Diversity of Puccinia striiformis on cereals and grasses

Dynamics of Puccinia striiformis f. sp. tritici Urediniospores and Its Relationship with Meteorological Factors in Mianyang, China

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the main diseases of wheat worldwide. Mianyang of Sichuan province in Southwest China is one of main regions for winter Pst inoculum production and spring epidemic and provides urediniospores for infecting wheat in the surrounding regions. Understanding the urediniospore dynamics is important to predict and manage stripe rust. In this study, spore trapping coupled with a TaqMan real-time quantitative PCR method was used to monitor airborne Pst urediniospores from December 2019 to December 2022 in Mianyang. Weather conditions (temperature, relative humidity, daily sunshine duration, and precipitation) were collected for the same period. These data were used to study the relationship of airborne urediniospore density with climatic conditions. The results showed that Pst urediniospores were captured all year round, and the annual peak of urediniospore densities occurred in the period from March to April in which the urediniospores accounted for the largest proportion of the annual total urediniospores. The density of urediniospores in the period of March to April was linearly related to the average sunshine duration of 20 days and average temperature of 15 days prior to the final day of a 7-day trapping period. This relationship needs to be tested in other regions where Pst can sporulate during the winter before it can be integrated with Pst infection conditions to predict rust development.

A fully haplotype-resolved and nearly gap-free genome assembly of wheat stripe rust fungus

Stripe rust fungus Puccinia striiformis f. sp. tritici (Pst) is a destructive pathogen of wheat worldwide. Pst has a macrocyclic-heteroecious lifecycle, in which one-celled urediniospores are dikaryotic, each nucleus containing one haploid genome. We successfully generated the first fully haplotype-resolved and nearly gap-free chromosome-scale genome assembly of Pst by combining PacBio HiFi sequencing and trio-binning strategy. The genome size of the two haploid assemblies was 75.59 Mb and 75.91 Mb with contig N50 of 4.17 Mb and 4.60 Mb, and both had 18 pseudochromosomes. The high consensus quality values of 55.57 and 59.02 for both haplotypes confirmed the correctness of the assembly. Of the total 18 chromosomes, 15 and 16 were gapless while there were only five and two gaps for the remaining chromosomes of the two haplotypes, respectively. In total, 15,046 and 15,050 protein-coding genes were predicted for the two haplotypes, and the complete BUSCO scores achieved 97.7% and 97.9%, respectively. The genome will lay the foundation for further research on genetic variations and the evolution of rust fungi.

Identification of a Locus for High-Temperature Adult-Plant Resistance to Stripe Rust in the Wheat Yr8 Near-Isogenic Line Through Mutagenesis and Molecular Mapping

Aegilops species are wheat relatives that harbor valuable disease resistance genes for wheat breeding. The wheat Yr8 near-isogenic line AvSYr8NIL has long been believed to carry only Yr8 for race-specific all-stage resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, derived from Aegilops comosa. However, AvSYr8NIL has been found to have high-temperature adult-plant (HTAP) resistance in our field and greenhouse tests. To confirm both HTAP and Yr8 resistance, seeds from AvSYr8NIL were treated with ethyl methanesulfonate to generate mutant lines. The mutant lines with only Yr8 (M641) and only HTAP resistance (M488) were crossed with the susceptible recurrent parent Avocet S (AvS). The F1 and F4 lines of AvS/M641 were phenotyped with Yr8-avirulent races in the seedling stage at the low-temperature (4 to 20°C) profile, while the F1, F2, F4, and F5 lines of AvS/M488 were phenotyped with Yr8-virulent races in the adult-plant stage at the high-temperature (10 to 30°C) profile. Both Yr8 and the HTAP resistance gene (YrM488) were recessive. The F4 populations of AvS/M641 and AvS/M488 were genotyped using polymorphic Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphisms. Yr8 was mapped to a 0.66-cM fragment, and YrM488 was mapped to a 1.22-cM interval on chromosome 2D. The physical distance between the two resistance genes was estimated to be more than 500 Mb, indicating their distinct loci. The mutant lines with separated resistance genes would be useful in enhancing our understanding of different types of resistance and in further studying the interactions between wheat and the stripe rust pathogen.

Comparative Analysis of Virulence and Molecular Diversity of Puccinia striiformis f. sp. tritici Isolates Collected in 2016 and 2023 in the Western Region of China

Puccinia striiformis f. sp. tritici (Pst) is adept at overcoming resistance in wheat cultivars, through variations in virulence in the western provinces of China. To apply disease management strategies, it is essential to understand the temporal and spatial dynamics of Pst populations. This study aimed to evaluate the virulence and molecular diversity of 84 old Pst isolates, in comparison to 59 newer ones. By using 19 Chinese wheat differentials, we identified 98 pathotypes, showing virulence complexity ranging from 0 to 16. Associations between 23 Yr gene pairs showed linkage disequilibrium and have the potential for gene pyramiding. The new Pst isolates had a higher number of polymorphic alleles (1.97), while the older isolates had a slightly higher number of effective alleles, Shannon's information, and diversity. The Gansu Pst population had the highest diversity (uh = 0.35), while the Guizhou population was the least diverse. Analysis of molecular variance revealed that 94% of the observed variation occurred within Pst populations across the four provinces, while 6% was attributed to differences among populations. Overall, Pst populations displayed a higher pathotypic diversity of H > 2.5 and a genotypic diversity of 96%. This underscores the need to develop gene-pyramided cultivars to enhance the durability of resistance.

Virulence Characterization of Puccinia striiformis f. sp. tritici in China Using the Chinese and Yr Single-Gene Differentials

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat. Identifying Pst races is essential for developing resistant cultivars and managing the disease. In this study, 608 isolates collected from China in 2021 were tested with the Chinese set of 19 wheat variety differentials and the set of 18 Yr single-gene differentials. Of the 119 races detected with the Chinese set of differentials, 94 were new. A higher number (149) of races were identified using the Yr single-gene differentials. The frequencies of virulence factors to 17 of the 19 Chinese differential varieties and to 10 of the 18 Yr single-gene differentials were high (>60%). None of the isolates were virulent to the differentials Zhong 4 (Yr genes unknown) and Triticum spelta Album (Yr5) in the Chinese set and the Yr5 and Yr15 lines in the single-gene set of differentials, indicating that these genes or varieties are effective against the Pst population detected in 2021. Using Nei's genetic distance, the 16 provincial Pst populations were clustered into six groups based on the Chinese set and eight groups based on the Yr single-gene set of differentials. In addition, we found that the same races identified using the Chinese differentials could be further differentiated into different races using the Yr single-gene differentials, suggesting a higher differential capability than the Chinese set of differentials. The results provide a scientific basis for monitoring Pst populations and guiding resistance breeding in China.

