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

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt across two consecutive years, 2022 and 2023, and compiled a genomic dataset of 415 Bgt isolates from 22 countries in Europe and surrounding regions. We identified a single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies

Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering.

Genome-wide Evidence of Host Specialization in Wild and Farmland Populations of the Fungal Leaf Spot Pathogen, Cercospora beticola

One of the most recent crop species to be domesticated is sugar beet (Beta vulgaris L. ssp. vulgaris Doell.), which was bred for high sucrose content within the last few centuries in Europe. Crop domestication can also lead to the evolution of novel pathogens, which may spread across large geographical distances with their crop host. In this study, we addressed the recent evolution of the fungal pathogen causing the disease Cercospora leaf spot, Cercospora beticola. This pathogen has become increasingly important in sugar beet and table beet production worldwide. We used genome sequences of 326 C. beticola isolates collected from 4 continents from 4 closely related Beta subspecies (3 domesticated and 1 wild). We applied population genomic analyses to identify signatures of population differentiation and host specialization in C. beticola populations derived from the cultivated and wild hosts. We found evidence that C. beticola populations in agro-ecosystems likely originate from sea beet-infecting isolates. Intriguingly, host jumps from wild to cultivated beet occurred in at least 2 independent events as evidenced by our population data of C. beticola from wild beet collected in the Mediterranean and the UK. We explore the occurrence of genetic variants associated with fungicide resistance and virulence and show that standing genetic variation in C. beticola populations from both wild and domesticated plants may serve as a reservoir of functionally important alleles. Overall, our results highlight the ability of C. beticola to invade the agro-ecosystem and establish new populations, demonstrating the rapid adaptation potential of the species.

An emerging fungal disease is spreading across the globe and affecting the blueberry industry

Powdery mildew is an economically important disease caused by c. 1000 different fungal species. Erysiphe vaccinii is an emerging powdery mildew species that is impacting the blueberry industry. Once confined to North America, E. vaccinii is now spreading rapidly across major blueberry-growing regions, including China, Morocco, Mexico, and the USA, threatening millions in losses. This study documents its recent global spread by analyzing both herbarium specimens, some over 150-yr-old, and fresh samples collected world-wide. Our findings were integrated into a 'living phylogeny' via T-BAS to simplify pathogen identification and enable rapid responses to new outbreaks. We identified 50 haplotypes, two primary introductions world-wide, and revealed a shift from a generalist to a specialist pathogen. This research provides insights into the complexities of host specialization and highlights the need to address this emerging global threat to blueberry production.

Population genomics of Marchantia polymorpha subsp. ruderalis reveals evidence of climate adaptation

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.

Migration of wheat stripe rust from the primary oversummering region to neighboring regions in China

Changing climate and changes in cropping systems have greatly affected outbreaks of plant diseases. Wheat stripe rust is a disease posing a threat to global wheat production, caused by Puccinia striiformis f. sp. tritici (Pst). Pst oversummering regions play a crucial role in the emergence of new races in China. To unveil the migration pattern of oversummering to adjacent regions, we develop a set of KASP-SNP marker from 28 Pst whole-genome sequences to investigate the population structure in the oversummering and its adjacent regions. A set of 19 Chinese wheat differentials is used to characterize the virulence patterns of 308 sampled Pst isolates. By integrating virulence characterization, population genetic analysis, air trajectory simulation and field disease monitoring, two main Pst dispersal routes are identified. Inocula from Eastern Qinghai are dispersed to Western and Eastern Liupan Mountain, and reach Guanzhong Plain. The second route originates from Middle Gansu, then through Longnan, and reaches the Guanzhong Plain via Eastern Liupan Mountain. Both dispersal routes result in Pst inoculum spreading to the Huang-Huai-Hai region, the main wheat-growing region in China. The proposed migration routes can be used to develop disease management strategies at a regional and national scale.

