Ug99

Puccinia graminis f. sp. tritici (Pgt) race TKTTF was reported as the dominant race in the wheat stem rust epidemics in Ethiopia during 2014–15 (Olivera et al. 2015). The race and variants hereof have also been recorded elsewhere in Africa, the Middle East, and Europe (www.wheatrust.org/stem-rust-tools-maps-and-charts/race-frequency-map). Here, we report the presence of additional virulence to Sr25 in the TKTTF population, a resistance gene transferred to several Australian and CIMMYT wheat genotypes. At the seedling stage, Sr25 confers infection type (IT) 2 or lower for isolates in the Ug99 race group and up to IT 2+ toward race TKTTF (Newcomb et al. 2016; Olivera et al. 2015). Our results are based on Pgt isolates of the TKTTF race from Ethiopia (2012, 2013, 2015), Egypt (2014), Azerbaijan (2014), Iran (2009, 2011, 2014), Iraq (2014), Lebanon, Sudan, and Turkey (2012), Denmark and Germany (2013), and Sweden (2014). Race typing was carried out at the Global Rust Reference Center according to Jin et al. (2008), except that we scored IT on both leaf 1 and 2; additional single pustule isolates of each sample were raised and stored in liquid nitrogen (–196°C). Sr25 response was assayed using seedling leaves and stems of adult plants of Misr1 (Oasis/Skauz//4*BCN/3/2*Pastor) and Agatha/9*LMPG (Sr25 carriers) along with two reference lines, Triumph 64 (SrTmp) and NA101/MqSr7a (Sr7a), and Morocco as a control. Seedling ITs were scored 17 days post-inoculation at 18 ± 2°C using a 0 to 4 scale (McIntosh et al. 1995). Isolates showing ITs of 33+ to 4 on Misr1, Agatha/9*LMPG, and susceptible check were considered Sr25 virulent, and clearly different from ITs conferred by Sr25 avirulent isolates. Results were confirmed for each isolate by race typing additional single-pustule isolates derived from cultivars Misr1 and/or Agatha, along with avirulent reference isolates. Virulence for Sr25 was observed in race TKTTF isolates from Azerbaijan, Egypt, Ethiopia, Iran, Iraq, and Sweden, collected in 2014 or 2015, but not in any sample collected earlier than 2014. The results were confirmed on adult plants of Misr1 and Agatha/9*LMPG by Sr25 virulent and avirulent isolates of TKTTF, TTKSK, and TTKST, respectively. Spore suspensions of ∼0.5 ml at concentration of ∼3 × 10⁵ spores/ml were injected into the stem internodes at Zadoks 45. The adult plant and seedling tests were carried out concurrently using the environmental conditions described above. The plants containing Sr25 were susceptible to the Sr25 virulent isolate and moderately resistant to moderately susceptible to the Sr25-avirulent isolates of TKTTF, TTKSK, and TTKST. The experiments were repeated two times with three replicates, using cv. Morocco as a susceptible check. Emergence of virulence to Sr25 in the race TKTTF is considered significant due to its spread into new areas and the potential loss of a significant source of resistance against Ug99.

Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F₆ recombinant inbred line and an F₂ population, two genes were identified that mapped to the short arm of chromosome 1S^sh, designated as Sr-1644-1Sh, and the long arm of chromosome 5S^sh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.

Stem rust, caused by Puccinia graminis f. sp. tritici, is a destructive disease of wheat that can be controlled by deploying effective stem rust resistance (Sr) genes. Highly virulent races of P. graminis f. sp. tritici in Africa have been detected and characterized. These include race TRTTF and the Ug99 group of races such as TTKSK. Several Canadian and U.S. spring wheat cultivars, including the widely grown Canadian cultivar ‘Harvest’, are resistant to TRTTF. However, the genetic basis of resistance to TRTTF in Canadian and U.S. spring wheat cultivars is unknown. The objectives of this study were to determine the number of Sr genes involved in TRTTF resistance in Harvest, genetically map the resistance with DNA markers, and use markers to assess the distribution of that resistance in a panel of Canadian cultivars. A doubled haploid (DH) population was produced from the cross LMPG-6S/Harvest. The DH population was tested with race TRTTF at the seedling stage. Of 92 DH progeny evaluated, 46 were resistant and 46 were susceptible which perfectly fit a 1:1 ratio indicating a single Sr gene was responsible for conferring resistance to TRTTF in Harvest. Mapping with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers placed the resistance gene distally on the chromosome 6AS genetic map, which corresponded to the location reported for Sr8. SSR marker gwm459 and 30 cosegregating SNP markers showed the closest linkage, mapping 2.2 cM proximal to the Sr gene. Gene Sr8a confers resistance to TRTTF and may account for the resistance in Harvest. Testing a panel of Canadian wheat cultivars with four SNP markers closely linked to resistance to TRTTF suggested that the resistance present in Harvest is present in many Canadian cultivars. Two of these SNP markers were also predictive of TRTTF resistance in a panel of 241 spring wheat lines from the United States, Canada, and Mexico.

Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BC₃F₂ families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940–7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest—including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.