Beneficial Microorganisms as Bioprotectants against Foliar Diseases of Cereals: A Review

Cereal production plays a major role in both animal and human diets throughout the world. However, cereal crops are vulnerable to attacks by fungal pathogens on the foliage, disrupting their biological cycle and photosynthesis, which can reduce yields by 15-20% or even 60%. Consumers are concerned about the excessive use of synthetic pesticides given their harmful effects on human health and the environment. As a result, the search for alternative solutions to protect crops has attracted the interest of scientists around the world. Among these solutions, biological control using beneficial microorganisms has taken on considerable importance, and several biological control agents (BCAs) have been studied, including species belonging to the genera Bacillus, Pseudomonas, Streptomyces, Trichoderma, Cladosporium, and Epicoccum, most of which include plants of growth-promoting rhizobacteria (PGPRs). Bacillus has proved to be a broad-spectrum agent against these leaf cereal diseases. Interaction between plant and beneficial agents occurs as direct mycoparasitism or hyperparasitism by a mixed pathway via the secretion of lytic enzymes, growth enzymes, and antibiotics, or by an indirect interaction involving competition for nutrients or space and the induction of host resistance (systemic acquired resistance (SAR) or induced systemic resistance (ISR) pathway). We mainly demonstrate the role of BCAs in the defense against fungal diseases of cereal leaves. To enhance a solution-based crop protection approach, it is also important to understand the mechanism of action of BCAs/molecules/plants. Research in the field of preventing cereal diseases is still ongoing.

The challenge of managing yellow rust (Puccinia striiformis f.sp. tritici) in winter wheat: how combined climate and pathogen stressors impact variability in genotype reactions

Despite the ongoing evolution of wheat pathogens due to the selection pressures of agro-ecological conditions, many studies have often overlooked the combined impact of both biotic and abiotic factors on disease occurrence. From 2016 to 2023, a comprehensive screening of obligate pathogens, including B. graminis f. sp. tritici, P. graminis f. sp. tritici, P. triticina, and P. striiformis f. sp. tritici, was carried out. This screening was conducted on a phenotyping platform encompassing 2715 winter wheat genotypes and their wild relatives, both with and without resistant genes (Lr, Yr, and Sr) for rust diseases. The data were analyzed using PCAmix, best subsets regression, and linear regression modeling. The findings from this study reveal that the plant reactions to leaf and yellow rust infections is far from straightforward. It is heavily influenced not only by prevalent rust races and climatic factors that impact pathogen life cycles but also by variations in the susceptibility reactions of wheat genotypes to the broader agro-ecological conditions. We also observed a tendency for leaf rust and yellow rust to coexist within the same host plant, even though yellow rust is typically considered more aggressive. We reported for the first time genes related to yellow rust resistance breakdown in Serbia in 2023. Lastly, we underscored the importance of investigating resistance responses to rust diseases not exclusively through the interrelation between resistance genes and pathogen virulence, but also by considering how plants respond to the combined stresses of abiotic and biotic factors. Consequently, our study sets the groundwork for further research into how plants respond to multiple stressors and contributes for further investigations related with effective integrated rust management.

Mycorrhizal colonization and Streptomyces viridosporus HH1 synergistically up-regulate the polyphenol biosynthesis genes in wheat against stripe rust

BACKGROUND

Stripe rust is considered one of the most devastating diseases of wheat all over the world, resulting in a high loss in its production. In this study, time-course changes in expression of the polyphenol biosynthesis pathways genes in wheat against stripe rust were investigated. The defense mechanisms triggered by mycorrhizal colonization and/or spraying with Streptomyces viridosporus HH1 against this disease were also investigated.

RESULTS

Results obtained revealed that C3H, which is considered the key gene in lignin biosynthesis, was the most expressed gene. Furthermore, most of the chlorogenic acid and flavonoid biosynthesis genes were also overexpressed. Volcano plots of the studied genes reveal that the dual treatment led to a high significant overexpression of 10 out of the 13 studied genes. Heatmap of these genes showed that the most frequent expressed gene in response to all applied treatments along the study period was DFR, the key gene in the biosynthesis of anthocyanidins. Gene co-expression network of the studied genes showed that HQT was the most central gene with respect to the other genes, followed by AN2 and DFR, respectively. Accumulation of different flavonoids and phenolic acids were detected in response to the dual treatment, in particular, cinnamic acid, coumarin, and esculetin, which recorded the highest elevation level recording 1000, 488.23, and 329.5% respectively. Furthermore, results from the greenhouse experiment showed that application of the dual treatment led to an 82.8% reduction in the disease severity, compared with the control treatment.

CONCLUSIONS

We can conclude that the biosynthesis of lignin, chlorogenic acid, and flavonoids contributed to the synergistic triggering effect of the dual treatment on wheat resistance to stripe rust.

Highly Aggressive Invasive Race Group PstS2 in Russian Populations of the Wheat Yellow Rust Pathogen

The expansion of the area of harmfulness of the wheat yellow rust pathogen (Puccinia striiformis) (Pst) has be observed all over the world in the 2000s. This is due to the emergence of new highly aggressive invasive groups of races PstS1 and PstS2, adopted to the high temperatures, and also as a result of virulence mutations of regional pathogen populations. SCAR-markers were developed for identification of invasive races, and pathogen collections from many countries were studied. In these studies in first in Russia, the analysis of regional populations of P. striiformis for the presence of invasive races PstS1 and PstS2 was carried out. Single pustule isolates were obtained from urediosamples collected from common and durum wheat, triticale and wild grasses in seven regions of the Russian Federation (North Caucasian, Northwestern, Central Black Earth, Lower Volga, Middle Volga, Volga-Vyatka, West Siberian) in 2019-2020. In total 82 isolates were studied. Using SCAR markers, three genotypes were identified in the studied collection of P. striiformis, and one of which belongs to the invasive group PstS2. The other two genotypes had a different origin (other). Isolates of PstS2 group were received from pathogen population samples collected in the Russian Northwest in 2020. Virulence analysis revealed two phenotypes among them: PstS2_R1 (3 isolates) and PstS2_R2 (1 isolate). According to information from the Global Rust Reference Center ( http://www.wheatrust.org/ ), the main characteristic of isolates from invasive PstS2 group is virulence to wheat lines with resistance genes Yr2, Yr6, Yr7, Yr8, Yr9, and Yr25. The Russian R1 phenotype PstS2 was also characterized by virulence to these genes, as well as to Yr1, Yr32, and YrSp. The PstS2_R2 phenotype differed from PstS2_R1 for avirulence to Yr25 and virulence to Yr3 and Yr4. The main difference of Russian PstS2 isolates with detected in other countries is virulence to wheat lines with genes Yr4, Yr32, and YrSp. The first detection of invasive races in the Northwest of Russia indicates the relevance of annual monitoring of regional populations of P. striiformis.

Characterizing the Response of Puccinia striiformis f. sp. tritici to Periods of Heat Stress that Are Common in Kansas and the Great Plains Region of North America

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is considered a disease of cool environments, and it has been observed that high temperatures can suppress disease development. However, recent field observations in Kansas suggest that the pathogen may be recovering from heat stress more quickly than expected. Previous research indicates that some strains of this pathogen were adapted to warm temperature regimes but did not consider how the pathogen responds to periods of heat stress that are common in the Great Plains region of North America. Therefore, the objectives of this study were to characterize the response of contemporary isolates of P. striiformis f. sp. tritici to periods of heat stress and to look for evidence of temperature adaptations within the pathogen population. These experiments evaluated nine isolates of the pathogen: eight isolates collected in Kansas between 2010 and 2021 and a historical reference isolate. Treatments compared the latent period and colonization rate of isolates given a cool temperature regime (12 to 20°C) and as they recovered from 7 days of heat stress (22 to 35°C). Results documented that contemporary isolates of the pathogen had similar latent periods and colonization rates as the historical reference under the cool temperature regime. Following exposure to 7 days of heat stress, the contemporary isolates had shorter latent periods and higher colonization rates than the historical isolate. There was also variability in how the contemporary isolates recovered from heat stress, with some isolates collected during 2019 to 2021 recovering sooner than those collected just 5 to 10 years ago.