Technical Advances Drive the Molecular Understanding of Effectors from Wheat and Barley Powdery Mildew Fungi

Pathogens manipulate host physiology through the secretion of virulence factors (effectors) to invade and proliferate on the host. The molecular functions of effectors inside plant hosts have been of interest in the field of molecular plant-microbe interactions. Obligate biotrophic pathogens, such as rusts and powdery mildews, cannot proliferate outside of plant hosts. In addition to the inhibition of the plant's immune components, these pathogens are under particular pressure to extract nutrients efficiently from the host. Understanding the molecular basis of infections mediated by obligate biotrophic pathogens is significant because of their impact in modern agriculture. In addition, powdery mildews serve as excellent models for obligate biotrophic cereal pathogens. Here, we summarize the current knowledge on the effectorome of the barley and wheat powdery mildews and putative molecular virulence functions of effectors. We emphasize the availability of comprehensive genomic, transcriptomic, and proteomic resources and discuss the methodological approaches used for identifying candidate effectors, assessing effector virulence traits, and identifying effector targets in the host. We highlight established and more recently employed methodologies, discuss limitations, and suggest additional strategies. We identify open questions and discuss how addressing them with currently available resources will enhance our understanding of Blumeria candidates for secretor effector proteins. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Long-distance gene flow and recombination shape the evolutionary history of a maize pathogen

The evolutionary history of crop pathogens is shaped by a complex interaction of natural and anthropogenic factors. The fungus Colletotrichumgraminicola causes maize anthracnose which results in significant yield losses worldwide. We conducted a comprehensive investigation into the evolutionary genomics of C.graminicola using a collection of 212 isolates from 17 countries across five continents. Genomic analyses supported the existence of three geographically isolated genetic lineages, with a significant pattern of isolation by distance. We identified two distinct gene flow patterns, driven by short- and long-distance dispersal, likely resulting from the natural spread of the pathogen and the exchange of contaminated seeds. We present evidence of genetic introgression between lineages, suggesting a long history of recombination. We identified significant recombination events coalescing at distinct points in time, with the North American lineage displaying evidence of the most ancient recombination. Demographic modelling has indicated that North America is an intermediate between Brazil, Europe and an ancestral, unsampled source population, which is hypothesised to be Mesoamerican. Our analyses revealed that the global genomic structure of C.graminicola is shaped by geographic differentiation driven by long-distance migration and a long history of recombination and introgression. We show historical relationships amongst these lineages, identifying a potential route for fungal spread, with the North American population emerging ancestrally, followed sequentially by the Brazilian and European populations. Our research indicates that the European lineage is more virulent, which has implications for the potential emergence of new outbreaks of maize anthracnose in Europe.

Fungal impacts on Earth's ecosystems

Over the past billion years, the fungal kingdom has diversified to more than two million species, with over 95% still undescribed. Beyond the well-known macroscopic mushrooms and microscopic yeast, fungi are heterotrophs that feed on almost any organic carbon, recycling nutrients through the decay of dead plants and animals and sequestering carbon into Earth's ecosystems. Human-directed applications of fungi extend from leavened bread, alcoholic beverages and biofuels to pharmaceuticals, including antibiotics and psychoactive compounds. Conversely, fungal infections pose risks to ecosystems ranging from crops to wildlife to humans; these risks are driven, in part, by human and animal movement, and might be accelerating with climate change. Genomic surveys are expanding our knowledge of the true biodiversity of the fungal kingdom, and genome-editing tools make it possible to imagine harnessing these organisms to fuel the bioeconomy. Here, we examine the fungal threats facing civilization and investigate opportunities to use fungi to combat these threats.

NUBP2 deficiency disrupts the centrosome-check point in the brain and causes primary microcephaly

Microcephaly affects 1 in 2,500 babies per year. Primary microcephaly results from aberrant neurogenesis leading to a small brain at birth. This is due to altered patterns of proliferation and/or early differentiation of neurons. Premature differentiation of neurons is associated with defects in the centrosome and/or primary cilia. In this study, we report on the first patients identified with NUBP2 -deficiency and utilize a conditional mouse model to ascertain the molecular mechanisms associated with NUBP2 -deficient primary microcephaly. We identified homozygous NUBP2 variants in these patients who displayed profound primary microcephaly in addition to intrauterine growth restriction, cervical kyphosis, severe contractures of joints, and facial dysmorphia. We then generated a mouse model using Emx1-Cre to ablate Nubp2 from the forebrain. The mice presented with severe microcephaly starting at E18.5. Neurospheres generated from the forebrain of Emx1-Cre; Nubp2 flox/flox conditional deletion mice were used to support the pathogenicity of the patient variants. We show that loss of Nubp2 increases both canonical and non-canonical cell death, but that loss of p53 fails to rescue microcephaly in the mouse model. Examination of neurogenesis in Emx1-Cre; Nubp2 flox/flox mice revealed distinct alterations in proliferation and cellular migration accompanied by supernumerary centrosomes and cilia. We therefore propose that NUBP2 is a novel primary microcephaly-related gene and that the role of Nubp2 in centrosome and cilia regulation is crucial for proper neurogenesis.

