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.
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Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant ‘Digalu’ in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in ‘Gabo 56’. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and ‘Chinese Spring’ exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a ‘Berkut’/‘Scalavatis’ population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.
Stem rust (Puccinia graminis f.sp.tritici) is a major disease of wheat that occurs more in the main wheat growing regions of Kenya. The objective of this study was to assess the incidence and severity of wheat stem rust during the 2015 growing season. A survey was conducted in Mau-Narok, Njoro and Kabatini regions. During the survey work, 149 small scale wheat growers’ fields were assessed. The results revealed that stem rust incidence of the three surveyed areas ranged from 11.3 to 77.8% and severity 20 to 60%. The survey confirmed that the incidence and severity were associated with the farming practices such as chemical control, varieties grown, use of certified or uncertified seed and cropping systems. The survey showed that high to moderate incidence and severity levels were found on fields with one or two sprays with a fungicide. The use of fungicide was the major practice by growers for stem rust control reporting Mau-Narok with 43.2%, Kabatini 38.9% and Njoro 17.8%. The varieties grown had a relationship to disease incidence and severity percent levels. The use of uncertified seed by farmers contributed to high disease incidence. About 50.6% growers preferred old varieties mainly Robin and NjoroBWII. About 97.8% of the farmers practiced crop rotation of wheat with legumes. A multi-tactic disease management approach mainly two fungicide sprays per growing season, use at recommended rates, planting of certified seed of resistant varieties and crop rotation of legumes with wheat are required as stem rust effective management strategies.
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.
A severe stem rust epidemic occurred in southern Ethiopia during November 2013 to January 2014, with yield losses close to 100% on the most widely grown wheat cultivar, ‘Digalu’. Sixty-four stem rust samples collected from the regions were analyzed. A meteorological model for airborne spore dispersal was used to identify which regions were most likely to have been infected from postulated sites of initial infection. Based on the analyses of 106 single-pustule isolates derived from these samples, four races of Puccinia graminis f. sp. tritici were identified: TKTTF, TTKSK, RRTTF, and JRCQC. Race TKTTF was found to be the primary cause of the epidemic in the southeastern zones of Bale and Arsi. Isolates of race TKTTF were first identified in samples collected in early October 2013 from West Arsi. It was the sole or predominant race in 31 samples collected from Bale and Arsi zones after the stem rust epidemic was established. Race TTKSK was recovered from 15 samples from Bale and Arsi zones at low frequencies. Genotyping indicated that isolates of race TKTTF belongs to a genetic lineage that is different from the Ug99 race group and is composed of two distinct genetic types. Results from evaluation of selected germplasm indicated that some cultivars and breeding lines resistant to the Ug99 race group are susceptible to race TKTTF. Appearance of race TKTTF and the ensuing epidemic underlines the continuing threats and challenges posed by stem rust not only in East Africa but also to wider-scale wheat production.
Landrace AUS28011 (Mahmoudi), collected from Ghardimaou, Tunisia, produced low stem rust response against Australian pathotypes of Puccinia graminis f. sp. tritici (Pgt) carrying virulence for several stem rust resistance genes deployed in modern wheat cultivars. Genetic analysis based on a Mahmoudi/Yitpi F3 population indicated the involvement of a single all-stage stem rust resistance gene and it was temporarily named SrM. Bulked segregant analysis using multiplex-ready SSR technology located SrM on the long arm of chromosome 5B. Since there is no other all-stage stem rust resistance gene located in chromosome 5BL, SrM was permanently designated Sr49. The Mahmoudi/Yitpi F3 population was enhanced to generate F6 recombinant inbred line (RIL) population for detailed mapping of Sr49 using publicly available genomic resources. Markers sun209 and sun479 flanked Sr49 at 1.5 and 0.9 cM distally and proximally, respectively. Markers sun209 and sun479 amplified PCR products different than the Sr49-linked alleles in 146 and 145 common wheat cultivars, respectively. Six and seven cultivars, respectively, carried the resistance-linked marker alleles sun209 148bp and sun479 200bp ; however, none of the cultivars carried both resistance-linked alleles. These results demonstrated the usefulness of these markers for marker-assisted selection of Sr49 in breeding programs.