Virulence and genetic analysis of Puccinia graminis tritici in the Indian sub-continent from 2016 to 2022 and evaluation of wheat varieties for stem rust resistance

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), has re-emerged as one of the major concerns for global wheat production since the evolution of Ug99 and other virulent pathotypes of Pgt from East Africa, Europe, Central Asia, and other regions. Host resistance is the most effective, economic, and eco-friendly approach for managing stem rust. Understanding the virulence nature, genetic diversity, origin, distribution, and evolutionary pattern of Pgt pathotypes over time and space is a prerequisite for effectively managing newly emerging Pgt isolates through host resistance. In the present study, we monitored the occurrence of stem rust of wheat in India and neighboring countries from 2016 to 2022, collected 620 single-pustule isolates of Pgt from six states of India and Nepal, analyzed them on Indian stem rust differentials, and determined their virulence phenotypes and molecular genotypes. The Ug99 type of pathotypes did not occur in India. Pathotypes 11 and 40A were most predominant during these years. Virulence phenotyping of these isolates identified 14 Pgt pathotypes, which were genotyped using 37 Puccinia spp.-specific polymorphic microsatellites, followed by additional phylogenetic analyses using DARwin. These analyses identified three major molecular groups, demonstrating fewer lineages, clonality, and long-distance migration of Pgt isolates in India. Fourteen of the 40 recently released Indian wheat varieties exhibited complete resistance to all 23 Pgt pathotypes at the seedling stage. Twelve Sr genes were postulated in 39 varieties based on their seedling response to Pgt pathotypes. The values of slow rusting parameters i.e. coefficient of infection, area under disease progress curve, and infection rates, assessed at adult plant stage at five geographically different locations during two crop seasons, indicated the slow rusting behavior of several varieties. Six Sr genes (Sr2, Sr57, Sr58, Sr24, Sr31, and Sr38) were identified in 24 wheat varieties using molecular markers closely linked to these genes. These findings will guide future breeding programs toward more effective management of wheat stem rust.

Insights into Diversity, Distribution, and Systematics of Rust Genus Puccinia

Puccinia, which comprises 4000 species, is the largest genus of rust fungi and one of the destructive plant pathogenic rust genera that are reported to infect both agricultural and nonagricultural plants with severe illnesses. The presence of bi-celled teliospores is one of the major features of these rust fungi that differentiated them from Uromyces, which is another largest genus of rust fungi. In the present study, an overview of the current knowledge on the general taxonomy and ecology of the rust genus Puccinia is presented. The status of the molecular identification of this genus along with updated species numbers and their current statuses in the 21st century are also presented, in addition to their threats to both agricultural and nonagricultural plants. Furthermore, a phylogenetic analysis based on ITS and LSU DNA sequence data available in GenBank and the published literature was performed to examine the intergeneric relationships of Puccinia. The obtained results revealed the worldwide distribution of Puccinia. Compared with other nations, a reasonable increase in research publications over the current century was demonstrated in Asian countries. The plant families Asteraceae and Poaceae were observed as the most infected in the 21st century. The phylogenetic studies of the LSU and ITS sequence data revealed the polyphyletic nature of Puccinia. In addition, the presences of too short, too lengthy, and incomplete sequences in the NCBI database demonstrate the need for extensive DNA-based analyses for a better understanding of the taxonomic placement of Puccinia.

The Biological Roles of Puccinia striiformis f. sp. tritici Effectors during Infection of Wheat

Puccinia striiformis f. sp. tritici (Pst) is the causative agent of wheat stripe rust, which can lead to a significant loss in annual wheat yields. Therefore, there is an urgent need for a deeper comprehension of the basic mechanisms underlying Pst infection. Effectors are known as the agents that plant pathogens deliver into host tissues to promote infection, typically by interfering with plant physiology and biochemistry. Insights into effector activity can significantly aid the development of future strategies to generate disease-resistant crops. However, the functional analysis of Pst effectors is still in its infancy, which hinders our understanding of the molecular mechanisms of the interaction between Pst and wheat. In this review, we summarize the potential roles of validated and proposed Pst effectors during wheat infection, including proteinaceous effectors, non-coding RNAs (sRNA effectors), and secondary metabolites (SMs effectors). Further, we suggest specific countermeasures against Pst pathogenesis and future research directions, which may promote our understanding of Pst effector functions during wheat immunity attempts.

Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China

Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting disease development and establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens wheat production through its long-distance migration. Because of wide variation in geographic features, climatic conditions, and wheat production systems, Pst sources and related dispersal routes in China are largely unclear. In the present study, we performed genomic analyses of 154 Pst isolates from all major wheat-growing regions in China to determine Pst population structure and diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, and field surveys, we investigated Pst sources and their contributions to wheat stripe rust epidemics. We identified Longnan, the Himalayan region, and the Guizhou Plateau, which contain the highest population genetic diversities, as the Pst sources in China. Pst from Longnan disseminates mainly to eastern Liupan Mountain, the Sichuan Basin, and eastern Qinghai; that from the Himalayan region spreads mainly to the Sichuan Basin and eastern Qinghai; and that from the Guizhou Plateau migrates mainly to the Sichuan Basin and the Central Plain. These findings improve our current understanding of wheat stripe rust epidemics in China and emphasize the need for managing stripe rust on a national scale.

Important wheat diseases in the US and their management in the 21st century

Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.

Pathogen Identification and Factors Influencing Infection Frequency and Severity of Fungal Rust in Four Native Grasses in Hulunber Grassland, China

A serious rust infection present in 2014 and 2015 on the dominant grass species (Leymus chinensis) in the Hulunber grassland of Inner Mongolia, China, and also present on three other grass species (Agropyron cristatum [wheat grass], Bromus inermis, and Festuca ovina) was investigated. Field surveys, laboratory determination of morphological characteristics, pathogenicity tests, and molecular identification methods were integrated to identify two rust-causing pathogens on L. chinensis. It was found that Puccinia elymi was the major pathogen of L. chinensis, and also infected A. cristatum and F. ovina. This is the first report of P. elymi on A. cristatum in China. P. striiformis caused stripe rust on L. chinensis and B. inermis. The incidence and severity of rust infection increased through the growing season, presumably from asexual spread by urediniospores, and was higher on grass species phylogenetically more closely related to common crop hosts of the pathogens. High host grass density and presence of a potential alternate host for P. elymi, Thalictrum squarrosum, were two further factors promoting rust incidence. These results provide insight into ecological factors linked to the rust epidemic and provide a theoretical basis for the formulation of control strategies.

Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India

Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.