Virulence, Structure, and Triadimefon Sensitivity of the Puccinia striiformis f. sp. tritici Population in Shaanxi Province, China

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is the most destructive fungal disease affecting wheat in China, especially in Shaanxi Province, an important epidemiological region connecting the western Pst oversummer regions and the central and eastern spring epidemic regions in the country. In the present study, 291 Pst isolates from Shaanxi Province were studied for their virulence using two sets of wheat differentials, population structure using single-nucleotide polymorphism (SNP) markers, and sensitivity to triadimefon. When the isolates were tested on the Chinese differentials of 19 wheat cultivars, 72 races were identified, which belonged to three groups, including the Guinong 22 group (48.45%), Hybrid 46 group (31.62%), and Suwon 11 group (19.93%). The three most predominant races were CYR34 (15.46%), G22-14 (11.68%), and CYR32 (10.65%). When the isolates were tested on the 18 Yr single-gene differentials, 95 races were identified, but none of the isolates were virulent to either Yr5 or Yr15. Cluster analyses of the virulence data based on the two sets of differentials and the SNP marker data consistently separated the Shaanxi Pst population into two clusters in the central part and southern part of the province. Triadimefon sensitivity testing across different concentrations showed a broad range of half-maximal effective concentration (EC50) values, from 0.03 to 5.99 μg ml-1, with a mean EC50 value of 0.46 μg ml-1. The majority of isolates (90.72%) were sensitive to the fungicide. The correlation analyses of the virulence, SNP marker, and the triadimefon sensitivity data showed no significant correlations, except a logarithmic relationship between the EC50 value and the number of avirulence factors. This study is the first to determine the relationship of virulence and SNP markers with triadimefon sensitivity in a regional Pst population. The findings provide valuable insights for breeding resistant wheat cultivars and integrated management of stripe rust.

Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew

Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt). Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. While R gene cloning has accelerated recently, AVR identification in many pathogens including Bgt lags behind, preventing pathogen-informed deployment of resistance sources. Here we describe a new "avirulence depletion (AD) assay" for rapid identification of AVR genes in Bgt. This assay relies on the selection of a segregating, haploid F1 progeny population on a resistant host, followed by bulk sequencing, thereby allowing rapid avirulence candidate gene identification with high mapping resolution. In a proof-of-concept experiment we mapped the AVR component of the wheat immune receptor Pm3a to a 25 kb genomic interval in Bgt harboring a single effector, the previously described AvrPm3a2/f2. Subsequently, we applied the AD assay to map the unknown AVR effector recognized by the Pm60 immune receptor. We show that AvrPm60 is encoded by three tandemly arrayed, nearly identical effector genes that trigger an immune response upon co-expression with Pm60 and its alleles Pm60a and Pm60b. We furthermore provide evidence that Pm60 outperforms Pm60a and Pm60b through more efficient recognition of AvrPm60 effectors, suggesting it should be prioritized for wheat breeding. Finally, we show that virulence towards Pm60 is caused by simultaneous deletion of all AvrPm60 gene paralogs and that isolates lacking AvrPm60 are especially prevalent in the US thereby limiting the potential of Pm60 in this region. The AD assay is a powerful new tool for rapid and inexpensive AVR identification in Bgt with the potential to contribute to pathogen-informed breeding decisions for the use of novel R genes and regionally tailored gene deployment.

First Reported Sexual Recombination Between Pyrenophora teres Isolates from Barley and Barley Grass

Barley grass (Hordeum leporinum), which often occurs in proximity to commercial barley (H. vulgare) cultivars, is an alternative host to Pyrenophora teres, an economically important pathogen causing net blotch in barley. This study is the first to report the sexual recombination of P. teres isolates collected from barley with those collected from barley grass. The sexual recombination between P. teres isolates from barley and barley grass was confirmed using a neighbor-net network and haploblock plots based on whole-genome sequencing of seven progeny isolates. Pathogenicity assays revealed that P. teres isolates from barley grass were not host specific and could infect both barley and barley grass, and the progeny isolates were virulent on commercially grown barley cultivars. Our results contradict previous population and pathogenicity studies of P. teres isolates obtained from barley and barley grass that have reported that the two populations are genetically distinct and host specific, suggesting that isolates collected from barley or barley grass could be two different entities. Despite the genetic divergence of P. teres isolates from barley and barley grass revealed through our phylogenomic analysis, there seems to be no complete host or reproductive separation between these populations. Therefore, there is a potential for generation of novel pathotypes through sexual recombination between P. teres isolates associated with barley and barley grass, with a risk of increased impacts on commercial barley cultivars that do not carry resistance to these pathotypes.

