Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici

Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.)

BACKGROUND

Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR).

RESULTS

Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype.

CONCLUSION

The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.

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.

Genetic Diversity and Population Structure of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) in Turkey

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening wheat production both in Turkey and worldwide. However, the underlying genetic dynamics of Pst populations are not fully known in Turkey. To determine the population genetic structure and migration network among regional Pst populations, a total of 140 Pst isolates collected from six geographical regions of Turkey from 2018 to 2020 were sampled and genotyped using 21 simple sequence repeat loci. A total of 70 multilocus genotypes were identified and classified into the three major genetic groups by Bayesian assignment. The highest genotypic diversity was detected in Southeastern Anatolia, showing its critical role as one of the source populations to trigger possible stripe rust epidemics. Analysis of molecular variance revealed the highest variation (90.25%) within isolates. The migration network generated by the number of effective migrants showed that the highest migration (1.0) was determined between Southeastern Anatolia and Central Anatolia, and considerable levels of migration (>0.2) were determined among the other regions, except for the Black Sea. Linkage equilibrium (P ≥ 0.05) was detected for many geographical regions, except for Marmara (P = 0.00) and the Mediterranean (P = 0.03), suggesting that reproduction of Pst populations is most likely sexual or mixed (sexual and clonal). To sum up, this is the first study on the genetic relationships and population genetic structure of the Pst population in Turkey, and these findings may provide critical information to develop management strategies for wheat stripe rust.

Field response and molecular screening of European wheat germplasm against powdery mildew at the Himalayan region of Pakistan

Wheat powdery mildew possesses a significant threat to wheat crops not only on a global scale but also in the northern region of Pakistan. Recognizing the need for effective measures, the exploration and utilization of exotic germplasm take on critical importance. To address this, a series of trials were made to investigate the response of 30 European (EU) lines, in addition to the local checks (Siran, Atta-Habib (AH) and Ghanimat-e-IBGE) against wheat powdery mildew at the Himalayan region of Pakistan. The study involved field testing from 2018 to 2022 across multiple locations, resulting in 38 different environments (location × year). In addition to field evaluations, molecular genotyping was also performed. The disease was absent on the tested lines during 2018, 2019, and 2020 whereas it ranged from 0 to 100% at Chitral location during 2021, where 100% was observed only for one EU wheat line "Matrix." The disease prevailed only at Gilgit location (0-60% for EU wheat line "F236") and at Nagar location (0-10% for EU wheat lines Substance and Nelson) during the disease season of 2022. Most of the EU wheat lines showed very low ACI values, due to an overall low disease pressure. Matrix showed the maximum ACI (1.54) followed by Ritter (1.25) and Bli_autrichion (0.87), whereas the minimum (0.1) was for Substance, JB_Asano, and KWS_Loft followed by Canon (0.19), all exhibiting partial resistance. The molecular marker-based screening revealed that Pm38 was the most prevalent and detected in 100% of wheat lines followed by Pm39 (60%) and Pm8 (30%). Six wheat lines (20%) possessed all three Pm genes (Pm8, Pm38, and Pm39) concurrently. The variability observed in this study can be utilized in future breeding efforts aimed at developing resistant wheat varieties.

Molecular Characterization of Ciborinia camelliae Kohn Shows Intraspecific Variability and Suggests Transcontinental Movement of the Pathogen

Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The fungus infects only the flowers of camellias. C. camelliae isolates obtained from symptomatic samples, collected in 13 different localities worldwide, were characterized by Multi-Locus Sequence Typing (MLST) using the following: (i) a nuclear ribosomal DNA internal transcribed spacer; (ii) subunit 2 of β-tubulin (β-TUB II), (iii) elongation factor 1-α (EF1α); and (iv) glycerol-3-phosphate dehydrogenase (GPDH). The variability of the strains was assessed using a universally primed-polymerase chain reaction (UP-PCR) with six universal primers. Gene sequence comparison showed high similarity among all the European strains and highlighted the diversity of the New Zealand and Chinese representative strains. The profiles obtained by UP-PCR confirmed the significant diversity of extra-European strains and identified subgroups within the European population. The presence of shared genetic profiles obtained from strains isolated in different countries (New Zealand and France) suggests the movement of strains from one location to another, which is probably due to the exchange of infected plant material. Moreover, our study shows the overall high intraspecific variability of C. camelliae, which is likely due to the sexual reproduction of the fungus, suggesting the risk of emergence of new pathotypes adapting to novel camellia varieties.

Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles

BACKGROUND

The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species.

RESULTS

We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015.

CONCLUSIONS

These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.

