Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat “Kronos”

Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.

Distribution, dynamics, and physiological races of wheat stem rust (Puccinia graminis f.sp. tritici) on irrigated wheat in the Awash River Basin of Ethiopia

Wheat is one of the high-value major crops in the world. However, wheat stem rust is considered one of the determinant threats to wheat production in Ethiopia and the world. So this study was conducted to assess the disease intensity, seasonal distribution dynamics pattern, the genetic variability of Puccinia graminis f. sp. tritici, and to determine the virulence spectrum in the irrigated ecology of the Awash River Basin. Totally 137 wheat farms were evaluated, from 2014/15–2019/20 in six districts representing the Upper, Middle, and Lower Awash River Basin. Farm plots were assessed, in every 5–10 km intervals, with ’X’ fashion, and data on disease incidence, severity, healthy plants were counted and recorded. Diseased samples were collected from the diseased wheat stem by Puccinia graminis physiological and genetic race analysis. The seasonal trend of stem rust disease progress showed its importance to infer the future progresses of the disease for the country’s potential production plan of irrigated wheat. The result revealed that the disease prevalence, disease incidence, and severity were significantly varied; among the different districts and seasons in the two regions. The survey results also indicated that about 71.7% of the wheat fields were affected by stem rust during the 2018/19 growing period. The disease’s overall incidence and mean severity during the same season were 49.02% and 29.27%, respectively. In 2019/20, about 63.7% of the wheat fields were affected by stem rust, disease incidence 30.97%, and severity 17.22% were lower than the previous season. In 2019/20, even though seasonal disease distribution decreased, the spatial distribution was expanding in Afambo and Dubti districts. Four, stem rust dominant races were identified (TTTTF, TKTTF TKKTF, and TTKTF) by physiological and genetic race analysis during 2018/19 and one additional race (TKPTF) in 2019/20, production year. The result indicated that the races are highly virulent and affect most Sr genes except Sr31 and Sr24. From the race analysis result, TTTTF, and TKKTF have the broadest virulence spectrum race, which affects 90% of the Sr genes. Generally, we can conclude that the spatial and seasonal distribution of the disease is expanding. Most of the races in the irrigated areas in the Basin were similar to that of rain-fed wheat production belts in Ethiopia, so care must be given, to effective management of the diseases, in both production ecologies towards controlling the spore pressure than race variability. Therefore, these findings provide inputs for wheat producers to reduce the spread and disease’ damage in the irrigated ecologies of Ethiopia. Also, it gives an insight for breeders to think about the breeding program in their crossing lines.

The wheat stem rust (Puccinia graminis f. sp. tritici) population from Washington contains the most virulent isolates reported on barley

A diverse sexual population of wheat stem rust, Puccinia graminis f. sp. tritici (Pgt), exist in the Pacific Northwest (PNW) region of the United States due to the natural presence of Mahonia spp. that serve as alternate hosts to complete its sexual life cycle. The region appears to be a center of stem rust diversity in North America where novel virulence gene combinations can emerge that could overcome deployed barley and wheat stem rust resistances. A total of 100 single pustule isolates derived from stem rust samples collected from barley in Eastern Washington during the 2019 growing season were assayed for virulence on the two known effective barley stem rust resistance genes/loci, Rpg1 and the rpg4/5-mediated resistance locus (RMRL) at the seedling stage. Interestingly, 99% of the Pgt isolates assayed were virulent on barley variety Morex carrying the Rpg1 gene, and 62% of the isolates were virulent on the variety Golden Promise transformant (H228.2c) that carries a single copy insertion of the Rpg1 gene from Morex and is more resistant than Morex to many Rpg1 avirulent isolates. Also, 16% of the isolates were virulent on the near isogenic line HQ-1, that carries the RMRL introgression from the barley line Q21861 in the susceptible Harrington background. Alarmingly, 10% of the isolates were virulent on barley line Q21861 that contains both Rpg1 and RMRL. Thus, we report on the first Pgt isolates worldwide with virulence on both Rpg1 and RMRL when stacked together representing the most virulent Pgt isolates reported on barley.

Characteristics of the virulence of the wheat stem rust pathogen in the conditions of the Saratov region

Stem rust (pathogen - biotrophic fungus Puccinia graminis f. sp. tritici Erikss. & Henning) – a particularly deleterious disease of bread wheat. In this article the results of the analysis of the structure of samples of Saratov populations of wheat stem rust pathogen by signs of virulence during 2016-2020 were presented. A total of 60 pathogen isolates were characterized for virulence. In general, Saratov P. graminis populations were characterized as highly virulent during the study period. The significant variation in the virulence frequencies of P. graminis was observed in lines with the genes Sr9b, Sr9g, Sr12, Sr21, Sr25, Sr27, Sr30, Sr32, Sr33, Sr7a+12, Sr17+13. The other Sr lines used in the analysis, the virulence rates remained consistently high in all the years of research. Genes and combinations of genes: SrSatu, Sr24, Sr25+9g, Sr25+31, Sr25+38 were shown to be effective to P. graminis populations in 2016-2020.