Identification and Biocontrol of Cladosporium Mold Caused by Cladosporium cladosporioides on Wheat Spikes in Central China

Wheat (Triticum aestivum L.) is one of the most agriculturally and economically important crops in the world. Wheat fungal diseases are becoming more severe and frequent due to global climate change, threatening wheat yields and security. While fungal diseases such as fusarium head blight, stripe rust, and powdery mildew have been extensively studied, the newly emerged fungal pathogens in wheat are still under-researched. In May 2023, black mold symptoms were observed on wheat spikes in Xinxiang City, Henan Province, China. However, the causal agent of this disease was not known. We employed a combination of morphological examination and molecular techniques to identify the pathogen. The internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (tef1), and actin (act) genes of the fungus were partially sequenced (accession no. OR186209, PQ271633 and PQ271632) and showed 99.59–100% identity with the previously reported Cladosporium cladosporioides, which affects wheat, pokeweed, and black-eyed pea. The pathogenicity of this fungus was confirmed by fulfilling Koch’s postulates. Through a rigorous screening process, we found Simplicillium aogashimaense, Trichothecium roseum, and Bacillus velezensis as effective biocontrol agents, with B. velezensis demonstrating the most potent antagonistic activity against the Cladosporium mold. This discovery showed the potential of B. velezensis as a biocontrol agent for wheat disease management. The findings underscore the importance of the present study in advancing the control of this disease.

Biocontrol Potential of Cladosporium sphaerospermum Against the Wheat Powdery Mildew Fungus Blumeria graminis f. sp. tritici

Cladosporium spp. are known to be mycoparasites and inhibit phytopathogenic fungi. However, so far, little information is available on the impact of Cladosporium spp. on powdery mildews. Based on the morphological characteristics and molecular analysis, C. sphaerospermum was identified as a mycoparasite on the wheat powdery mildew fungus Blumeria graminis f. sp. tritici (Bgt), recently named B. graminis s. str. C. sphaerospermum was capable of preventing colony formation and conidial distribution of Bgt. The biomasses of Bgt notably decreased by 1.3, 2.2, 3.6, and 3.8 times at 2, 4, 6, and 8 days postinoculation (dpi), respectively. In addition, biomasses of C. sphaerospermum at 2, 4, 6, and 8 dpi significantly increased to 5.6, 13.9, 18.2, and 67.3 times, respectively. In vitro, C. sphaerospermum exudates significantly impaired appressorial formation of Bgt. Thus, C. sphaerospermum acts as a potential biological control agent by suppressing the formation, distribution, and development of Bgt conidia and is a viable alternative for managing the wheat powdery mildew. These results suggest that C. sphaerospermum is an antagonistic parasite of the wheat powdery mildew fungus and, hence, provide new knowledge about the biological control of phytopathogenic fungi.

Analysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination

KEY MESSAGE

This study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat. Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such "alien" introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.

Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration

Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To understand the impact of human migration and changes in agricultural practices on crop pathogens, here population genomic analysis with 245 representative strains from a collection of 4,427 field isolates of Fusarium asiaticum, the causal agent of FHB in Southern China is conducted. Three populations with distinct evolution trajectories are identifies over the last 10,000 years that can be correlated with historically documented changes in agricultural practices due to human migration caused by the Southern Expeditions during the Jin Dynasty. The gradual decrease of 3ADON-producing isolates from north to south along with the population structure and spore dispersal patterns shows the long-distance (>250 km) dispersal of F. asiaticum. These insights into population dynamics and evolutionary history of FHB pathogens are corroborated by a genome-wide analysis with strains originating from Japan, South America, and the USA, confirming the adaptation of FHB pathogens to cropping systems and human migration.

A kinase fusion protein from Aegilops longissima confers resistance to wheat powdery mildew

Many disease resistance genes have been introgressed into wheat from its wild relatives. However, reduced recombination within the introgressed segments hinders the cloning of the introgressed genes. Here, we have cloned the powdery mildew resistance gene Pm13, which is introgressed into wheat from Aegilops longissima, using a method that combines physical mapping with radiation-induced chromosomal aberrations and transcriptome sequencing analysis of ethyl methanesulfonate (EMS)-induced loss-of-function mutants. Pm13 encodes a kinase fusion protein, designated MLKL-K, with an N-terminal domain of mixed lineage kinase domain-like protein (MLKL_NTD domain) and a C-terminal serine/threonine kinase domain bridged by a brace. The resistance function of Pm13 is validated through transient and stable transgenic complementation assays. Transient over-expression analyses in Nicotiana benthamiana leaves and wheat protoplasts reveal that the fragment Brace-Kinase122-476 of MLKL-K is capable of inducing cell death, which is dependent on a functional kinase domain and the three α-helices in the brace region close to the N-terminus of the kinase domain.

