A prebreeding study of introgression spring bread wheat lines carrying combinations of stem rust resistance genes, Sr22+Sr25 and Sr35+Sr25

The Sr22, Sr35, and Sr25 genes attract the attention of bread wheat breeders with their effectiveness against Puccinia graminis f. sp. tritici race Ug99 and its biotypes. The effectiveness and impact of Sr22+Sr25 and Sr35+Sr25 gene combinations on agronomic traits have not yet been studied. In the present article, these traits were studied using the spring bread wheat lines L503/W3534//L503, L503/Sr35//L503/3/L503 carrying the Sr22+Sr25 and Sr35+Sr25 genes during 2016–2020. These lines were assessed for resistance to P. graminis f. sp. tritici under natural epiphytotics and to the Saratov, Lysogorsk and Omsk populations of the pathogen and to the PgtZ1 (TKSTF) and PgtF18.6 fungus isolates in laboratory conditions (TKSTF + Sr33). The presence of the studied Sr-genes was confirmed by using molecular markers. Prebreeding studies were conducted during 2018–2020 vegetation periods. Under the natural epiphytotics of the pathogen and in the laboratory conditions, the Sr22+Sr25 combination was highly effective, while Sr35+Sr25 was ineffective. For grain yield, the lines with the Sr22+Sr25 and Sr35+Sr25 genes were superior to the recipient cultivar L503 in one year (Sr22+Sr25 in 2019; Sr35+Sr25 in 2018), with a decrease in 2020, but in general there were no differences. For the period 2018–2020, both combinations showed a decrease in 1000 grains weight and an increase in the germination-earing period. The line with Sr22+Sr25 genes showed insignificant effects on gluten and dough tenacity, but the ratio of dough tenacity to extensibility was higher, and flour strength, porosity and bread volume were lower; in the line with Sr35+Sr25 genes, the gluten content was lower, but the strength, tenacity of the dough and the ratio of dough tenacity to extensibility were higher, flour strength and the porosity of the bread were at the recipient level, but the volume of bread was lower.

Aeciospore ejection in the rust pathogen Puccinia graminis is driven by moisture ingress

Fungi have evolved an array of spore discharge and dispersal processes. Here, we developed a theoretical model that explains the ejection mechanics of aeciospore liberation in the stem rust pathogen Puccinia graminis. Aeciospores are released from cluster cups formed on its Berberis host, spreading early-season inoculum into neighboring small-grain crops. Our model illustrates that during dew or rainfall, changes in aeciospore turgidity exerts substantial force on neighboring aeciospores in cluster cups whilst gaps between spores become perfused with water. This perfusion coats aeciospores with a lubrication film that facilitates expulsion, with single aeciospores reaching speeds of 0.053 to 0.754 m·s−1. We also used aeciospore source strength estimates to simulate the aeciospore dispersal gradient and incorporated this into a publicly available web interface. This aids farmers and legislators to assess current local risk of dispersal and facilitates development of sophisticated epidemiological models to potentially curtail stem rust epidemics originating on Berberis.

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.

Virulence Characterization of Puccinia graminis f. sp. avenae and Resistance of Oat Cultivars in China

Oat stem rust, caused by Puccinia graminis f. sp. avenae (Pga), is one of the most devastating diseases of oat. The most cost-effective and eco-friendly strategy to control this disease is the use of resistant cultivars. However, P. graminis f. sp. avenae can overcome the resistance of cultivars by rapidly changing its virulence. Thus, information on the virulence of P. graminis f. sp. avenae populations and resistance of cultivars is critical to control the disease. The current study was conducted to monitor the virulence composition and dynamics in the P. graminis f. sp. avenae population in China and to evaluate resistance of oat cultivars. Oat leaves naturally infected by P. graminis f. sp. avenae were collected during 2018 and 2019 and 159 isolates were derived from single uredinia. The isolates were tested on 12 international differential lines, and eight races, TJJ, TBD, TJB, TJD, TJL, TJN, TGD, and TKN, were identified for the first time in China. The predominant race was TJD, virulent against Pg1, Pg2, Pg3, Pg4, Pg8, Pg9, and Pg15, accounting for 35.8% and 37.8% in 2018 and 2019, respectively. The sub-predominant races were TJN (30.2% in 2018, 28.3% in 2019) and TKN (20.8% in 2018, 12.3% in 2019). All isolates were virulent to Pg1, Pg2, Pg3, and Pg4, and avirulent to Pg6 and Pg16. The three predominant races (TJD, TJN, and TKN) were used to evaluate resistance in 30 Chinese oat cultivars at the seedling and adult-plant stages. Five cultivars, Bayan 1, Baiyan 2, Baiyan 3, Baiyan 5, and Baiyan 9, were highly resistant to the three races at both seedling and adult-plant stages. The results of the virulences and frequencies of P. graminis f. sp. avenae races and the resistant cultivars will be useful in understanding the pathogen migration and evolution and for breeding oat cultivars with stem rust resistance.

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.

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation

Background Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. Results We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5′ uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5′ adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. Conclusions We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation.

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.

Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection

Diseases caused by Puccinia graminis are some of the most devastating diseases of wheat. Extensive genomic understanding of the pathogen has proven helpful not only in understanding host- pathogen interaction but also in finding appropriate control measures. In the present study, whole-genome sequencing of four diverse P. graminis pathotypes was performed to understand the genetic variation and evolution. An average of 63.5 Gb of data per pathotype with about 100× average genomic coverage was achieved with 100-base paired-end sequencing performed with Illumina Hiseq 1000. Genome structural annotations collectively predicted 9273 functional proteins including ~583 extracellular secreted proteins. Approximately 7.4% of the genes showed similarity with the PHI database which is suggestive of their significance in pathogenesis. Genome-wide analysis demonstrated pathotype 117-6 as likely distinct and descended through a different lineage. The 3–6% more SNPs in the regulatory regions and 154 genes under positive selection with their orthologs and under negative selection in the other three pathotypes further supported pathotype 117-6 to be highly diverse in nature. The genomic information generated in the present study could serve as an important source for comparative genomic studies across the genus Puccinia and lead to better rust management in wheat.