Pretorius et al. 2012). In this study, 84 stem rust samples from the 2014 surveys of wheat fields in Africa (Kenya, 9; Uganda, 28; Rwanda, 41; and Egypt, 6) were sent to the Global Rust Reference Center (GRRC, Denmark) for race analysis. Puccinia graminis f. sp. tritici (Pgt) samples were recovered on cv. Morocco, and resulting urediniospores of 53 single-pustule isolates were inoculated onto 20 North American stem rust differential lines using standard procedures (Jin et al. 2008). The pathotyping was repeated in two or three independent experiments. Twelve of the derived isolates were also typed at the USDA-ARS Cereal Disease Laboratory (USA) for an independent confirmation. Among the Kenyan samples, four collected from Njoro (Central Rift, cvs. Robin and Kwale) and two from Ntulumeti and Olgilai (South Rift, cv. Robin), were typed as TTKTK. Race TTKTK was similar to TTKSK except for additional virulence to SrTmp (Infection Type 4). An additional single-pustule isolate derived from one sample from Njoro showed a high infection type on LcSr24Ag and CnsSrTmp, testers for Sr24 and SrTmp, respectively, and was typed as TTKTT. These isolates were also tested on Siouxland (PI 483469, Sr24+Sr31), Sisson (PI 617053, Sr31+Sr36), and Triumph 64 (CI 13679, donor of SrTmp) to confirm their virulence/avirulence combinations to Sr24, Sr31, Sr36, and SrTmp. Race TTKTK was also detected at two locations in Uganda (Rubaya and Muko in Kabale region) and at five locations in Rwanda (Kinigi, Rwerere, Rufungo, Gatebe, and Kamenyo). Three isolates derived from stem rust samples collected on cv. PBW343 (carrying Sr31) in Sakha in the Nile Delta region in Egypt were also typed as TTKTK. In addition, DNA from isolates of race TTKTK were analyzed using a diagnostic qPCR assay (Ug99 RG stage-1, Szabo, unpublished data), which confirmed that these samples belong to the Ug99 lineage. The identification of SrTmp virulence in the Ug99 race group in several countries in one year emphasizes the relevance of coordinated international surveillance efforts and utilization of diverse sources of resistance to control stem rust in wheat. Further studies are in progress to determine the detailed relationship of the newly emerged races and other Pgt isolates identified in the Ug99 group.
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, causes severe losses in wheat production under epidemic conditions. The detection of isolate Ug99 in east Africa (Pretorius et al. 2000) has raised global concerns of the vulnerability of wheat to stem rust. Since initial detection, 10 variants of Ug99 have been reported across 13 countries (Patpour et al. 2015). Wheat stem rust infection was widespread in Kenya in 2014. Fifty-two samples from common wheat were collected from the Mount Kenya and North, South, and Central Rift regions and analyzed for race identity in a level-3 biocontainment laboratory in Canada. Of these samples, 41 yielded viable spores for race pathotyping. Each sample was inoculated on 8-day-old seedlings of 20 single-gene differential lines using an inoculator, incubated for 16 h in a dew chamber in the dark, and subsequently moved to a growth cabinet set at 18 ± 1°C and 16-h photoperiod. Infected plants were rated 14 days postinoculation using a 0 to 4 infection type scale. Virulence analysis using the letter-code nomenclature system (Jin et al. 2008) identified two new races in the Ug99 race group from repeated experiments. Race TTHSK was identified from samples collected at Ngorengore (South Rift) and Njoro (field 13), which differs from the original Ug99 isolate (race TTKSK) by avirulence on gene Sr30. Race TTHSK is similar to race TTHST, which was detected previously by Newcomb et al. (manuscript in preparation). Race PTKTK was identified from samples collected at Rotian and Eor-Enkitok in the South Rift region, Cheplasgei and Kaplogoi in the North Rift region, and at the technology farm in Njoro in the Central Rift region. Race PTKTK differs from race PTKSK (first identified in 2007) by additional virulence to gene SrTmp, or alternatively differs from race TTKTK by avirulence to gene Sr21. Races TTKTK and TTKTT in the Ug99 race group with virulence to gene SrTmp were also found in 2014 (Patpour et al. 2015; Patpour et al. 2016). Virulence to SrTmp was detected soon after the deployment of the variety ‘Kenya Robin’ (which has SrTmp) in 2011. This report now brings the total number of variants in the Ug99 race group to 13 and highlights the importance of stem rust surveillance and race pathotyping, particularly in Kenya and surrounding countries in eastern Africa where evolution of new stem rust virulence is frequent.