Virulence Survey of Puccinia striiformis in Israel Revealed Considerable Changes in the Pathogen Population During the Period 2001 to 2019

A total of 353 urediniospore isolates of Puccinia striiformis f. sp. tritici (Pst) collected in Israel during 2001 to 2019 were analyzed. Pst pathogenicity was studied with a set of 20 differentials (17 Avocet and 3 other lines). Three periods were compared: 2001 to 2007, 2009 to 2016, and 2017 to 2019. No virulence to Yr5 or Yr15 was detected. Virulence frequencies on Yr4, Yr10, Yr24, and YrSp genes rose to the moderate level (0.28 to 0.44) in 2017 to 2019. Virulence frequencies to Yr2 and Yr9 decreased. One Pst phenotype was identified in all three periods, but its frequency drastically decreased from 0.74 in 2001 to 2016 to 0.21 in 2017 to 2019. The most probable scenario of emergence of wheat yellow rust in Israel is wind dissemination of Pst urediniospores from the Horn of Africa. Variability of the Pst population increased amid considerable evolution with two major transformations in 2009 and 2017. The first modification can be attributed to changes in wheat genetic background in Israel due to deployment of new cultivars resistant to yellow rust since 2004. The second shift in 2017 can be primarily explained by intensive deployment of wheat cultivars resistant to the stem rust race Ug99 in the 2010s in the Horn of Africa. This led to changing genetic backgrounds of the cultivated wheats in the donor region and development and long-distance spread of new Pst phenotypes to Israel. Two singular multivirulent Pst phenotypes were identified in 2019, one of them being closely related to the aggressive Warrior race. Such phenotypes may potentially defeat existing resistances.

Long-Distance Transport of Puccinia striiformis f. sp. tritici by Upper Airflow on the Yunnan-Guizhou Plateau Disrupts the Balance of Agricultural Ecology in Central China

Long-distance dispersal of plant pathogens in the air can establish diseases in other areas and lead to an increased risk of large-scale epidemics. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat in China. Hubei is an important overwintering region for Pst in China, and this overwintering region is a determinant of stripe rust severity in eastern China. In 2017, stripe rust disease caused a pandemic in the Hubei region and resulted in great yield losses of wheat. To explain the disease pandemic, a total of 595 single-lesion samples of stripe rust were collected in spring, including 204 in five provinces in 2017 and 391 in four provinces in 2018, and genotyped with 13 simple sequence repeat makers. The samples were classified into 12 subpopulations based on the locations and year of collection. Genetic diversity was determined for the collection and each subpopulation. Differentiation and gene flow were determined between subpopulations. STRUCTURE analyses and discriminant analysis of principal components were conducted, and the results were used to infer the relationships between subpopulations. Our study revealed a new route of Pst transmission from the Yunnan-Guizhou Plateau to the Hubei region. The Pst inoculum of northwestern Hubei came from Gansu in the northwest, whereas the inoculum in southern Hubei came from the Yunnan-Guizhou Plateau via upper airflow. After the initial inocula infected wheat plants and multiplied in northern and southern Hubei, urediniospores produced in these regions further spread together along the middle reach of Hanshui Valley and made exchanges there. The finding of the new transmission route of Pst is important for improving integrated stripe rust disease management, which should have a profound impact on the balance of agricultural ecology in China.

Changes of Barley Stripe Rust Populations in the United States from 1993 to 2017

Barley stripe rust is a relatively new disease in the United States. The pathogen, Puccinia striiformis f. sp. hordei (Psh), was first observed in Texas in 1991 and has spread north and westwards and mainly caused epidemics in the western United States. A total of 447 isolates collected from 1993 to 2017 were identified as 382 multilocus genotypes (MLGs) using 14 simple sequence repeat markers. The MLGs were clustered into six molecular groups (MGs) using the discriminant analysis of principal components and the hierarchical cluster analysis, and the MGs had significant differences in frequency in different years. MG1 was present in the population prior to the year 2000. MG2, MG3, and MG4 became predominate after 2000. MG5 was detected in all 24 years but more frequent from 2010 to 2017. MG6 was the most recent group detected mainly from 2011 to 2017 and had the highest correlation coefficient with the virulence phenotypes among the MGs. The heterozygosity and genotypic diversity of the Psh populations increased from 2000 to 2017, even more from 2010 to 2017. The results indicate rapid genetic changes from year to year, with major molecular group changes around 2000 and 2010. The possible mechanisms underlying the population changes are discussed.

Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm

We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity but lack causal association. Here, we show that Rps8-mediated resistance in barley to the pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: Pur1 and Exo70FX12, which are together necessary and sufficient. Pur1 encodes a leucine-rich repeat receptor kinase and is the ortholog of rice Xa21, and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.

Elucidating the Population Structure and Genetic Diversity of Indian Puccinia striiformis f. sp. tritici Pathotypes Based on Microsatellite Markers

In India, systematic wheat yellow rust survey and pathotype (race) analysis work began in 1930. However, information on population structure and genetic diversity of yellow rust pathogen has not been available. To address this, we conducted studies on population structure and genetic diversity of Puccinia striiformis f. sp. tritici (Pst) pathotypes using 38 simple sequence repeat primer-pairs. Bayesian assignment and discriminant analysis of principal components indicated the presence of two distinct Pst subpopulations (Pop1 and Pop2) along with 37.9% admixed pathotypes. The unweighted pair-group method with arithmetic mean also categorized these pathotypes into two major clusters. Principal coordinates analysis explained 20.06 and 12.50% variance in horizontal and vertical coordinates, respectively. Index of association (I_A) and the standardized index of association ([Formula: see text]) values showed that Pst subpopulations reproduced asexually (clonally). In total, 102 alleles were detected, with the expected heterozygosity (H_exp) per locus ranging from 0.13 to 0.73, with a mean of 0.47. The average polymorphic information content value of 0.40 indicated high genetic diversity among pathotypes. Analysis of molecular variance revealed 12% of the total variance between subpopulations, 11% among the pathotypes of each subpopulation, and 77% within pathotypes. A significant moderate level of genetic differentiation (F_ST = 0.122, P < 0.001) and gene flow (N_m = 1.80) were observed between subpopulations. The Pst virulence phenotypes showed a weak positive correlation (R² = 0.027, P < 0.02) with molecular genotypes.

QTL Mapping of Adult Plant Resistance to Stripe Rust in a Doubled Haploid Wheat Population

Stripe rust caused by Puccinia striiformis Westend. f. sp. tritici. is a major bread wheat disease worldwide with yield losses of up to 100% under severe disease pressure. The deployment of resistant cultivars with adult plant resistance to the disease provides a long-term solution to stripe rust of wheat. An advanced line from the International Winter Wheat Improvement Program (IWWIP) 130675 (Avd/Vee#1//1-27-6275/Cf 1770/3/MV171-C-17466) showed a high level of adult plant resistance to stripe rust in the field. To identify the adult plant resistance genes in this elite line, a mapping population of 190 doubled haploid (DH) lines was developed from a cross between line 130675 and the universal stripe rust-susceptible variety Avocet S. The DH population was evaluated at precision wheat stripe rust phenotyping platform, in Izmir during 2019, 2020, and 2021 cropping seasons under artificial inoculations. Composite interval mapping (CIM) identified two stable QTLs QYr.rcrrc-3B.1, and QYr.rcrrc-3B.2, which were detected in multiple years. In addition to these two QTLs, five more QTLs, QYr.rcrrc-1B, QYr.rcrrc-2A, QYr.rcrrc-3A, QYr.rcrrc-5A, and QYr.rcrrc-7D, were identified, which were specific to the cropping year (environment). All QTLs were derived from the resistant parent, except QYr.rcrrc-3A. The significant QTLs explained 3.4-20.6% of the phenotypic variance. SNP markers flanking the QTL regions can be amenable to marker-assisted selection. The best DH lines with high yield, end-use quality, and stripe rust resistance can be used for further selection for improved germplasm. SNP markers flanking the QTL regions can aid in identifying such lines.

