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Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness. Combining fungal-resistance genes into a single cassette enables the generation of highly resistant wheat lines.

Stem rust in recent years has acquired an epiphytotic character, causing significant economic damage for wheat production in some parts of Western Siberia. On the basis of a race composition study of the stem rust populations collected in 2016-2017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 in Altai population were identified. The race differentiation of stem rust using a tester set of 20 North American Sr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulent only to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A low frequency of virulence (10-25 %) of the Omsk population pathotypes was found for Sr11, Sr24, Sr30, and for Altai population - Sr7b, Sr9b, Sr11, SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stem rust were made in 2016-2018 in Omsk region in the varieties and spring wheat lines from three different sources. The first set included 58 lines and spring bread wheat varieties with identified Sr genes - the so-called trap nursery (ISRTN - International Stem Rust Trap Nursery). The second set included spring wheat lines from the Arsenal collection, that were previously selected according to a complex of economically valuable traits, with genes for resistance to stem rust, including genes introgressed into the common wheat genome from wild cereal species. The third set included spring bread wheat varieties created in the Omsk State Agrarian University within the framework of a shuttle breeding program, with a synthetic wheat with the Ae. tauschii genome in their pedigrees. It was established that the resistance genes Sr31, Sr40, Sr2 complex are effective against stem rust in the conditions of Western Siberia. The following sources with effective Sr genes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10, Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24, 1RS-Am), Siouxland (Sr24, Sr31), Roughrider (Sr6, Sr36), Sisson (Sr6, Sr31, Sr36), and Fleming (Sr6, Sr24, Sr36, 1RS-Am), Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC1F2 (96 × 113) × 145 × 113 (Sr2, Sr36, Sr44), No. 14а F3 (96 × 113) × 145 (Sr36, Sr44), No. 19 BC2F3 (96 × 113) × 113 (Sr2, Sr36, Sr44), and No. 20 F3 (96 × 113) × 145 (Sr2, Sr36, Sr40, Sr44) from the Arsenal collection; and the Omsk State Agrarian University varieties Element 22 (Sr31, Sr35), Lutescens 27-12, Lutescens 87-12 (Sr23, Sr36), Lutescens 70-13, and Lutescens 87-13 (Sr23, Sr31, Sr36). These sources are recommended for inclusion in the breeding process for developing stem rust resistant varieties in the region.Стеблевая ржавчина пшеницы в последние годы приобрела эпифитотийный характер, нанося значительный экономический ущерб производству зерна пшеницы в отдельных областях Западной Сибири. По результатам изучения расового состава популяций стеблевой ржавчины, собранной в 2016–2017 гг. в Омской области и Алтайском крае, выявлено 13 патотипов в омской популяции и 10 – в алтайской. Диффе- ренцирование рас стеблевой ржавчины проводили с помощью тестерного набора 20 североамериканских линий-дифференциаторов Sr генов. Гены патотипов стеблевой ржавчины омской популяции авирулентны только к гену устойчивости Sr31, алтайские изоляты авирулентны, помимо Sr31, к генам Sr24, Sr30. Низкая частота вирулентности (10–25 %) патотипов омской популяции установлена для Sr11, Sr24, Sr30, а патотипов алтайской – для Sr7b, Sr9b, Sr11, SrTmp, которые неэффективны в Омской области. Полевая оценка устойчивости к стеблевой ржавчине проводилась в 2016–2018 гг. в Омской области в динамике в течение вегетационного периода у сортов и линий мягкой пшеницы из трех различных источников. Первый набор включал 58 линий и сортов яровой мягкой пшеницы с идентифицированными генами Sr, условно называемыми «питомник- ловушка» (ISRTN – international stem rust trap nursery). Второй набор включал линии яровой пшеницы из коллекции «Арсенал», отобранные ранее по комплексу хозяйственно ценных признаков и несущие пирамиду генов устойчивости к стеблевой ржавчине, в том числе интрогрессированных в геном мягкой пшеницы от дикорастущих видов злаков. Третий набор включал сорта яровой мягкой пшеницы, созданные в Омском аграрном университете по программе челночной селекции, имеющие в родословной синтетическую пшеницу с геномом Ae. tauschii. Установлено, что линии с генами Sr31, Sr40, Sr2 complex невосприимчивы к стеблевой ржавчине в условиях Западно-Сибирского региона. Выделены источники с эффективными гена- ми Sr : из питомника ISRTN – (Benno)/6*LMPG-6 DK42 (Sr31), Seri 82 (Sr31), Cham 10 (Sr31), Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24, 1RS-Am), Siouxland (Sr24, Sr31), Roughrider (Sr6, Sr36), Sisson (Sr6, Sr31, Sr36), Fleming (Sr6, Sr24, Sr36, 1RS-Am), Pavon 76 (Sr2 complex); из коллекции «Арсенал» – № 1 BC1F2 (96 × 113) × 145 × 113 (Sr2, Sr36, Sr44), № 14а F3 (96 × 113) × 145 (Sr36, Sr44), № 19 BC2F3 (96 × 113) × 113 (Sr2, Sr36, Sr44), № 20 F3 (96 × 113) × 145 (Sr2, Sr36, Sr40, Sr44); сорта Омского аграрного университета – Элемент 22 (Sr31, Sr35), Лютесценс 27-12, Лютес- ценс 87-12 (Sr23, Sr36), Лютесценс 70-13, Лютесценс 87- 13 (Sr23, Sr31, Sr36). Выделенные источники рекомен- дуются для включения в селекционный процесс при создании сортов, устойчивых к стеблевой ржавчине в условиях региона.