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.

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.

Genetic Characterization of Advance Bread Wheat Lines for Yield and Stripe Rust Resistance

Wheat (Triticum aestivum L.) is a prominent grain crop. The goal of the current experiment was to examine the genetic potential of advanced bread wheat genotypes for yield and stripe rust resistance. Ninety-three bread wheat genotypes including three varieties (Kohat-2017, Pakistan-2013, and Morocco) were field tested in augmented design as observational nurseries at three locations (i.e., Kohat, Nowshera, and Peshawar) during the 2018-19 crop season. Various parameters related to yield and stripe rust resistance showed significant differences among genotypes for most of the characters with few exceptions. The analysis of variance revealed significant variations for all the genotypes for all the traits at all three sites with few exceptions where nonsignificant differences were noticed among genotypes. Averaged over three locations, genotypes exhibiting maximum desirable values for yield and yield components were KT-86 (325 tillers) for tillers m^-2, KT-50 (2.86 g) for grain weight spike^-1, KT-49 (41.6 g) for 1000-grain weight, KT-50 (74 grains) for grains spikes^-1, KT-55 (4.76 g) for spike weight, and KT-36 and KT-072 (4586 kg ha^-1) for grain yield. Correlation analysis revealed that grain yield had a significant positive correlation with grain spike^-1 and grain weight spike^-1 at Kohat, with grains spike^-1, tillers m^-2, and grain weight spike^-1 at Nowshera, and with plant height, spike weight, 1000-grain weight, and tillers m^-2 at Peshawar. Molecular marker data and host response in the field at the adult stage revealed that Yr15 and Yr10 are both still effective in providing adequate resistance to wheat against prevalent races of stripe rust. Four lines showing desirable lower average coefficient of infection (ACI) values without carrying Yr15 and Yr10 genes show the presence of unique/new resistance gene(s) in the genetic composition of these four lines. Genotype KT-072 (4586 kg ha^-1 and 1.3 ACI), KT-07 (4416 kg ha^-1 and 4.3 ACI), KT-10 (4346 kg ha^-1 and 1.0 ACI), and KT-62 (4338 kg ha^-1 and 2.7 ACI) showed maximum values for grain yield and low desirable ACI values, and these lines could be recommended for general cultivation after procedural requirements of variety release.

Mapping and validation of a novel major QTL for resistance to stripe rust in four wheat populations derived from landrace Qishanmai

Wheat yield has been constrained by stripe rust disease globally. A wheat landrace (Qishanmai, QSM) consistently showed lower stripe rust severities in multiple year studies than susceptible check varieties including Suwon11 (SW) at the adult plant stage. To detect QTL for reducing the severity in QSM, 1218 recombinant inbred lines (RILs) were developed from SW × QSM. QTL detection was conducted firstly using 112 RILs selected for similarity in pheno-morphological characters. The 112 RILs were assessed for stripe rust severity at the 2nd leaf, 6th leaf and flag leaf stages under field and greenhouse conditions, and genotyping was done primarily with a single nucleotide polymorphism (SNP) array. On the basis of these phenotypic and genotypic data, a major QTL (QYr.cau-1DL) was detected on chromosome 1D at the 6th leaf and flag leaf stages. Further mapping was conducted by genotyping 1218 RILs using new simple sequence repeat (SSR) markers, which were developed by referring to the sequences of the wheat line Chinese Spring (IWGSC RefSeq v1.0). QYr.cau-1DL was mapped within a 0.5 cM (5.2 Mb) interval delimited by the SSR markers 1D-320.58 and 1D-325.79. These markers were applied to select for QYr.cau-1DL by screening F₂ or BC₄F₂ plants of the wheat crosses RL6058 × QSM, Lantian10 × QSM and Yannong21 × QSM. F_2:3 or BC₄F_2:3 families derived from the selected plants were assessed for stripe rust resistance in the fields of two locations and in a greenhouse. Wheat plants carrying the resistant marker haplotype in homozygous state for QYr.cau-1DL showed lower stripe rust severities (by 44% to 48%) than plants lacking this QTL. The trial of RL6058 (a carrier of Yr18) × QSM also indicated that QYr.cau-1DL had larger effect than Yr18 on reducing severity; they acted synergistically, yielding an elevated level of stripe rust resistance.

Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen

Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

Races CYR34 and Suwon11-1 of Puccinia striiformis f. sp. tritici Played an Important Role in Causing the Stripe Rust Epidemic in Winter Wheat in Yili, Xinjiang, China

Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease. Its pathogen frequently adapts to newly invaded regions and overcomes resistance in wheat cultivars. This disease is especially important in China due to its favorable conditions for the stripe rust epidemic and the recombination population structure of pathogens. Xinjiang is a vast epidemic region in China, but very limited research on this disease has been performed in this region. In this study, we identified 25 races from 129 isolates collected from winter wheat fields from five different regions (Nileke, Xinyuan, Gongliu, Huocheng, and Qapqal) of Yili, Xinjiang, using the Chinese set of 19 differential wheat lines. All isolates were virulent on the differentials Fulhad and Early Premium, but no isolates were virulent on Yr5. Among the 25 races, Suwon11-1 was the most prevalent, followed by CYR34. Both races were found in four out of the five locations. It is important to continue monitoring stripe rust and its pathogen races in this region, as it forms a pathway between China and Central Asia. Collaborative research is essential for controlling stripe rust in this region, other regions in China, and neighboring countries.

Direct Evidence Demonstrates that Puccinia striiformis f. sp. tritici Infects Susceptible Barberry to Complete Sexual Cycle in Autumn

Wheat stripe rust is an airborne and destructive disease caused by a heteroecious rust fungus Puccinia striiformis f. sp. tritici (Pst). Studies have demonstrated that the rust pathogen accomplishes sexual reproduction on susceptible barberry under natural conditions in spring, whereas Pst infection on barberry is still in blank in other seasons. In late October 2016, aecial production on barberry shrubs were observed in Linzhi, Tibet, China. Therefore, experimental tests were conducted to verify the existence of sexual cycles of Pst in this season. By inoculating 52 aecial clusters from 30 rusted barberry leaves, four Pst samples, T1 to T4, were successfully recovered from the rusted barberry shrubs. Sixty-five single uredinium (SU) isolates were derived from the four Pst samples. Based on virulence tests on the Chinese differential hosts, T1 to T4 samples were unknown races and showed mixed reactions on some differentials. Twenty-one known races and 44 unknown races belonging to five race groups were identified among the 65 SU isolates. Meanwhile, the 65 SU isolates produced 26 various virulence patterns (VPs; called VP1-VP26) on 25 single Yr gene lines and 15 multilocus genotypes (MLGs) at nine simple sequence repeat marker loci. Clustering analysis showed similar lineage among subpopulations and different lineage between subpopulations. Linkage disequilibrium analysis indicated that the SU population was produced sexually. This study first reported that Pst infects susceptible barberry to complete sexual reproduction in autumn. The results update the knowledge of disease cycle and management of wheat stripe rust and contribute to the understanding of rust genetic diversity in Tibet.

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.

Global dispersal and diversity of rust fungi in the context of plant health

Long-distance dispersal of plant pathogens at the continental scale may have strong implications on plant health, in particular when incursions result in spread of disease to new territories where the disease was previously absent or insignificant. These dispersions may be caused by airborne transmission of spores or accidental spread via human travel and trade. Recent surveillance efforts of cereal rust fungi have demonstrated that incursion of new strains with superior fitness into areas where the disease is already established may have similar implications on plant health. Since dispersal events are highly stochastic, irrespective of transmission mechanism, critical mitigation efforts include preparedness by coordinated pathogen surveillance activities, host crop diversification, and breeding for disease resistance with low vulnerability to sudden changes in the pathogen population.

Wheat Stem Rust Detection and Race Characterization in Tunisia

Climate changes over the past 25 years have led to conducive conditions for invasive and transboundary fungal disease occurrence, including the re-emergence of wheat stem rust disease, caused by Puccinia graminis f.sp. tritici (Pgt) in East Africa, Europe, and the Mediterranean basin. Since 2018, sporadic infections have been observed in Tunisia. In this study, we investigated Pgt occurrence at major Tunisian wheat growing areas. Pgt monitoring, assessment, and sampling from planted trap nurseries at five different locations over two years (2021 and 2022) revealed the predominance of three races, namely TTRTF (Clade III-B), TKKTF (Clade IV-F), and TKTTF (Clade IV-B). Clade III-B was the most prevalent in 2021 as it was detected at all locations, while in 2022 Pgt was only reported at Beja and Jendouba, with the prevalence of Clade IV-B. The low levels of disease incidence during these two years and Pgt population diversity suggest that this fungus most likely originated from exotic incursions and that climate factors could have caused disease establishment in Tunisia. Further evaluation under the artificial disease pressure of Tunisian wheat varieties and weather-based modeling for early disease detection in the Mediterranean area could be helpful in monitoring and predicting wheat stem rust emergence and epidemics.