First report of yellow rust (Puccinia striiformis f. sp. tritici) in wheat (Triticum aestivum) in Paraguay

Wheat yellow (stripe) rust caused by Puccinia striiformis Westend. f. sp. tritici Eriks. (Pst) is an important disease worldwide (Chen 2005; Afzal et al., 2007; Hovmøller et al. 2011). In Latin America, the disease has been reported in Argentina, Bolivia, Chile, Colombia, Ecuador, Peru, Brazil, and Uruguay (van Beuningen and Kohli, 1986; German et al., 2007). The disease was observed for the first time in Paraguay at Capitán Miranda (Itapúa) (27°12'07.5888''S, 55°47'20.3640''W) in an environment with average minimum temperature below 10°C in July 2021 (coldest month). Symptoms were yellow rust pustules distributed linearly on the leaves of adult host plants (Fig. 1). Oval-shaped uredinia contained unicellular, yellow to orange, spherical urediniospores (28, 82 × 26, 83 μm), within the range reported by Rioux et al. (2015). Black telia produced yellow to orange teliospores (64, 12 × 15, 46 μm), which were within the range reported by Chen et al. (2014). All susceptible wheat cultivars had up to 100% disease severity. Ten- day-old seedlings of the susceptible cultivars were inoculated in a greenhouse using urediniospores collected from the field. Two weeks after inoculation, extensive sporulation was observed on the seedlings. For pathogen identification, DNA was extracted from wheat leaf segments containing urediniospores using the PureLink® Plant Total DNA Purification Kit (Invitrogen). PCR and sequencing were carried out by Macrogen (Korea), using the following species-specific primers: PSF (5`-GGATGTTGAGTGCTGCTGTAA-3`) / PSR (5`-TTGAGGTCTTAAGGTTAAAATTG-3`), which amplifies an internal transcribed spacer (ITS) region (Zhao et al. 2007); LidPs9 (TCGGTAAAACTGCACCAATACCT) / LidPs10 (TCCCAACAGTCCCCTTCTGT), which amplifies a fragment of the RNA polymerase II gene encoding the second largest subunit (rpb2); and LidPs11 (TTACGACATCTGCTTCCGCA) / LisPs12 (TGCGATGTCAACTCTGGGAC) and LidPs13 (TACGACATCTGCTTCCGCAC) / LidPs14 (GATTGCCCGGTATTGTTGGC), both pairs amplifying fragments of the β-tubulin 1 gene (tub1) (Kuzdraliński et al. 2017). The sequences obtained were OM631935, OM638432, OM718000, and OM718001 and were aligned using the GenBank BLAST tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi), obtaining a 100% match with the following sequences: KC677574.1, KY411522.1, KY411533.1, and KY411542.1, respectively. Yellow-rust-infected leaf samples were collected from a field trial and sent to the Global Rust Reference Center (GRRC), Denmark. Simple sequence repeat (SSR) genotyping of samples from two different cultivars exhibited the genetic lineage PstS13 (www.wheatrust.org), which had previously been detected in South America (Carmona et al., 2019), thereby confirming the first report of wheat yellow rust in Paraguay. Considering that the Paraguayan wheat germplasm is highly susceptible to yellow rust, further studies are required to monitor potential spread and establishment of yellow rust in Paraguay and to explore potential sources of resistance to prevent future epidemics.

Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust

Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.

Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from the Longnan, Longdong, and Central Shaanxi Regions of China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases of wheat worldwide. In China, Longnan (LN) and Longdong (LD) in the south and east of Gansu province, respectively, are important P. striiformis f. sp. tritici oversummering areas and are a source of P. striiformis f. sp. tritici inoculum for the major wheat-growing regions in eastern China. Central Shaanxi (CS) is a wheat-growing region that acts as an important bridge zone for stripe rust epidemic development between LN and LD in the west and the Huanghuai wheat-growing region in the east, and thus, it plays an essential role in P. striiformis f. sp. tritici epidemics in China. To study the relationships among P. striiformis f. sp. tritici populations in the three regions (LN, LD, and CS), we sampled 284 isolates from different geographic locations. Based on 10 simple sequence repeat markers, the results demonstrated high genetic diversity in all three regions, although diversity did vary among regions, with LN > LD > CS. Genetic differentiation was lower, with more extensive gene flow between LD and CS. P. striiformis f. sp. tritici populations in the CS region were genetically closer to those from LD than those from LN, which may be a result of geographical proximity and topography. A positive and significant correlation existed between linearized fixation index (F_ST) and the log of geographical distances among all subpopulations. Linkage disequilibrium analysis showed that subpopulations of P. striiformis f. sp. tritici from Qinzhou, Qincheng, Beidao, and Maiji from LN and Qianyang and Longxian from CS were in equilibrium (P > 0.05), suggesting that somatic hybridization and/or sexual reproduction may exist in these subpopulations.

Distribution of Puccinia striiformis f. sp. tritici Races and Virulence in Wheat Growing Regions of Kenya from 1970 to 2014

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a major threat to wheat (Triticum spp.) production worldwide. The objective of this study was to determine the virulence of P. striiformis f. sp. tritici races prevalent in the main wheat growing regions of Kenya, which includes Mt. Kenya, Eastern Kenya, and the Rift Valley (Central, Southern, and Northern Rift). Fifty P. striiformis f. sp. tritici isolates collected from 1970 to 1992 and from 2009 to 2014 were virulence phenotyped with stripe rust differential sets, and 45 isolates were genotyped with sequence characterized amplified region (SCAR) markers to differentiate the isolates and identify aggressive strains PstS1 and PstS2. Virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, and Yr27 and the seedling resistance in genotype Avocet S were detected. Ten races were detected in the P. striiformis f. sp. tritici samples obtained from 1970 to 1992, and three additional races were detected from 2009 to 2014, with a single race being detected in both periods. The SCAR markers detected both Pst1 and Pst2 strains in the collection. Increasing P. striiformis f. sp. tritici virulence was found in the Kenyan P. striiformis f. sp. tritici population, and different P. striiformis f. sp. tritici race groups were found to dominate different wheat growing regions. Moreover, recent P. striiformis f. sp. tritici races in East Africa indicated possible migration of some race groups into Kenya from other regions. This study is important in elucidating P. striiformis f. sp. tritici evolution and virulence diversity and useful in breeding wheat cultivars with effective resistance to stripe rust.

Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance

The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.