Global Spread, Genetic Differentiation, and Selection of Barley Spot Form Net Blotch Isolates

Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen

Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

KEY MESSAGE

A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

Mutagenesis of Wheat Powdery Mildew Reveals a Single Gene Controlling Both NLR and Tandem Kinase-Mediated Immunity

Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal wheat pathogen. Some wheat genotypes contain powdery mildew resistance (Pm) genes encoding immune receptors that recognize specific fungal-secreted effector proteins, defined as avirulence (Avr) factors. Identifying Avr factors is vital for understanding the mechanisms, functioning, and durability of wheat resistance. Here, we present AvrXpose, an approach to identify Avr genes in Bgt by generating gain-of-virulence mutants on Pm genes. We first identified six Bgt mutants with gain of virulence on Pm3b and Pm3c. They all had point mutations, deletions or insertions of transposable elements within the corresponding AvrPm3b2/c2 gene or its promoter region. We further selected six mutants on Pm3a, aiming to identify the yet unknown AvrPm3a3 recognized by Pm3a, in addition to the previously described AvrPm3a2/f2. Surprisingly, Pm3a virulence in the obtained mutants was always accompanied by an additional gain of virulence on the unrelated tandem kinase resistance gene WTK4. No virulence toward 11 additional R genes tested was observed, indicating that the gain of virulence was specific for Pm3a and WTK4. Several independently obtained Pm3a-WTK4 mutants have mutations in Bgt-646, a gene encoding a putative, nonsecreted ankyrin repeat-containing protein. Gene expression analysis suggests that Bgt-646 regulates a subset of effector genes. We conclude that Bgt-646 is a common factor required for avirulence on both a specific nucleotide-binding leucine-rich repeat and a WTK immune receptor. Our findings suggest that, beyond effectors, another type of pathogen protein can control the race-specific interaction between powdery mildew and wheat. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Emergence and spread of the barley net blotch pathogen coincided with crop domestication and cultivation history

Fungal pathogens cause devastating disease in crops. Understanding the evolutionary origin of pathogens is essential to the prediction of future disease emergence and the potential of pathogens to disperse. The fungus Pyrenophora teres f. teres causes net form net blotch (NFNB), an economically significant disease of barley. In this study, we have used 104 P. teres f. teres genomes from four continents to explore the population structure and demographic history of the fungal pathogen. We showed that P. teres f. teres is structured into populations that tend to be geographically restricted to different regions. Using Multiple Sequentially Markovian Coalescent and machine learning approaches we demonstrated that the demographic history of the pathogen correlates with the history of barley, highlighting the importance of human migration and trade in spreading the pathogen. Exploring signatures of natural selection, we identified several population-specific selective sweeps that colocalized with genomic regions enriched in putative virulence genes, and loci previously identified as determinants of virulence specificities by quantitative trait locus analyses. This reflects rapid adaptation to local hosts and environmental conditions of P. teres f. teres as it spread with barley. Our research highlights how human activities can contribute to the spread of pathogens that significantly impact the productivity of field crops.

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.

Identification of a Novel Pm65 Allele Conferring a Wide Spectrum of Resistance to Powdery Mildew in Wheat Accession PI 351817