Clonal Expansion and Dispersal Pathways of Puccinia polysora in China

Southern corn rust (SCR) caused by Puccinia polysora is one of the most devastating diseases in the world. In recent years, SCR has been upgraded from a minor to a major disease around the world, including in China. However, little is known about its population genetics and structure in China. In this study, we analyzed 288 isolates collected from various localities during 2017 in seven Chinese provinces: Guangxi, Guangdong, Anhui, Hunan, Shandong, Henan, and Shaanxi. The isolates were analyzed using nine microsatellite markers. The population structure, genetic diversity, and reproduction mode of P. polysora were investigated based on genotype data. Strong genotypic diversity was detected and clonal reproduction was dominant. The populations collected from the pathogen's winter-reproductive regions harbored more genotypes than those collected from the pathogen's epidemic regions. The spatial differences in genotypic richness, and evenness among the populations were significant, and showed a decreasing trend from south to north. Most isolates were clustered into two clonal groups. Two high-frequency multilocus genotypes (MLGs), MLG1 and MLG2, were widely distributed in all populations. Our analyses confirmed that P. polysora employed clone dispersal from the pathogen's winter-reproductive regions to the pathogen's epidemic regions, and in addition to the sources from the pathogen's winter-reproductive regions, the pathogen in Anhui and Hunan might also have other sources from areas such as Taiwan, China, or/and Southeast Asia, and the pathogen went through a genetic bottleneck during its dispersal. These findings provide initial insights into the reproduction mode and dispersal pathways of P. polysora in China.

Early detection of stripe rust infection in wheat using light-induced fluorescence spectroscopy

In the current study, the application of fluorescence spectroscopy along with the advanced statistical technique and confocal microscopy was investigated for the early detection of stripe rust infection in wheat grown under field conditions. The indigenously developed Fluorosensor fitted with LED, emitting monochromatic light was used that covered comparatively larger leaf area for recording fluorescence data thus presenting more reliable current status of the leaf. The examined leaf samples covered the entire range of stripe rust disease infection from no visible symptoms to the complete disease prevalence. The molecular changes were also assessed in the leaves as the disease progresses. The emission spectra mainly produce two fluorescence emission classes, namely the blue-green fluorescence (400-600 nm range) and chlorophyll fluorescence (650-800 nm range). The chlorophyll fluorescence region showed lower chlorophyll bands both at 685 and 735 nm in the asymptomatic (early diseased) and symptomatic (diseased) leaf samples than the healthy ones as a result of partial deactivation of PSII reaction centers. The 735 nm chlorophyll fluorescence band was either slight or completely absent in the leaf samples with lower to higher disease incidence and thus differentiate between the healthy and the infected leaf samples. The Hydroxycinnamic acids (caffeic and sinapic acids) showed decreasing trend, whereas the ferulic acid increased with the rise in disease infection. Peak broadening/shifting has been observed in case of ferulic acid and carotenes/carotenoids, with the increase in the disease intensity. While using the LEDs (365 nm), the peak broadening and the decline in the chlorophyll fluorescence bands could be used for the early prediction of stripe rust disease in wheat crop. The PLSR statistical techniques discriminated well between the healthy and the diseased samples, thus showed promise in early disease detection. Confocal microscopy confirmed the early prevalence of stripe rust disease infection in a susceptible variety at a stage when the disease is not detectable visually. It is inferred that fluorescence emission spectroscopy along with the chemometrics aided in the effective and timely diagnosis of plant diseases and the detected signatures provide the basis for remote sensing.

Himalayan mountains imposing a barrier on gene flow of wheat yellow rust pathogen in the bordering regions of Pakistan and China

The wheat yellow rust pathogen has been shown to be diverse and potentially originated in the Himalayan region. Although Himalayan populations of Pakistan, Nepal and Bhutan have been previously compared, little is known about the relative divergence and diversity in Puccinia striiformis populations in the bordering regions of Pakistan and China. To assess the relative diversity and divergence in these regions of Pakistan (Gilgit-Baltistan, Hazara and Azad Jammu Kashmir) and China (Xinjiang, Qinghai, Tibet, Sichuan, Guizhou and Yunnan), a total of 1245 samples were genotyped using 17 microsatellite SSR markers. A clear divergence was observed between the bordering regions of Pakistan and China (F_ST = 0.28) without any resampling of genetic groups and multilocus genotypes across two sides of the Himalayan mountains. The closest subpopulations across the two countries were Xinjiang and Gilgit-Baltistan (Nei's distance = 0.147), which were close geographically. A very high diversity and recombinant population structure was observed in both populations, though slightly higher in China (Genotypic diversity = 0.970; r¯d = 0.000) than in Pakistan (Genotypic diversity = 0.902; r¯d = 0.065). The distribution of genetic groups and resampling of MLGs revealed more gene flow across Yunnan, Guizhou and Sichuan regions in China, while between Hazara and Azad-Jammu Kashmir in Pakistan. The lack of gene flow between Pakistan and China populations is due to geographical barriers and a large patch of land without wheat. The information on the relative diversity and divergence in different geographical zones of the pathogen center of diversity and neighboring region should be considered in resistant wheat deployment while considering the invasion potential of the pathogen at regional and global contexts.

