Structure and Migration in U.S. Blumeria graminis f. sp. tritici Populations

Multiple routes to fungicide resistance: Interaction of Cyp51 gene sequences, copy number and expression

We examined the molecular basis of triazole resistance in Blumeria graminis f. sp. tritici (wheat mildew, Bgt), a model organism among powdery mildews. Four genetic models for responses to triazole fungicides were identified among US and UK isolates, involving multiple genetic mechanisms. Firstly, only two amino acid substitutions in CYP51B lanosterol demethylase, the target of triazoles, were associated with resistance, Y136F and S509T (homologous to Y137F and S524T in the reference fungus Zymoseptoria tritici). As sequence variation did not explain the wide range of resistance, we also investigated Cyp51B copy number and expression, the latter using both reverse transcription-quantitative PCR and RNA-seq. The second model for resistance involved higher copy number and expression in isolates with a resistance allele; thirdly, however, moderate resistance was associated with higher copy number of wild-type Cyp51B in some US isolates. A fourth mechanism was heteroallelism with multiple alleles of Cyp51B. UK isolates, with significantly higher mean resistance than their US counterparts, had higher mean copy number, a high frequency of the S509T substitution, which was absent from the United States, and in the most resistant isolates, heteroallelism involving both sensitivity residues Y136+S509 and resistance residues F136+T509. Some US isolates were heteroallelic for Y136+S509 and F136+S509, but this was not associated with higher resistance. The obligate biotrophy of Bgt may constrain the tertiary structure and thus the sequence of CYP51B, so other variation that increases resistance may have a selective advantage. We describe a process by which heteroallelism may be adaptive when Bgt is intermittently exposed to triazoles.

Population Genetic Structure of the Rubber Tree Powdery Mildew Pathogen (Erysiphe quercicola) from China

In order to manage agricultural pathogens, it is crucial to understand the population structure underlying epidemics. Rubber tree powdery mildew, caused by Erysiphe quercicola, is a serious threat to rubber plantations worldwide, especially in subtropical environments including all rubber tree-growing regions in China. However, the population structure of the pathogen is uncertain. In this study, 16 polymorphic microsatellite markers were used to genotype powdery mildew samples from the main rubber tree-growing regions including Yunnan (YN), Hainan (HN), western Guangdong (WG), and eastern Guangdong (EG). YN had higher genotypic diversity (Simpson's indices), genotypic evenness, Nei's gene diversity, allelic richness, and private allelic richness than the other regions. Cluster analysis, discriminant analysis of principal components, pairwise divergence, and shared multilocus genotype analyses all showed that YN differed significantly from the other regions. The genetic differentiation was small among the other three regions (HN, WG, and EG). Analysis of molecular variance indicated that the variability among regions accounted for 22.37% of the total variability. Genetic differentiation was significantly positively correlated (Rxy = 0.772, P = 0.001) with geographic distance. Linkage equilibrium analysis suggested possible occurrence of sexual recombination although asexual reproduction predominates in E. quercicola. The results suggested that although significant genetic differentiation of E. quercicola occurred between YN and the other regions, pathogen populations from the other three regions lacked genetic differentiation.

Virulence and Genetic Types of Blumeria graminis f. sp. hordei in Tibet and Surrounding Areas

Barley (Hordeum vulgare L.) is the most important cereal crop in the Qinghai-Tibet Plateau, and the yield has been seriously threatened by Blumeria graminis f. sp. hordei (Bgh) in recent years. To understand the virulence and genetic traits of different Bgh populations, 229 isolates of Bgh were collected from Tibet, Sichuan, Gansu and Yunnan provinces of China during 2020 and 2021, and their pathogenicity to 21 barley lines of different genotypes was assessed. A total of 132 virulent types were identified. The Bgh isolates from Yunnan showed the highest diversity in terms of virulence complexity (Rci) and genetic diversity (KWm), followed by those from Sichuan, Gansu, and Tibet, in that order. Single nucleotide polymorphism (SNP) in genes coding for alternative oxidase (AOX), protein kinase A (PKA), and protein phosphatase type 2A (PPA) were detected at seven polymorphic sites. Nine haplotypes (H1–H9) with an average haplotype diversity (Hd) and nucleotide diversity π of 0.564 and 0.00034, respectively, were observed. Of these, haplotypes H1 and H4 accounted for 88.8% of the isolates, and H4 was predominant in Tibet. Genetic diversity analysis using the STRUCTURE (K = 2) and AMOVE indicated that the inter-group variation accounted for 54.68%, and inter- and intra-population genotypic heterogeneity accounted for 23.90% and 21.42%, respectively. The results revealed the recent expansion of the Bgh population in Tibet, accompanied by an increase in virulence and a loss of genetic diversity.

Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade

The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization.

Sensitivity of the U.S. Wheat Powdery Mildew Population to Quinone Outside Inhibitor Fungicides and Determination of the Complete Blumeria graminis f. sp. tritici Cytochrome b Gene

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is managed primarily with cultivar resistance and foliar fungicides. Quinone outside inhibitors (QoIs), which target the mitochondrial cytochrome b (cytb) gene, are one of the two main fungicide classes used on wheat. While European populations of B. graminis f. sp. tritici are widely insensitive to QoIs, largely because of the cytb mutation G143A, the QoI sensitivity of the U.S. B. graminis f. sp. tritici population had never been evaluated despite years of QoI use on U.S. wheat. A total of 381 B. graminis f. sp. tritici isolates from 15 central and eastern U.S. states were screened for sensitivity to QoI fungicides pyraclostrobin and picoxystrobin. A modest range of sensitivities was observed, with maximum resistance factors of 11.2 for pyraclostrobin and 5.3 for picoxystrobin. The F129L, G137R, and G143A cytb mutations were not detected in the U.S. B. graminis f. sp. tritici population, nor were mutations identified in the PEWY loop, a key part of the Qo site. Thus, no genetic basis for the observed quantitative variation in QoI sensitivity of U.S. B. graminis f. sp. tritici was identified. Isolate sporulation was weakly negatively associated with reduced QoI sensitivity, suggesting a fitness cost. In the course of the study, the complete B. graminis f. sp. tritici cytb gene sequence was determined for the first time in the isolate 96224 v. 3.16 reference genome. Contrary to previous reports, the gene has an intron that appears to belong to intron group II, which is unusual in fungi. The study was the first QoI sensitivity screening of a large, geographically diverse set of U.S. B. graminis f. sp. tritici isolates, and while the population as a whole remains relatively sensitive, some quantitative loss of efficacy was observed.

Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.)

Powdery mildew is one of the most destructive diseases in the world, causing substantial grain yield losses and quality reduction in cereal crops. At present 23 powdery mildew resistance genes have been identified in rye, of which the majority are in wheat-rye translocation lines developed for wheat improvement. Here, we investigated the genetics underlying powdery mildew resistance in the Gülzow-type elite hybrid rye (Secale cereale L.) breeding germplasm. In total, 180 inbred breeding lines were genotyped using the state-of-the-art 600 K SNP array and phenotyped for infection type against three distinct field populations of B. graminis f. sp. secalis from Northern Germany (2013 and 2018) and Denmark (2020). We observed a moderate level of powdery mildew resistance in the non-restorer germplasm population, and by performing a genome-wide association study using 261,406 informative SNP markers, we identified a powdery mildew resistance locus, provisionally denoted PmNOS1, on the distal tip of chromosome arm 7RL. Using recent advances in rye genomic resources, we investigated whether nucleotide-binding leucine-rich repeat genes residing in the identified 17 Mbp block associated with PmNOS1 on recent reference genomes resembled known Pm genes.

De novo transcriptome assembly, polymorphic SSR markers development and population genetics analyses for southern corn rust (Puccinia polysora)

Southern corn rust is a destructive maize disease caused by Puccinia polysora Underw that can lead to severe yield losses. However, genomic information and microsatellite markers are currently unavailable for this disease. In this study, we generated a total of 27,295,216 high-quality cDNA sequence reads using Illumina sequencing technology. These reads were assembled into 17,496 unigenes with an average length of 1015 bp. The functional annotation indicated that 8113 (46.37%), 1933 (11.04%) and 5516 (31.52%) unigenes showed significant similarity to known proteins in the NCBI Nr, Nt and Swiss-Prot databases, respectively. In addition, 2921 (16.70%) unigenes were assigned to KEGG database categories; 4218 (24.11%), to KOG database categories; and 6,603 (37.74%), to GO database categories. Furthermore, we identified 8,798 potential SSRs among 6653 unigenes. A total of 9 polymorphic SSR markers were developed to evaluate the genetic diversity and population structure of 96 isolates collected from Guangdong Province in China. Clonal reproduction of P. polysora in Guangdong was dominant. The YJ (Yangjiang) population had the highest genotypic diversity and the greatest number of the multilocus genotypes, followed by the HY (Heyuan), HZ (Huizhou) and XY (Xinyi) populations. These results provide valuable information for the molecular genetic analysis of P. polysora and related species.