Phenotyping and Genotyping Analyses Reveal the Spread of Puccinia striiformis f. sp. tritici Aeciospores From Susceptible Barberry to Wheat in Qinghai of China

Puccinia striiformis f. sp. tritici Eriks., the cause of wheat yellow or stripe rust on wheat, undergoes sexual reproduction on barberry, but it is unclear if barberry plays any role in stripe rust epidemics under natural conditions. P. striiformis f. sp. tritici was isolated from its alternate host barberry (Berberis spp.) and primary host wheat in the vicinity of barberry by inoculation of aeciospores and urediniospores on Mingxian 169 cultivar in Qinghai province of China in 2018. The P. striiformis f. sp. tritici isolates from barberry and wheat were characterized to virulence patterns by inoculation on 24 differentials bearing Yr gene under control conditions and analyzed using 12 polymorphic simple sequence repeat (SSR) markers. The occurrence frequency of P. striiformis f. sp. tritici on barberry was 1.87% by inoculation aecia, collected from barberry on Mingxian 169 of wheat. A close virulence relationship was presented between P. striiformis f. sp. tritici isolates from both barberry and wheat based on virulence simple matching coefficient and principal coordinates analysis (PCoA). Additionally, the same genetic ancestry, based on structure analysis by STRUCTURE program and genetic relationship analyses using discriminant analysis of principal components and PCoA, was shared between P. striiformis f. sp. tritici isolates from barberry and those from wheat. Together, all the results indicated that the role of barberry in providing aeciospores as an inoculum source causing wheat stripe rust epidemic in Qinghai in spring is of considerable importance.

The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics

Crop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes, Rps6, Rps7, and Rps8, contribute to immunity in barley to wheat stripe rust. Rps7 cosegregates with barley powdery mildew resistance at the Mla locus. Using transgenic complementation of different Mla alleles, we confirm allele-specific recognition of wheat stripe rust by Mla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.

Analysis of Host-Specific Differentiation of Puccinia striiformis in the South and North-West of the European Part of Russia

Yellow (stripe) rust, caused by Puccinia striiformis Westend. (Pst), is a major disease of cereals worldwide. We studied Pst virulence phenotypes on Triticum aestivum, Triticum durum, and triticale in three geographically distant regions of the European part of Russia (Dagestan and Krasnodar in North Caucasus, and Northwest) with different climate and environmental conditions. Based on the set of twenty differential lines, a relatively high level of population diversity was determined with 67 different Pst pathotypes identified among 141 isolates. Only seven pathotypes were shared by at least two hosts or occurred in the different regions. No significant differentiation was found between regional Pst collections of pathotypes either from T. aestivum or from T. durum. A set of Pst pathotypes from triticale was subdivided into two groups. One of them was indistinguishable from most durum and common wheat pathotypes, whereas the second group differed greatly from all other pathotypes. All sampled Pst isolates were avirulent on lines with Yr5, Yr10, Yr15, and Yr24 genes. Significant variation in virulence frequency among all Pst collections was observed on lines containing Yr1, Yr3, Yr17, Yr27, and YrSp genes and cvs Strubes Dickkopf, Carstens V, and Nord Desprez. Relationships between Russian regional collections of Pst from wheat did not conform to those for P. triticina.

Wild grasses as the reservoirs of infection of rust species for winter soft wheat in the Northern Caucasus

Common winter wheat is the main grain crop cultivated in the North Caucasus. Rust disease damage is one of the factors limiting wheat productivity. There are three species of rust in the region: leaf (Puccinia triticina), stem (P. graminis) and stripe rust (P. striiformis), and their signif icance varies from year to year. The most common is leaf rust, but in the last decade the frequency of its epiphytotic development has signif icantly decreased. At the same time, an increase in the harmfulness of stripe rust (P. striiformis) is noted. Stem rust in the region is mainly absent or observed at the end of the wheat growing season to a weak degree. Only in some years with favorable weather conditions its mass development is noted on susceptible cultivars. It is believed that the sources of infection with rust species in the North Caucasus are infested soft wheat crops, wild-growing cereals and exodemic infection carried by air currents from adjacent territories. In the North Caucasus, forage and wild grasses are affected by Puccinia species almost every year. Depending on weather conditions, the symptom expression is noted from late September to December and then from late February to May–June. Potentially, an autumn infection on grasses can serve as a source for infection of winter soft wheat cultivars sown in October. The purpose of these studies is to characterize the virulence of P. triticina, P. graminis, P. striiformis on wild cereals and to assess the specialization of causative agents to winter wheat in the North Caucasus. Infectious material represented by leaves with urediniopustules of leaf, stem and stripe rusts was collected from wild cereals (Poa spp., Bromus spp.) in the Krasnodar Territory in October–November 2019. Uredinium material from P. triticina, P. striiformis, and P. graminis was propagated and cloned. Monopustular Puccinia spp. isolates were used for virulence genetics analysis. In experiments to study the specialization of rust species from wild-growing cereals on common wheat, 12 winter cultivars were used (Grom, Tanya, Yuka, Tabor, Bezostaya 100, Yubileynaya 100, Vekha, Vassa, Alekseich, Stan, Gurt, Bagrat). These cultivars are widely cultivated in the North Caucasus region and are characterized by varying degrees of resistance to rust. Additionally, wheat material was inoculated with Krasnodar populations of P. triticina, P. striiformis, P. graminis from common wheat. In the virulence analysis of P. triticina on cereal grasses, four phenotypes (races) were identif ied: MCTKH (30 %), TCTTR (30 %), TNTTR (25 %), MHTKH (15 %), and f ive were identif ied in P. graminis (RKMTF (60 %), TKTTF, RKLTF, QKLTF, LHLPF (10 % each). Among P. striiformis isolates, three phenotypes were identif ied using the International and European sets of differentiating cultivars – 111E231 (88 %), 111E247 (6 %) and 78E199 (6 %). Using isogenic Avocet lines, 3 races were also identif ied, which differed among themselves in virulence to the Yr1, Yr11, Yr18 genes (with the prevalence of virulent ones (94 %)). Composite urediniums’ samples (a mixture of all identif ied races) of grass rust of each species were used to inoculate winter wheat cultivars. The most common winter wheat cultivars (75 %) were characterized by a resistant response when infected with P. graminis populations from common wheat and cereal grasses. All these cultivars were developed using donors of the rye translocation 1BL.1RS, in which the Lr26, Sr31, and Yr9 genes are localized. The number of winter wheat cultivars resistant to leaf rust in the seedling phase was lower (58 %). At the same time, all the studied cultivars in the seedling phase were susceptible to P. striiformis to varying degrees. The virulence analysis of the leaf, stem and stripe rust populations did not reveal signif icant differences in the virulence of the pathogens between wild-growing cereals and soft wheat. Urediniomaterial of all studied rust species successfully infested soft wheat cultivars. The results obtained indicate that grasses are rust infection reservoirs for common wheat crops in the North Caucasus.