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.

Populations of Puccinia striiformis f. sp. tritici in Winter Spore Production Regions Spread from Southwestern Oversummering Areas in China

Stripe rust, caused by Puccinia striifomis f. sp. tritici (Pst), is one of the most destructive wheat diseases in China. Understanding the interregional dispersal of Pst inoculum is important for controlling the disease. In the present study, wheat stripe rust samples collected from the winter spore production and oversummering regions in November 2018 to March 2019 were studied through virulence testing and molecular characterization. From 296 isolates, 96 races were identified using a set of 19 Chinese wheat cultivars and 111 races were identified using 18 Yr single-gene lines as differentials. The isolates from Hubei province in the winter spore production area had the highest similarity in virulence with those from eastern Yunnan in the oversummering area. Molecular characterization using 13 simple-sequence repeat and 43 Kompetitive allele specific PCR-single nucleotide polymorphism markers supported the conclusion that the Pst populations in the winter spore production regions were from Guizhou and eastern Yunnan, key oversummering areas in the southwest. Furthermore, an analysis of wind movement at the 700-hPa high altitude also supported the conclusion of spore dispersal from the southwestern oversummering region to the south-central winter spore production region. The results of this study provide an epidemiological basis for deploying various effective resistance genes in different regions to control stripe rust.

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.

Two Main Routes of Spore Migration Contributing to the Occurrence of Wheat Stripe Rust in the Jiangsu and Zhejiang Coastal Sporadic Epidemiological Region in 2019, Based on Phenotyping and Genotyping Analyses

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive disease in many countries. In China, wheat stripe rust generally occurs in northwestern and southwestern China and sporadically in the Jiangsu and Zhejiang coastal epidemiological region (JZER), where an outbreak of the disease occurred in 2019. To understand the population structure and potential inoculum sources of the pathogen in this region, 171 isolates collected from 93 wheat fields of 53 counties in 10 provinces were phenotyped with two sets of wheat differentials and genotyped with 20 pairs of single-nucleotide polymorphism primers. Phenotype tests indicated that identical races (CYR34, CYR33, Su11-139, and Su11-14-1) detected in Jiangsu and Zhejiang were shared with the oversummering regions (Gansu), overwintering regions (Hubei, Henan, and Shaanxi), and Yun-Gui epidemiological regions (Yunnan and Guizhou). In JZER, races CYR32, G22-14, and G22-68 were detected in Jiangsu, but not in Zhejiang, and Su11-208 was identified in Zhejiang, but not in Jiangsu. Genotypic analysis revealed remarkable gene flows among the Jiangsu, Yunnan, Henan, and Anhui populations, as well as those of Zhejiang, Guizhou, and Sichuan, showing that wheat stripe rust in Zhejiang and Jiangsu was from spores that migrated from different routes. Major gene flows were detected between the Jiangsu and Zhejiang populations. P. striiformis f. sp. tritici from both overwintering regions (Yunnan, Sichuan, Guizhou, Henan, Hubei, and Shaanxi) and oversummering regions (Gansu) contributed to the wheat stripe rust epidemic in the JZER region in 2019.

Multi-Layer Biosensor for Pre-Symptomatic Detection of Puccinia strifformis, the Causal Agent of Yellow Rust

The yellow rust of wheat (caused by Puccinia striiformis f. sp. tritici) is a devastating fungal infection that is responsible for significant wheat yield losses. The main challenge with the detection of this disease is that it can only be visually detected on the leaf surface between 7 and 10 days after infection, and by this point, counter measures such as the use of fungicides are generally less effective. The hypothesis of this study is to develop and use a compact electrochemical-based biosensor for the early detection of P. striiformis, thus enabling fast countermeasures to be taken. The biosensor that was developed consists of three layers. The first layer mimics the wheat leaf surface morphology. The second layer consists of a sucrose/agar mixture that acts as a substrate and contains a wheat-derived terpene volatile organic compound that stimulates the germination and growth of the spores of the yellow rust pathogen P. s. f. sp. tritici. The third layer consists of a nonenzymatic glucose sensor that produces a signal once invertase is produced by P. striiformis, which comes into contact with the second layer, thereby converting sucrose to glucose. The results show the proof that this innovative biosensor can enable the detection of yellow rust spores in 72 h.