High Genetic Diversity in Predominantly Clonal Populations of the Powdery Mildew Fungus Podosphaera leucotricha from U.S. Apple Orchards

Apple powdery mildew (APM), caused by Podosphaera leucotricha, is a constant threat to apple production worldwide. Very little is known about the biology and population structure of this pathogen in the United States and other growing regions, which affects APM management. A total of 253 P. leucotricha isolates, sampled from 10 apple orchards in Washington, New York, and Virginia, were genetically characterized with novel single sequence repeat and mating type markers. Eighty-three multilocus genotypes (MLGs) were identified, most of which were unique to a given orchard. Each isolate carried either a MAT1-1 or a MAT1-2 idiomorph at the mating type locus, indicating that P. leucotricha is heterothallic. Virulence tests on detached apple leaves showed that the 10 most frequent P. leucotricha MLGs were avirulent on a line containing a major resistance gene. Analysis of molecular variance showed significant differentiation (P < 0.001) among populations, a result supported by principal coordinate analysis revealing three genetic groups, each represented by nonoverlapping MLGs from Washington, New York, and Virginia. A Bayesian cluster analysis showed genetic heterogeneity between Washington populations, and a relative migration analysis indicated substantial gene flow among neighboring orchards. Random mating tests indicated that APM epidemics during the active cycle were dominated by clonal reproduction. However, the presence of sexual structures in orchards, the likelihood that five repeated MLGs resulted from sexual reproduction, and high genotypic diversity observed in some populations suggest that sexual spores play some role in APM epidemics. IMPORTANCE Understanding the population biology and epidemiology of plant pathogens is essential to develop effective strategies for controlling plant diseases. Herein, we gathered insights into the population biology of P. leucotricha populations from conventional and organic apple orchards in the United States. We showed genetic heterogeneity between P. leucotricha populations in Washington and structure between populations from different U.S. regions, suggesting that short-distance spore dispersal plays an important role in the disease's epidemiology. We presented evidence that P. leucotricha is heterothallic and that populations likely result from a mixed (i.e., sexual and asexual) reproductive system, revealing that the sexual stage contributes to apple powdery mildew epidemics. We showed that the major resistance gene Pl-1 is valuable for apple breeding because virulent isolates have most likely not emerged yet in U.S. commercial orchards. These results will be important to achieve sustainability of disease management strategies and maintenance of plant health in apple orchards.

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

Sensitivity of the U.S. Blumeria graminis f. sp. tritici Population to Demethylation Inhibitor Fungicides

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is managed in the United States with cultivar resistance and foliar fungicides. Despite high levels of fungicide sensitivity in other cereal mildew populations, fungicide sensitivity of U.S. B. graminis f. sp. tritici has never been evaluated. Almost 400 B. graminis f. sp. tritici isolates were collected from 15 U.S. states over 2 years and phenotyped for sensitivity to two widely used demethylation inhibitor (DMI) fungicides, tebuconazole and prothioconazole. A large range of sensitivity to both DMIs was observed, with more insensitive isolates originating from the eastern United States (Great Lakes, Mid-Atlantic, and Southeast regions) and more sensitive isolates from central states (Plains region, Arkansas, and Missouri). Cross-resistance was indicated by a positive although weak association between tebuconazole and prothioconazole sensitivities at all levels of analysis (EC₅₀ values, P < 0.0001). A possible fitness cost was also associated with prothioconazole insensitivity (P = 0.0307) when analyzed at the state population level. This is the first assessment of fungicide sensitivity in the U.S. B. graminis f. sp. tritici population, and it produced evidence of regional selection for reduced DMI efficacy. The observation of reduced sensitivity to DMI fungicides in the eastern United States underlines the importance of rotating between chemistry classes to maintain the effectiveness of DMIs in U.S. wheat production. Although cross-resistance was demonstrated, variability in the relationship of EC₅₀ values for tebuconazole and prothioconazole also suggests that multiple mechanisms influence B. graminis f. sp. tritici isolate responses to these two DMI fungicides.