First Report of Races TKTTP and TKKTP of Puccinia graminis f. sp. tritici with Virulence to Wheat Stem Rust Resistance Gene Sr24 in Turkey and Tunisia

Severe wheat stem rust caused by Puccinia graminis Pers.:Pers. f. sp. tritici Erikss. (Pgt) can result in complete crop failure. In recent years, the increasing frequency and the early onset of stem rust in Central West Asia and North Africa (CWANA) has become a big concern. The Sr24 resistance gene, one of the most effective stem rust resistance genes effective against most P. graminis f. sp. tritici races worldwide, has been widely deployed. Until the recent establishment of virulence to Sr24 within the Ug99 lineage of the pathogen in Africa (Hei et al. 2020; Jin et al. 2008; Patpour et al. 2015), Iraq (Nazari et al., 2021), occasional detections of races virulent to Sr24 were reported in South Africa (Le Roux and Rijkenberg 1987), India (Bhardwaj et al. 1990), Germany (Olivera Firpo et al. 2017), Georgia (Olivera, et al. 2019), and Western Siberia (Skolotneva et al., 2020). During the rust surveys conducted in Sinops, Samsun, and Kastomonu in the Black Sea region in northern Turkey in 2018, 19 isolates were collected. Single pustule (SP) isolates were developed and used in race analysis in the Biosafety Rust Laboratory, Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey. Sample recovery, experimental procedures for pre-inoculation, inoculation, incubation, and race typing were conducted as previously described (Nazari et al. 2021). Among the tested SP isolates, two isolates showed a high infection type (IT) of 33+ on the Sr24 tester line (Little Club/Agent) and a low infection type of 11+ for the source of Sr31 (Benno/6*LMPG-6). Eight SP isolates were further developed from the high IT 33+ pustules collected from the Sr24 tester line. After spore multiplications, they were used in inoculation of the 20 North American stem rust single-gene lines used to differentiate races of P. graminis f. sp. tritici, plus Trident (Sr38+), Siouxland (Sr24+Sr31), and Sisson (Sr31+Sr36). Five SP-derived isolates with IT 33+ on the Sr24 single-gene line collected from Samsun (Alacam – Etyemez; Location: N 41.61889 E 35.55722) and Sinop (Merkez-Sanlıoglu; Location: N 41.85556 E 35.04889) were identified as race TKKTP and the remaining three SP isolates as race TKTTP. In 2020, we detected two isolates of TKKTP among the stem rust samples from Tunisia submitted to RCRRC. These two isolates were collected from bread wheat cultivars Heydna and Tahmet at a trial site near Bou Salem in Western Tunisia (Location: N 36.5351 E 8.95486). Based on the negative results of the Stage 1 test using a suite of four real-time polymerase chain reaction assays diagnostic for the Ug99 race group developed by Szabo (2012), these two races should not belong to the Ug99 race group when compared to the reference Ug99 race TTKTT from Kenya. These races were virulent to Sr5, Sr21, Sr9e, Sr7b, Sr6, Sr8a, Sr9g, Sr9b, Sr30, Sr17, Sr9a, Sr9d, Sr10, SrTmp, Sr24, Sr38, and SrMcN. In addition to these genes, race TKTTP was virulent to Sr36. Both races were avirulent to Sr11 and Sr31. To our knowledge, this is the first report of P. graminis f. sp. tritici races with the Sr24 virulence in Turkey and Tunisia. The results reflect an increasing trend of virulence to Sr24 in the pathogen populations, and raise a great concern given the deployment of the Sr24 resistance gene in widely grown wheat cultivars worldwide.

Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population

Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RIL) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping (CIM) using 762 Genotyping-by-Sequencing (GBS) markers, identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37 and Yr17. Three QTL were mapped on chromosomes 2B, two QTL on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27-39% less stem rust coefficient of infection in all field environments compared to RILs with none of these genes and this gene combination was most effective in the US environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.

A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon

Plants resist infection by pathogens using both preexisting barriers and inducible defense responses. Inducible responses are governed in a complex manner by various hormone signaling pathways. The relative contribution of hormone signaling pathways to nonhost resistance to pathogens is not well understood. In this study, we examined the molecular basis of disrupted nonhost resistance to the fungal species Puccinia graminis, which causes stem rust of wheat, in an induced mutant of the model grass Brachypodium distachyon. Through bioinformatic analysis, a 1 base pair deletion in the mutant genotype was identified that introduces a premature stop codon in the gene Bradi1g24100, which is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC). In Arabidopsis, TIC is central to the regulation of the circadian clock and plays a crucial role in jasmonate signaling by attenuating levels of the transcription factor protein MYC2, and its mutational disruption results in enhanced susceptibility to the hemi-biotroph Pseudomonas syringae. Our similar finding for an obligate biotroph suggests that the biochemical role of TIC in mediating disease resistance to biotrophs is conserved in grasses, and that the correct modulation of jasmonate signaling during infection by Puccinia graminis may be essential for nonhost resistance to wheat stem rust in B. distachyon.