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.

Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace

Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.

Identification and molecular mapping of YrBm for adult plan resistance to stripe rust in Chinese wheat landrace Baimangmai

A new adult plan resistance gene YrBm for potentially durable resistance to stripe rust was mapped on wheat chromosome arm 4BL in landrace Baimangmai. SSR markers closely flanking YrBm were developed and validated for use in marker-assisted selection. The wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) frequently acquires new virulences and rapidly adapts to environmental stress. New virulences in Pst populations can cause previously resistant varieties to become susceptible. If those varieties were widely grown, consequent epidemics can lead to yield losses. Identification and deployment of genes for durable resistance are preferred method for disease control. The Chinese winter wheat landrace Baimangmai showed a high level of adult plant resistance (APR) to stripe rust in a germplasm evaluation trial at Langfang in Hebei province in 2006 and has continued to confer high resistance over the following 15 years in field nurseries in Hebei, Sichuan and Gansu. A recombinant inbred line population of 200 F₁₀ lines developed from a cross of Baimangmai and a susceptible genotype segregated for APR at a single locus on chromosome 4BL; the resistance allele was designated YrBm. Allelism tests of known Yr genes on chromosome 4B and unique closely flanking marker alleles Xgpw7272₁₈₉ and Xwmc652₁₆₄ among a panel of Chinese wheat varieties indicated that YrBm was located at a new locus. Moreover, those markers can be used for marker-assisted selection in breeding for stripe rust resistance.

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.

Role of Sexual Reproduction in the Evolution of the Wheat Stripe Rust Fungus Races in China

Experimental and population genetic approaches have reshaped our view of how fungal pathogens reproduce, with consequences for our understanding of fungal invasions. Puccinia striiformis f. sp. tritici, the causal agent of stripe rust, poses a severe threat to wheat production worldwide. The sexual stage of P. striiformis f. sp. tritici was discovered >10 years ago, but how it affects the evolution of the pathogen, especially the emergence of the new virulent races, remains largely unknown. Here, using population genetic analyses, we demonstrate that sexual reproduction plays an important role in the evolution of P. striiformis f. sp. tritici races in China, specifically the newly emerged and devastating race virulent to resistance gene Yr26, which is widely used in China and exerts strong selective pressure on the pathogen population. Association analysis identified six genes encoding secreted proteins as candidates for virulence on wheat cultivars carrying the Yr26 resistance gene. Our results highlight the important role of sexual reproduction and selection exerted by hosts in the emergence of new virulent races in China.

Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat (Triticum aestivum L.) Accessions

Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.

Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.

Incidence of Coffee Leaf Rust in Vietnam, Possible Original Sources and Subsequent Pathways of Migration

This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863-869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.

The evolving battle between yellow rust and wheat: implications for global food security

Wheat (Triticum aestivum L.) is a global commodity, and its production is a key component underpinning worldwide food security. Yellow rust, also known as stripe rust, is a wheat disease caused by the fungus Puccinia striiformis Westend f. sp. tritici (Pst), and results in yield losses in most wheat growing areas. Recently, the rapid global spread of genetically diverse sexually derived Pst races, which have now largely replaced the previous clonally propagated slowly evolving endemic populations, has resulted in further challenges for the protection of global wheat yields. However, advances in the application of genomics approaches, in both the host and pathogen, combined with classical genetic approaches, pathogen and disease monitoring, provide resources to help increase the rate of genetic gain for yellow rust resistance via wheat breeding while reducing the carbon footprint of the crop. Here we review key elements in the evolving battle between the pathogen and host, with a focus on solutions to help protect future wheat production from this globally important disease.

Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range

Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.