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability., The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production. Clare Lewis et al. report the first identification in nearly 60 years of a cultivated wheat plant infected with the fungal pathogen Puccinia graminis f.sp. tritici (wheat stem rust) in the United Kingdom. They find that only 20% of UK wheat varieties are resistant to this strain and urge growers to resume resistance breeding programs.

Since the first detection of race TTKSK (Ug99) of Puccinia graminis f. sp. tritici in Uganda in 1998 (Pretorius et al. 2000), it has been a priority to track its further spread to other wheat growing areas. To date, 10 variants in the Ug99 race group have been detected in 12 countries, i.e., Uganda, Kenya, Ethiopia, Sudan, Tanzania, Eritrea, Rwanda, South Africa, Zimbabwe, Mozambique, Yemen, and Iran (Patpour et al. 2015). In the 2014 crop season, the presence of virulence to Sr31 in Egypt was suspected based on preliminary field observations of high infection on sources of Sr31 planted as international stem rust trap nursery at i) Sakha Agricultural Research Station in Kafrelsheikh (31.094059° N, 30.933899° E), ii) Al-Sharqia (30.601400° N, 31.510383° E), and iii) Nubaria (30.91464° N, 29.95543° E). At Sakha, wheat cv. PBW343 (carrying Sr31) was scored 30MS-S, and the monogenic line Benno Sr31/6*LMPG was scored 20MS-S at Al-Sharqia. Three samples from each of these lines were sent to the Global Rust Reference Center (GRRC, Denmark). At Nubaria, stem rust was observed on wheat cvs. Misr-1, Misr-2, Giza 168, and Giza 171, and infected samples were collected and sent under permit to the Foreign Disease-Weed Science Research Unit (Fort Detrick, MD). Urediniospores of each sample were recovered on susceptible wheat cv. Morocco and McNair 701. Twenty-three and 11 single pustule isolates were derived and analyzed at GRRC and USDA-ARS Cereals Disease Laboratory, respectively, using 20 North American stem rust differential lines following standard race-typing procedure and infection type (IT) criteria determining virulence and avirulence (Jin et al. 2008). In addition, three supplemental tester lines of Siouxland (carrying Sr24+Sr31), Sisson (carrying Sr31+Sr36), and Triumph 64 (donor of SrTmp) were included to confirm virulence/avirulence to Sr24, Sr31, Sr36, and SrTmp. The experiments were repeated two to three times. Three races in the Ug99 race group were detected; TTKST (four isolates, IT 3+4 for Sr24, Sr31, and cv. Siouxland) from Al-Sharqia, TTKTK (13 isolates, IT 4 for Sr31, SrTmp, and cv. Triumph 64) from Sakha, and TTKSK (2 isolates, IT 4 for Sr31) from Nubaria. This is the first confirmation of races in the Ug99 race group in Egypt, thereby extending the geographical distribution of Ug99-related races. Since Egypt may play a role as green-bridge for P. graminis f. sp. tritici between East and North African countries and the wheat belts in the Middle East and Mediterranean regions, the rust surveillance efforts should be intensified in affected countries as well as in neighboring regions.

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.