The transfer of alien genes to crop plants using chromosome engineering has been attempted infrequently in tetraploid durum wheat (Triticum turgidum L. subsp. durum). Here, we report a highly efficient approach for the transfer of two genes conferring resistance to stem rust race Pgt-TTKSK (Ug99) from goatgrass (Aegilops speltoides) to tetraploid wheat. The durum line DAS15, carrying the stem rust resistance gene Sr47 derived from Ae. speltoides, was crossed, and backcrossed, to durum 5D(5B) aneuploids to induce homeologous pairing. After a final cross to ‘Rusty’ durum, allosyndetic recombinants were recovered. The Ae. speltoides chromosomal segment carrying Sr47 was found to have two stem rust resistance genes. One gene conditioning an infection type (IT) 2 was located in the same chromosomal region of 2BS as Sr39 and was assigned the temporary gene symbol SrAes7t. Based on ITs observed on a diverse set of rust races, SrAes7t may be the same as Sr39. The second gene conditioned an IT 0; and was located on chromosome arm 2BL. This gene retained the symbol Sr47 because it had a different IT and map location from other stem rust resistance genes derived from Ae. speltoides. Allosyndetic recombinant lines carrying each gene on minimal alien chromosomal segments were identified as were molecular markers distinguishing each alien segment. This study demonstrated that chromosome engineering of Ae. speltoides segments is feasible in tetraploid wheat. The Sr47 gene confers high-level and broad spectrum resistance to stem rust and should be very useful in efforts to control TTKSK.
A stem rust resistance gene, originally derived from Triticum tauschii accession RL5289 and present in the germplasm line 87M66-2-1, is here designated Sr45. Sr45 was found to be closely linked to Sr33 (9 ± 1.9 map units) and the centromere (21 ± 3.4 map units) on chromosome arm 1DS. Sr45 is believed to be the same gene as SrX. The Russian wheat aphid resistance gene, Dn5, was loosely linked (32 ± 5 map units) to Ep-D1b, which occurs on a translocation derived from T. ventricosum, and to the cn?D1 locus (37 ± 6.3 map units) on chromosome arm 7DL. Dn5 derives from T. aestivum accession Pl294994 which was found to express two novel Ep-1 alleles (proposed designations Ep-A1d and Ep-D1e). A gene (here designated Dn7) for Russian wheat aphid resistance that was derived from the rye accession, Turkey 77', mapped 14.5 ± 3.9 map units from Lr26 on the 1BL.1RS translocation.
The emergence of the highly virulent Ug99 race complex of the stem rust fungus (Puccinia graminis Pers. f. sp. tritici Eriks. and Henn.) threatens wheat (Triticum aestivum L.) production worldwide. One of the effective genes against the Ug99 race complex is Sr44, which was derived from Thinopyrum intermedium (Host) Barkworth and D.R. Dewey and mapped to the short arm of 7J (designated 7J#1S) present in the noncompensating T7DS-7J#1L∙7J#1S translocation. Noncompensating wheat-alien translocations are known to cause genomic duplications and deficiencies leading to poor agronomic performance, precluding their direct use in wheat improvement. The present study was initiated to produce compensating wheat-Th. intermedium Robertsonian translocations with Sr44 resistance. One compensating RobT was identified consisting of the wheat 7DL arm translocated to the Th. intermedium 7J#1S arm resulting in T7DL∙7J#1S. The T7DL∙7J#1S stock was designated as TA5657. The 7DL∙7J#1S stock carries Sr44 and has resistance to the Ug99 race complex. This compensating RobT with Sr44 resistance may be useful in wheat improvement. In addition, we identified an unnamed stem rust resistance gene located on the 7J#1L arm that confers resistance not only to Ug99, but also to race TRTTF, which is virulent to Sr44. However, the action of the second gene can be modified by the presence of suppressors in the recipient wheat cultivars.