Identification of a novel stripe rust resistance gene from the European winter wheat cultivar 'Acienda': A step towards rust proofing wheat cultivation

All stage resistance to stripe rust races prevalent in India was investigated in the European winter wheat cultivar 'Acienda'. In order to dissect the genetic basis of the resistance, a backcross population was developed between 'Acienda' and the stripe rust susceptible Indian spring wheat cultivar 'HD 2967'. Inheritance studies revealed segregation for a dominant resistant gene. High density SNP genotyping was used to map stripe rust resistance and marker regression analysis located stripe rust resistance to the distal end of wheat chromosome 1A. Interval mapping located this region between the SNP markers AX-95162217 and AX-94540853, at a LOD score of 15.83 with a phenotypic contribution of 60%. This major stripe rust resistance locus from 'Acienda' has been temporarily designated as Yraci. A candidate gene search in the 2.76 Mb region carrying Yraci on chromosome 1A identified 18 NBS-LRR genes based on wheat RefSeqv1.0 annotations. Our results indicate that as there is no major gene reported in the Yraci chromosome region, it is likely to be a novel stripe rust resistance locus and offers potential for deployment, using the identified markers, to confer all stage stripe rust resistance.

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.

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.

Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici

KEY MESSAGE

Analysis of a wheat multi-founder population identified 14 yellow rust resistance QTL. For three of the four most significant QTL, haplotype analysis indicated resistance alleles were rare in European wheat. Stripe rust, or yellow rust (YR), is a major fungal disease of wheat (Triticum aestivum) caused by Puccinia striiformis Westend f. sp. tritici (Pst). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties previously showing durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map YR resistance to such new Pst races. Genetic analysis of five field trials at three UK sites identified 14 quantitative trait loci (QTL) conferring resistance. Of these, four highly significant loci were consistently identified across all test environments, located on chromosomes 1A (QYr.niab-1A.1), 2A (QYr.niab-2A.1), 2B (QYr.niab-2B.1) and 2D (QYr.niab-2D.1), together explaining ~ 50% of the phenotypic variation. Analysis of these four QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL, and genetic markers were developed that distinguished resistant and susceptible alleles. Haplotype analysis in a collection of wheat varieties found that the haplotypes associated with YR resistance at three of these four major loci were rare (≤ 7%) in European wheat, highlighting their potential utility for future targeted improvement of disease resistance. Notably, the physical interval for QTL QYr.niab-2B.1 contained five nucleotide-binding leucine-rich repeat candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp.

Meta-QTLs and candidate genes for stripe rust resistance in wheat

In bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders' MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning.

Chromosome-level genomes provide insights into genome evolution, organization and size in Epichloe fungi

Epichloe fungi are endophytes of cool season grasses, both wild species and commercial cultivars, where they may exhibit mutualistic or pathogenic lifestyles. The Epichloe-grass symbiosis is of great interest to agricultural research for the fungal bioprotective properties conferred to host grasses but also serves as an ideal system to study the evolution of fungal plant-pathogens in natural environments. Here, we assembled and annotated gapless chromosome-level genomes of two pathogenic Epichloe sibling species. Both genomes have a bipartite genome organization, with blocks of highly syntenic gene-rich regions separated by blocks of AT-rich DNA. The AT-rich regions show an extensive signature of RIP (repeat-induced point mutation) and the expansion of this compartment accounts for the large difference in genome size between the two species. This study reveals how the rapid evolution of repeat structure can drive divergence between closely related taxa and highlights the evolutionary role of dynamic compartments in fungal genomes.

Population Genetic Structures of Puccinia striiformis f. sp. tritici in the Gansu-Ningxia Region and Hubei Province, China

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a destructive wheat disease in China. The Gansu–Ningxia region (GN) is a key area for pathogen over-summering in China, and northwestern Hubei (HB) is an important region for pathogen over-wintering, serving as a source of inoculum in spring epidemic regions. The spatiotemporal population genetic structure of Pst in HB and the pathogen population exchanges between GN and HB are important for estimating the risk of interregional epidemics. Here, 567 isolates from GN and HB were sampled from fall 2016 to spring 2018 and were genotyped using simple sequence repeat markers. The genotypic and genetic diversity of Pst subpopulations in HB varied among seasons and locations. Greater genetic diversification levels were found in the spring compared with fall populations using principal coordinate analysis and Bayesian assignments. In total, there were 17 common genotypes among the 208 determined, as shown by a small overlap of genotypes in the principal coordinate analysis and dissimilar Bayesian assignments in both regions, which revealed the limited genotype exchange between the populations of GN and HB.

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.