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a devastating disease of wheat worldwide. Development of cultivars with effective resistance has been the primary means to control this disease, but the appearance of new virulent strains such as Ug99 has rendered most wheat varieties vulnerable. The stem rust resistance gene SrCad located on chromosome arm 6DS has provided excellent resistance to various strains of Ug99 in field nurseries conducted in Njoro, Kenya since 2005. Three genetic populations were used to identify SNP markers closely linked to the SrCad locus. Of 220 SNP markers evaluated, 27 were found to be located within a 2 cM region surrounding SrCad. The diagnostic potential of these SNPs was evaluated in a diverse set of 50 wheat lines that were primarily of Canadian origin with known presence or absence of SrCad. Three SNP markers tightly linked proximally to SrCad and one SNP that co-segregated with SrCad were completely predictive of the presence or absence of SrCad. These markers also differentiated SrCad from Sr42 and SrTmp which are also located in the same region of chromosome arm 6DS. These markers should be useful in marker-assisted breeding to develop new wheat varieties containing SrCad-based resistance to Ug99 stem rust.
To determine phenotypic diversity of Puccinia graminis f. sp. tritici (Pgt), the cause of stem rust of wheat, samples of infected stems were collected during 2009–2013 from commercial wheat fields, experimental plots, and rust trap nurseries across major wheat growing regions of South Africa (SA). Pgt races were identified based on their avirulence/virulence profiles on seedlings of 20 standard and five supplemental differential lines. Nine Pgt races were identified from 521 isolates pathotyped. Predominant races were TTKSF (2SA88, South African race notation) with 39%–85% frequency and BPGSC + Sr27,Kiewiet,Satu (2SA105) with 10%–20% frequency. Race TTKSF is virulent on major resistance genes such as Sr5, Sr6, Sr9e, and Sr38 and is one of the variants of the highly virulent Ug99 race group originally detected in East Africa. Race TTKSP (2SA106), also a member of the Ug99 lineage, was detected in 2009 and 2010. A new race virulent on Sr31, PTKST (2SA107), was detected in 2009. Two new races, TTKSF + Sr9h (2SA88 + Sr9h) and BFBSC (2SA108), were identified in 2010. Race TTKSF + Sr9h is similar to TTKSF except for its virulence on Sr9h. Race BFBSC appears related to Pgt races characterized by avirulence for Sr5 and often attacking triticale. Simple sequence repeat (SSR) analysis indicated that race BFBSC forms part of the non-Ug99 group of South African Pgt races. Despite some similarity in avirulence/virulence phenotype with the non-Ug99 races, BFBSC represents a third distinct genetic lineage within this group. Genes Sr13, 14, 22, 25, 26, 29, 32, 33, 35, 36, 37, 39, 42, and 43 that are effective against the new and other Pgt races can be used in resistance breeding in SA. Races like PTKST and TTKSF + Sr9h were also reported in other Southern African countries suggesting that they probably spread to SA from neighbouring regions. The new races are additions to nearly 30 Pgt races identified since the early 1980s, and suggest continued variability of the Pgt population in SA. Therefore, surveys should be conducted regularly to timely detect and manage new races, and utilize the latter in screening and identification of effective sources of resistance.
The recently identified Puccinia graminis f. sp. tritici (Pgt) race TTKSK (Ug99) poses a severe threat to global wheat production because of its broad virulence on several widely deployed resistance genes. Additional virulences have been detected in the Ug99 group of races, and the spread of this race group has been documented across wheat growing regions in Africa, the Middle East (Yemen), and West Asia (Iran). Other broadly virulent Pgt races, such as TRTTF and TKTTF, present further difficulties in maintaining abundant genetic resistance for their effective use in wheat breeding against this destructive fungal disease of wheat. In an effort to identify loci conferring resistance to these races, a genome-wide association study was carried out on a panel of 250 spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT), six wheat breeding programs in the United States and three wheat breeding programs in Canada.
The lines included in this study were grouped into two major clusters, based on the results of principal component analysis using 23,976 SNP markers. Upon screening for adult plant resistance (APR) to Ug99 during 2013 and 2014 in artificial stem rust screening nurseries at Njoro, Kenya and at Debre Zeit, Ethiopia, several wheat lines were found to exhibit APR. The lines were also screened for resistance at the seedling stage against races TTKSK, TRTTF, and TKTTF at USDA-ARS Cereal Disease Laboratory in St. Paul, Minnesota; and only 9 of the 250 lines displayed seedling resistance to all the races. Using a mixed linear model, 27 SNP markers associated with APR against Ug99 were detected, including markers linked with the known APR gene Sr2. Using the same model, 23, 86, and 111 SNP markers associated with seedling resistance against races TTKSK, TRTTF, and TKTTF were identified, respectively. These included markers linked to the genes Sr8a and Sr11 providing seedling resistance to races TRTTF and TKTTF, respectively. We also identified putatively novel Sr resistance genes on chromosomes 3B, 4D, 5A, 5B, 6A, 7A, and 7B.
Our results demonstrate that the North American wheat breeding lines have several resistance loci that provide APR and seedling resistance to highly virulent Pgt races. Using the resistant lines and the SNP markers identified in this study, marker-assisted resistance breeding can assist in development of varieties with elevated levels of resistance to virulent stem rust races including TTKSK.