Genotyping Puccinia striiformis f. sp. tritici Isolates with SSR and SP-SNP Markers Reveals Dynamics of the Wheat Stripe Rust Pathogen in the United States from 1968 to 2009 and Identifies Avirulence-Associated Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating disease of wheat (Triticum aestivum) in the United States. The fungal pathogen can rapidly evolve, producing new virulent races infecting previously resistant cultivars and genotypes adapting to different environments. The objective of this study was to investigate the long-term population dynamics of P. striiformis f. sp. tritici in the United States. Through genotyping 1,083 isolates taken from 1968 to 2009, using 14 simple sequence repeat (SSR) markers and 92 secreted protein single nucleotide polymorphism (SP-SNP) markers, 614 and 945 genotypes were detected, respectively. In general, the two types of markers produced consistent genetic relationships among the P. striiformis f. sp. tritici populations over the 40-year period. The prior-to-2000 and the 2000-to-2009 populations were significantly different, with the latter showing higher genotypic diversity and higher heterozygosity than the earlier populations. Clustering analyses using genotypes of either SSR or SP-SNP markers revealed three molecular groups (MGs), MG1, MG2, and MG3. The prior-to-2000 and the 2000-to-2009 groups both had evidence of MG1 and MG2; however, MG3 was only found in the 2000-to-2009 population. Some of the isolates in the period of 2000 to 2009 formed individual clusters, suggesting exotic incursions. Other isolates of the same period were clustered with prior-to-2000 isolates, indicating that they were developed from the previously established populations. The data suggest the coexistence of newly introduced populations alongside established populations in the United States. Twenty SP-SNP markers were significantly associated to individual avirulence genes. These results are useful for developing more accurate monitoring systems and provide guidance for disease management.

Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis

Long-distance migration and host adaptation by transboundary plant pathogens often brings detrimental effects to important agroecosystems. Efficient surveillance as a basis for responding to the dynamics of such pathogens is often hampered by a lack of information on incursion origin, evolutionary pathways and the genetic basis of rapidly evolving virulence across larger timescales. Here, we studied these genetic features by using historical isolates of the obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst), which causes one of the most widespread and devastating diseases, stripe (yellow) rust, of wheat. Through a combination of genotypic, phenotypic and genomic analyses, we assigned eight Pst isolates representing putative exotic Pst incursions into Australia to four previously defined genetic groups, PstS0, PstS1, PstS10 and PstS13. We showed that isolates of an additional incursion of P. striiformis, known locally as P. striiformis f. sp. pseudo-hordei, had a new and unique multilocus SSR genotype (MLG). We provide results of overall genomic variation of representative Pst isolates from each genetic group by comparative genomic analyses. We showed that isolates within the PstS1 and PstS13 genetic groups are most distinct at the whole-genome variant level from isolates belonging to genetic group PstS0, whereas the isolate from the PstS10 genetic group is intermediate. We further explored variable gene content, including putative effectors, representing both shared but also unique genetic changes that have occurred following introduction, some of which may additionally account for local adaptation of these isolates to triticale. Our genotypic and genomic data revealed new genetic insights into the evolution of diverse phenotypes of rust pathogens following incursion into a geographically isolated continental region.

Spatiotemporal Changes in Varietal Resistance to Wheat Yellow Rust in France Reveal an Increase in Field Resistance Level During the Period 1985-2018

Monitoring spatiotemporal changes in varietal resistance and understanding its drivers seem essential to managing plant diseases but require having access to the genetic basis of disease resistance and to its deployment. In this study, we focused on yellow rust (Puccinia striiformis f. sp. tritici) for three decades in France, by using field adult plant resistance levels, Yr race-specific resistance genes of varieties, presence of Puccinia striiformis f. sp. tritici pathotypes and their virulence profiles, and systematic surveys of the acreages of bread wheat varieties available at a yearly survey time and at a district level. Based on these data, we studied spatiotemporal changes in varietal resistance over the period from 1985 to 2018 in 54 French administrative districts (hereafter "departments") by using a set of relevant indicators weighted by the relative acreage proportion of the varieties sown at the department level. Our analyses revealed an increase in varietal resistance over decades that would be due to the accumulation of both quantitative resistance and different race-specific resistance genes. We suggest that, beyond breeders, several actors, including examination offices, agricultural advisory services, and farmers, may have had a substantial influence on these spatiotemporal changes, promoting more resistant varieties and the rapid replacement of newly susceptible varieties by still resistant ones at the beginning of each epidemic.

Genetic Diversity of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Yunnan, China

The stripe rust of wheat is one of the devastating diseases in China, which is caused by fungus Puccinia striiformis f. sp. tritici (Pst). The Yunnan Province of China is located in the south-western part, and holds distinctive geographical and climate features, while wheat growth and epidemics of stripe rust fungus are fully dissimilar to the major wheat-growing regions of China. It is important to discover its origin and migration to control the disease. In this study, 352 isolates were sampled from 11 spots of the Yunnan Province during the wheat growing season from 2004 to 2015 and analyzed with SNPs markers of housekeeping genes. Results revealed that 220 haplotypes were inferred from the concatenating sequences; among them, 5 haplotypes (viz., 'H86', 'H18', 'H8', 'H15' and 'H23') comprised over 24.5% of the population. The haplotype diversity, nucleotide diversity, mutation rate and recombination events were 0.992, 6.04 × 10^-3, 4.46 × 10^-3 and 18.0 respectively, which revealed the genetic diversity of Pst populations among all locations. Four grouping methods, such as UPGMA-tree, PCA, PLS-DA and STRUCTURE, were employed for the categorization of the Pst populations conferring to their races and topographical localities. All methods were found significant and mostly had co-linear relations with each other. The analysis of molecular variance (AMOVA) conferred total variation was 9.09%, and 86.20% of variation was within the populations. The current study also exposed a comparatively high genetic multiplicity within the population, while low genetic inconsistency among the populations. Furthermore, the molecular records on the gene pole (Nm = 18.45) established that the migration of the stripe rust pathogen occurred among all locations in Yunnan province. The ancestral haplotype was detected in Yuxi. Based on the trajectories of upper airflow and genetic diversity of Pst populations in different locations, it is suggested that the locations Dehong, Dali, Lincang and Baoshan are probably a major source of Pst in Yunnan.

Potential Infection Risks of the Wheat Stripe Rust and Stem Rust Pathogens on Barberry in Asia and Southeastern Europe

Barberry (Berberis spp.) is an alternate host for both the stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), and the stem rust pathogen, P. graminis f. sp. tritici (Pgt), infecting wheat. Infection risk was assessed to determine whether barberry could be infected by either of the pathogens in Asia and Southeastern Europe, known for recurring epidemics on wheat and the presence of barberry habitats. For assessing infection risk, mechanistic infection models were used to calculate infection indices for both pathogens on barberry following a modeling framework. In East Asia, Bhutan, China, and Nepal were found to have low risks of barberry infection by Pst but high risks by Pgt. In Central Asia, Azerbaijan, Iran, Kazakhstan, southern Russia, and Uzbekistan were identified to have low to high risks of barberry infection for both Pst and Pgt. In Northwest Asia, risk levels of both pathogens in Turkey and the Republic of Georgia were determined to be high to very high. In Southwest Asia, no or low risk was found. In Southeastern Europe, similar high or very high risks for both pathogens were noted for all countries. The potential risks of barberry infection by Pst and/or Pgt should provide guidelines for monitoring barberry infections and could be valuable for developing rust management programs in these regions. The framework used in this study may be useful to predict rust infection risk in other regions.