The Changing Virulence of Stripe Rust in Canada from 1984 to 2017

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is an important wheat disease worldwide. In this study, the P. striiformis f. sp. tritici population in Canada, representing a time period from 1984 to 2017, was analyzed for virulence diversity and geographical distribution. Virulence of 140 P. striiformis f. sp. tritici isolates was evaluated on 17 near-isogenic wheat lines in the 'Avocet S' background, each containing a single resistance gene along with an 18th line 'Tyee'. Seedlings were inoculated with a urediniospore/talc mixture and infection types were evaluated on a scale of 0 to 9. In total, 89 races were identified with various combinations of defeated Yr genes. Clear changes in pathogen virulence have been observed through time that are confirmed by clustering algorithms. The results showed that the tested P. striiformis f. sp. tritici isolates remained avirulent on Yr1, Yr5, and Yr15, and have very low frequency of virulence on Yr76, but had high frequencies of virulence on Yr6, Yr7, Yr8, Yr9, Yr17, Yr43, Yr44, YrTr1, and YrExp2. P. striiformis f. sp. tritici virulence spiked on Yr7, Yr8, and Yr9 for the first time in 2000, and on Yr10 and Yr27 in 2010. Overall, the predominant races in Canada were very similar to those reported in the United States (PSTv-37, PSTv-41, and PSTv-52), which indicates long-distance migration of P. striiformis f. sp. tritici from the United States to Canada. Sixty-four races had unique virulence combinations that had not been previously reported in the United States, which suggested that evolution of virulence/avirulence for host resistance by mutation at local scale, is possible. Analysis of diversity between Canadian isolates and races from the United States since 2010 showed that the P. striiformis f. sp. tritici population in western Canada is similar to that in the western states of the United States, and that the population in eastern Canada is similar to the eastern and/or central regions of the United States, supporting the hypothesis that specific P. striiformis f. sp. tritici populations in North America travel through different wind trajectories.

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.

Molecular Characterization of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Collections from Nine Countries

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. To understand the worldwide distribution of its molecular groups, as well as the diversity, differentiation, and migration of the Pst populations, 567 isolates collected from nine countries (China, Pakistan, Italy, Egypt, Ethiopia, Canada, Mexico, Ecuador, and the U.S.) in 2010–2018 were genotyped using 14 codominant simple sequence repeat markers. A total of 433, including 333 new multi-locus genotypes (MLGs), were identified, which were clustered into ten molecular groups (MGs). The MGs and country-wise populations differed in genetic diversity, heterozygosity, and correlation coefficient between the marker and virulence data. Many isolates from different countries, especially the isolates from Mexico, Ecuador, and the U.S., were found to be identical or closely related MLGs, and some of the MGs were present in all countries, indicating Pst migrations among different countries. The analysis of molecular variance revealed 78% variation among isolates, 12% variation among countries, and 10% variation within countries. Only low levels of differentiation were found by the pairwise comparisons of country populations. Of the 10 MGs, 5 were found to be involved in sexual and/or somatic recombination. Identical and closely related MLGs identified from different countries indicated international migrations. The study provides information on the distributions of various Pst genetic groups in different countries and evidence for the global migrations, which should be useful in understanding the pathogen evolution and in stressing the need for continual monitoring of the disease and pathogen populations at the global scale.

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.

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.

Population Diversity, Dynamics, and Differentiation of Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici From 2010 to 2017 and Comparison With 1968 to 2009 in the United States

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious disease on wheat in the United States, especially after 2000. In the present study, 2,247 Pst isolates collected over all stripe rust epidemiological regions in the United States from 2010 to 2017 were genotyped at 14 simple sequence repeat (SSR) loci to investigate the population diversity, dynamics, and differentiation. A total of 1,454 multilocus genotypes (MLGs) were detected. In general, the populations in the west (regions 1-6) had more MLGs and higher diversities than the populations in the east (regions 7-12). The populations of 2010 and 2011 were more different from the other years. Genetic variation was higher among years than among regions, indicating the fast changes of the population. The divergence (Gst) was bigger between the west population and east population than among regions within either the west or east population. Gene flow was stronger among the regional populations in the east than in the west. Clustering analyses revealed 3 major molecular groups (MGs) and 10 sub-MGs by combining the genotypic data of 2010-2017 isolates with those of 1968-2009. MG1 contained both 1968-2009 isolates (23.1%) and 2010-2017 isolates (76.9%). MG2 had 99.4% of isolates from 1968-2009. MG3, which was the most recent and distinct group, had 99.1% of isolates from 2010-2017. Of the 10 sub-MGs, 5 (MG1-3, MG1-5, MG3-2, MG3-3, and MG3-4) were detected only from 2011 to 2017. The SSR genotypes had a moderate, but significant correlation (r = 0.325; p < 0.0001) with the virulence phenotype data. The standard index values of association (rbarD = 0.11) based on either regional or yearly populations suggest clonal reproduction. This study indicated high diversity, fast dynamics, and various levels of differentiation of the Pst population over the years and among epidemiological regions, and the results should be useful for managing wheat stripe rust.