Powdery mildew is caused by the highly adaptive biotrophic fungus Blumeria graminis f. sp. tritici infecting wheat worldwide. Novel powdery mildew resistance genes are urgently needed that can be used rapidly in wheat cultivar development with minimal disruption of trait advances elsewhere. PI 351817 is a German cultivar exhibiting a wide spectrum of resistance to B. graminis f. sp. tritici isolates collected from different wheat-growing regions of the United States. Evaluation of an F2 population and 237 F2:3 lines derived from OK1059060-2C14 × PI 351817 for responses to B. graminis f. sp. tritici isolate OKS(14)-B-3-1 identified a single dominant gene, designated Pm351817, for powdery mildew resistance in PI 351817. Using bulked segregant analysis (BSA) and simple sequence repeat (SSR) markers, Pm351817 was mapped in the terminal region of the long arm of chromosome 2A. Deep sequencing of the genotyping-by-sequencing libraries of the two parental lines identified a set of single-nucleotide polymorphism (SNP) markers in the 2AL candidate gene region. Those SNP markers was subsequently converted to Kompetitive allele-specific PCR (KASP) markers for genotyping the mapping population. Linkage analysis delimited Pm351817 to a 634-kb interval between Stars-KASP656 (771,207,512 bp) and Stars-KASP662 (771,841,609 bp) on 2AL, based on the Chinese Spring reference sequence IWGSC RefSeq v 2.1. Tests of allelism indicated that Pm351817 is located at the Pm65 locus. Pm351817 shows resistance to all B. graminis f. sp. tritici isolates used in this study and can be used to enhance powdery mildew resistance in the United States. KASP markers flanking Pm351817 can be used to select Pm351817 in wheat breeding programs after further tests for polymorphism.

Wheat powdery mildew resistance: from gene identification to immunity deployment

Powdery mildew is one of the most devastating diseases on wheat and is caused by the obligate biotrophic phytopathogen Blumeria graminis f. sp. tritici (Bgt). Due to the complexity of the large genome of wheat and its close relatives, the identification of powdery mildew resistance genes had been hampered for a long time until recent progress in large-scale sequencing, genomics, and rapid gene isolation techniques. Here, we describe and summarize the current advances in wheat powdery mildew resistance, emphasizing the most recent discoveries about the identification of genes conferring powdery mildew resistance and the similarity, diversity and molecular function of those genes. Multilayered resistance to powdery mildew in wheat could be used for counteracting Bgt, including durable, broad spectrum but partial resistance, as well as race-specific and mostly complete resistance mediated by nucleotide-binding and leucine rich repeat domain (NLR) proteins. In addition to the above mentioned layers, manipulation of susceptibility (S) and negative regulator genes may represent another layer that can be used for durable and broad-spectrum resistance in wheat. We propose that it is promising to develop effective and durable strategies to combat powdery mildew in wheat by simultaneous deployment of multilayered immunity.

Hybridisation has shaped a recent radiation of grass-feeding aphids

BACKGROUND

Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called "super clones" have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals-the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids.

RESULTS

Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression.

CONCLUSIONS

Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born "frozen hybrids" via asexual reproduction, increasing the likelihood of hybrid lineage formation.

Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a

Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal pathogen of wheat that can rapidly evolve to defeat wheat powdery mildew (Pm) resistance genes. Despite periodic regional deployment of the Pm1a resistance gene in US wheat production, Bgt strains that overcome Pm1a have been notably nonpersistent in the United States, while on other continents, they are more widely established. A genome-wide association study (GWAS) was conducted to map sequence variants associated with Pm1a virulence in 216 Bgt isolates from six countries, including the United States. A virulence variant apparently unique to Bgt isolates from the United States was detected in the previously mapped gene AvrPm1a (BgtE-5612) on Bgt chromosome 6; an in vitro growth assay suggested no fitness reduction associated with this variant. A gene on Bgt chromosome 8, Bgt-51526, was shown to function as a second determinant of Pm1a virulence, and despite < 30% amino acid identity, BGT-51526 and BGTE-5612 were predicted to share > 85% of their secondary structure. A co-expression study in Nicotiana benthamiana showed that BGTE-5612 and BGT-51526 each produce a PM1A-dependent hypersensitive response. More than one member of a B. graminis effector family can be recognized by a single wheat immune receptor, and a two-gene model is necessary to explain virulence to Pm1a.

A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.

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.

The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen

BACKGROUND

Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, wheat breeding for disease resistance heavily relied on the introgression of chromosomal segments from related species as genetic sources of new resistance. The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation encompassing multiple disease resistance genes and yield components. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome by the powdery mildew pathogen. The long-term use of Pm8 at a global scale provided the unique opportunity to study the consequences of such extensive resistance gene application on pathogen evolution.

RESULTS

Using genome-wide association studies in a population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8. Haplovariant mining in a global mildew population covering all major wheat growing areas of the world revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two functional categories. The first one comprised amino acid polymorphisms at a single position along the AvrPm8 protein, which we confirmed to be crucial for the recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use.

CONCLUSIONS

In this study, we show that the broad and prolonged use of the Pm8 gene in wheat production worldwide resulted in a multitude of gain-of-virulence mechanisms affecting the AvrPm8 gene in the wheat powdery mildew pathogen. Based on our findings, we conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression.

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

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