Genome-wide association study of resistance to PstS2 and Warrior races of Puccinia striiformis f. sp. tritici (stripe rust) in bread wheat landraces

Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding programs an association mapping (AM) panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the AM panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers across 19 chromosomes with significant SNP-trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study do not correspond to previously reported Yr genes or QTL, suggesting new genomic regions for stripe rust resistance.

Pathogen Incursions - Integrating Technical Expertise in a Socio-Political Context

The incursion of a plant pathogen into a new geographic area initiates a series of decisions about appropriate control or eradication efforts. Incomplete, erroneous, and/or selective information may be used by diverse stakeholders to support individual goals and positions on how an incursion should be managed. We discuss the complex social, political, and technical factors that shape a biosecurity response prior to reviewing information needs and common stakeholder misunderstandings. Selected examples focus on the rust fungi (order Pucciniales). We then explore how plant pathologists, as technical experts, can interact with biosecurity stakeholders to build empathy and understanding that in turn allows a shift from being a distant subject matter expert to an active participant helping to structure problems and shape knowledge flows for better outcomes.

Breeding progress for pathogen resistance is a second major driver for yield increase in German winter wheat at contrasting N levels

Breeding has substantially increased the genetic yield potential, but fungal pathogens are still major constraints for wheat production. Therefore, breeding success for resistance and its impact on yield were analyzed on a large panel of winter wheat cultivars, representing breeding progress in Germany during the last decades, in large scale field trials under different fungicide and nitrogen treatments. Results revealed a highly significant effect of genotype (G) and year (Y) on resistances and G × Y interactions were significant for all pathogens tested, i.e. leaf rust, strip rust, powdery mildew and Fusarium head blight. N-fertilization significantly increased the susceptibility to biotrophic and hemibiotrophic pathogens. Resistance was significantly improved over time but at different rates for the pathogens. Although the average progress of resistance against each pathogen was higher at the elevated N level in absolute terms, it was very similar at both N levels on a relative basis. Grain yield was increased significantly over time under all treatments but was considerably higher without fungicides particularly at high N-input. Our results strongly indicate that wheat breeding resulted in a substantial increase of grain yield along with a constant improvement of resistance to fungal pathogens, thereby contributing to an environment-friendly and sustainable wheat production.

Evolutionary Genomics of High Fecundity

Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.

Diversity in Puccinia striiformis populations causing the 2013 yellow rust epidemics on major wheat cultivars of Pakistan

Wheat yellow/stripe rust pathogen Puccinia striiformis is highly diverse and recombinant in the north of Pakistan in the Himalayan region. However, little is known about the role of this diversity in disease epidemics in areas where wheat yellow rust is an important disease in both irrigated and rain-fed wheat (i.e., in the plains of Pakistan). We explored the population diversity in P. striiformis during the rust epidemics of 2013 in the major wheat-growing regions of Pakistan (the Himalayan region, central Khyber Pakhtunkhwa [KP], southern KP, central and northern Punjab). Disease severities among commonly grown cultivars ranged from 5% to 100%. Microsatellite genotyping with 16 simple sequence repeat (SSR) markers revealed a high diversity among 266 isolates collected during the season, with the Simpson diversity index (Simpson 1949) ranging from 0.870 (Himalayan) to 0.955 (southern KP). The recombination signature was stronger in the Himalayan population and central KP compared with wheat-growing regions of Punjab and southern KP. The overall diversity was higher in Pakistan relative to the clonal populations present in Europe, Australia, and the Americas. Analyses of population subdivision revealed no clear evidence of spatial structure for samples from Pakistan, with a maximum fixation index (F_ST) value of only 0.10. The lack of clear population subdivision could be attributed to migration of pathogen. In turn, the high diversity of P. striiformis in Pakistan represents a potential threat to wheat production in the region and worldwide, as a possible source to found clonal populations in diverse wheat-growing areas.

Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust

First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.

Alternate Hosts of Puccinia striiformis f. sp. tritici and Their Role

Understanding the interactions between the host and the pathogen is important in developing resistant cultivars and strategies for controlling the disease. Since the discovery of Berberis and Mahonia spp. as alternate hosts of the wheat stripe rust pathogen, Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), their possible role in generating new races of Pst through sexual reproduction has become a hot topic. To date, all the investigations about the role of alternate hosts in the occurrence of the wheat stripe rust epidemics revealed that it depends on alternate host species and environmental conditions. In this review, we summarized the current status of alternate hosts of Pst, their interactions with the pathogen, their importance in genetic diversity and disease epidemics. Most importantly, the recent research progress in understanding the role of alternate hosts of Pst is provided.

An ankyrin-repeat and WRKY-domain-containing immune receptor confers stripe rust resistance in wheat

Perception of pathogenic effectors in plants often relies on nucleotide-binding domain (NBS) and leucine-rich-repeat-containing (NLR) proteins. Some NLRs contain additional domains that function as integrated decoys for pathogen effector targets and activation of immune signalling. Wheat stripe rust is one of the most devastating diseases of crop plants. Here, we report the cloning of YrU1, a stripe rust resistance gene from the diploid wheat Triticum urartu, the progenitor of the A genome of hexaploid wheat. YrU1 encodes a coiled-coil-NBS-leucine-rich repeat protein with N-terminal ankyrin-repeat and C-terminal WRKY domains, representing a unique NLR structure in plants. Database searches identify similar architecture only in wheat relatives. Transient expression of YrU1 in Nicotiana benthamiana does not induce cell death in the absence of pathogens. The ankyrin-repeat and coiled-coil domains of YrU1 self-associate, suggesting that homodimerisation is critical for YrU1 function. The identification and cloning of this disease resistance gene sheds light on NLR protein function and may facilitate breeding to control the devastating wheat stripe rust disease.

Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan

The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by F_ST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions.

Multilocus Genotypes of the Wheat Leaf Rust Fungus Puccinia triticina in Worldwide Regions Indicate Past and Current Long-Distance Migration

Many plant pathogenic fungi have a global distribution across diverse ecological zones and agricultural production systems. Puccinia triticina, the wheat leaf rust fungus, is a major pathogen in many wheat production areas of the world. The objective of this research was to determine the genetic relatedness of P. triticina in different worldwide regions. A total of 831 single-uredinial isolates collected from 11 regions were characterized for multilocus genotype at 23 simple sequence repeat loci and for virulence to 20 lines of wheat with single genes for leaf rust resistance. A total of 424 multilocus genotypes and 497 virulence phenotypes were found. All populations had high heterozygosity and significant correlation between virulence and molecular variation, which indicated clonal reproduction. The populations from North America and South America, Central Asia and Russia, and the Middle East and Europe were closely related for multilocus genotypes and many individual isolates from other continental regions were closely related. Twenty-seven multilocus genotypes were found in more than one continental region, and 13 of these had isolates with identical virulence phenotypes. The wide geographic distribution of identical and highly related multilocus genotypes of P. triticina indicated past and more recent migration events facilitated by the spread of clonally produced urediniospores.

Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei)

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.