Evaluating the Profitability of Foliar Fungicide Programs in Mid-Atlantic Soft-Red Winter Wheat Production

In mid-Atlantic soft-red winter wheat (SRWW) production, the standard timing for a fungicide application is between flag leaf emergence (Feekes growth stage [FGS] 8) and heading (FGS 10.5). However, two-pass and anthesis (FGS 10.5.1) applications are becoming common, although these programs have not been thoroughly evaluated for disease control, yield, and profitability. Experiments were conducted in the mid-Atlantic in 2015 and 2016 to evaluate fungicide programs with applications at FGS 8, FGS 10.5.1, and two-pass programs with an early application at green-up (FGS 5) followed by (FB) applications at either FGS 8 or FGS 10.5.1. Fungicide programs that included an application at FGS 10.5.1 resulted in the highest probability of no disease on the flag leaf (0.29 to 0.40). The estimated mean yield increases ( D¯ ) relative to the nontreated check ranged from 253.65 to 634.16 kg ha^-1. Using a grain price of $0.18 kg^-1 ($5 bushel^-1), probabilities were similar between applications at FGS 8 (0.49 to 0.56) and FGS 10.5.1 (0.53). The probability of profitability ranged from 0.48 to 0.57 for FGS 5 FB FGS 8 applications and 0.52 to 0.59 for FGS 5 FB FGS 10.5.1 applications, indicating limited benefit to two-pass programs.

Virulence Differences in Blumeria graminis f. sp. tritici from the Central and Eastern United States

Wheat powdery mildew is a disease of global importance that occurs across a wide geographic area in the United States. A virulence survey of Blumeria graminis f. sp. tritici, the causal agent, was conducted by sampling 36 wheat fields in 15 U.S. states in the years 2013 and 2014. Using a hierarchical sampling protocol, isolates were derived from three separated plants at each of five separated sites within each field in order to assess the spatial distribution of pathotypes. In total, 1,017 isolates from those fields were tested individually on single-gene differential cultivars containing a total of 21 powdery mildew resistance (Pm) genes. Several recently introgressed mildew resistance genes from wild wheat relatives (Pm37, Pm53, MlAG12, NCAG13, and MlUM15) exhibited complete or nearly complete resistance to all local B. graminis f. sp. tritici populations from across the sampled area. One older gene, Pm4b, also retained at least some efficacy across the sampled area. The B. graminis f. sp. tritici population sampled from Arkansas and Missouri, on the western edge of the eastern soft red winter wheat region, had virulence profiles more similar to other soft wheat mildew populations than to the geographically closer population from hard wheat fields in the Plains states of Oklahoma, Nebraska, and Kansas. The Plains population differed in that it was avirulent to several Pm genes long defeated in the soft-wheat-growing areas. Virulence complexity was greatest east of the Mississippi River, and diminished toward the west. Several recently introgressed Pm genes (Pm25, Pm34, Pm35, and NCA6) that are highly effective against mildew in the field in North Carolina were unexpectedly susceptible to eastern-U.S. B. graminis f. sp. tritici populations in detached-leaf tests. Sampled fields displayed a wide range of pathotype diversity and spatial distribution, suggesting that epidemics are caused by varying numbers of pathotypes in all regions. The research confirmed that most long-used Pm genes are defeated in the eastern United States, and the U.S. B. graminis f. sp. tritici population has different virulence profiles in the hard- and soft-wheat regions, which are likely maintained by host selection, isolation by distance, and west-to-east gene flow.

Identification of Pm58 from Aegilops tauschii

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP™ markers were developed for MAS. Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The D-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n = 2x = DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n = 6x = AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ = 2.0, P value = 0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value < 0.01). KASP™ assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

Differentiation Among Blumeria graminis f. sp. tritici Isolates Originating from Wild Versus Domesticated Triticum Species in Israel

Israel and its vicinity constitute a center of diversity of domesticated wheat species (Triticum aestivum and T. durum) and their sympatrically growing wild relatives, including wild emmer wheat (T. dicoccoides). We investigated differentiation within the forma specialis of their obligate powdery mildew pathogen, Blumeria graminis f. sp. tritici. A total of 61 B. graminis f. sp. tritici isolates were collected from the three host species in four geographic regions of Israel. Genetic relatedness of the isolates was characterized using both virulence patterns on 38 wheat lines (including 21 resistance gene differentials) and presumptively neutral molecular markers (simple-sequence repeats and single-nucleotide polymorphisms). All isolates were virulent on at least some genotypes of all three wheat species tested. All assays divided the B. graminis f. sp. tritici collection into two distinct groups, those from domesticated hosts and those from wild emmer wheat. One-way migration was detected from the domestic wheat B. graminis f. sp. tritici population to the wild emmer B. graminis f. sp. tritici population at a rate of five to six migrants per generation. This gene flow may help explain the overlap between the distinct domestic and wild B. graminis f. sp. tritici groups. Overall, B. graminis f. sp. tritici is significantly differentiated into wild-emmer and domesticated-wheat populations, although the results do not support the existence of a separate f. sp. dicocci.