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Rhynchosporium is one of the main biotic stresses on barley production worldwide. A set of 312 spring barley accessions was tested in four different locations over 3 years, to identify novel genetic resistances to rhynchosporium and to explore the allelic diversity for resistance genes present in this global germplasm collection. High-density genotypes from exome capture and RNA-seq were used to conduct high-resolution association mapping. Seven quantitative trait loci (QTL) were detected, including one in the Rrs2 region, amongst five containing known resistances. Relatively short physical intervals harbouring these resistances were proposed, providing a platform for the identification of underlying genes and tightly linked genetic markers for use in marker assisted selection. Genes encoding kinases were present in four of the QTL, in addition to Rrs1 and Rrs18, two loci known to contribute to rhynchosporium resistance. The frequencies and distributions of these novel and known QTL were superimposed on the regional origin of the landrace genotypes comprising the genome-wide association studies (GWAS) panel, highlighting the value of genetic resources as a source of diverse genetically controlled resistance to rhynchosporium. The detected QTL along with their linked genetic markers, could be exploited either directly for breeding purposes or for candidate gene identification in future studies. [ABSTRACT FROM AUTHOR]

Barley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare) is an important crop in Turkey. In this study, 37 barley fields in Batman central district and Beşiri (Batman), Gercüş (Batman), Hasankeyf (Batman), Kozluk (Batman), Sason (Batman), Kocaköy (Diyarbakır), Kurtalan (Siirt), and Midyat (Mardin) districts were examined for the presence of leaf diseases. In addition, 24 naturally grown wild barley (H. spontaneum) populations in Batman central district and Beşiri, Hasankeyf, Kurtalan, and Midyat districts were inspected for the presence of leaf diseases. In barley fields, scald caused by Rhynchosporium commune was the most common disease, followed by the spot form of net blotch caused by Drechslera teres f. maculata, barley stripe caused by Drechslera graminea, the net form of net blotch caused by Drechslera teres f. teres, spot blotch caused by Cochliobolus sativus, powdery mildew caused by Blumeria graminis f. sp. hordei and brown rust caused by Puccinia hordei. Among the Hordeum spontaneum populations the most common disease was scald, followed by the spot form of net blotch, the net form of net blotch, powdery mildew, and brown rust. [ABSTRACT FROM AUTHOR]

Rhynchosporium is one of the main biotic stresses on barley production worldwide. A set of 312 spring barley accessions was tested in four different locations over 3 years, to identify novel genetic resistances to rhynchosporium and to explore the allelic diversity for resistance genes present in this global germplasm collection. High-density genotypes from exome capture and RNA-seq were used to conduct high-resolution association mapping. Seven quantitative trait loci (QTL) were detected, including one in the Rrs2 region, amongst five containing known resistances. Relatively short physical intervals harbouring these resistances were proposed, providing a platform for the identification of underlying genes and tightly linked genetic markers for use in marker assisted selection. Genes encoding kinases were present in four of the QTL, in addition to Rrs1 and Rrs18, two loci known to contribute to rhynchosporium resistance. The frequencies and distributions of these novel and known QTL were superimposed on the regional origin of the landrace genotypes comprising the genome-wide association studies (GWAS) panel, highlighting the value of genetic resources as a source of diverse genetically controlled resistance to rhynchosporium. The detected QTL along with their linked genetic markers, could be exploited either directly for breeding purposes or for candidate gene identification in future studies.

Spermospora avenae causes the economically important red leather leaf disease of oats, which reduces grain yield and hay quality. It was first reported in the USA in 1936 and subsequently in Australia in 1978. Despite this, its phylogenetic placement is unknown, attributed merely to Ascomycota. Twenty-three S. avenae single spore isolates were obtained from affected crops in South Australia and western Victoria from 2008 to 2016. DNA was extracted from each and sequenced using Illumina technology. To identify its closest relatives, a draft genome was de novo assembled and contigs with the highest depth, hypothesised to be the rRNA gene region, were compared to NCBI using the BLASTN function. Contigs that had homologous sequence to the rRNA gene region were used to identify closely related species, which turned out to be Rhynchosporium species. Sequence data from the α-tubulin, β-tubulin, and ITS gene regions of Rhynchosporium species, identified as phylogenetically informative for this genus, were mapped to the S. avenae contigs. Phylogenetic analysis of the ITS region and multilocus concatenation demonstrated that S. avenae is nested within Rhynchosporium, closely related to R. orthosporum and R. lolii. When ITS sequences from other related genera sourced from GenBank were added to the analysis, it appears that Rhynchosporium is paraphyletic and should be split into two genera. Culturally, S. avenae prefers a semi-solid low nutrient medium (ie. ¼ strength PDA made with 1.25% agar) and cool temperature (optimum 15 °C). This corresponds well with the cold wet seasonal conditions required for disease development in the field. [ABSTRACT FROM AUTHOR]

There are five described Rhynchosporium species, Rhynchosporium commune, R. secalis, R. agropyri, R. orthosporum and R. lolii, that cause scald diseases on Poaceae. This study used morphological (conidial shape and size) and phylogenetic analyses of two loci (the internal transcribed spacer region (ITS) and β-tubulin (TUBB)) to identify Rhynchosporium species and their host ranges in Iran. Despite the large variation observed for Rhynchosporium conidial dimensions, the phylogenetic analyses of the ITS region and concatenated ITS and TUBB loci revealed that all isolates from wild grasses in Iran belong to R. commune. R. commune was isolated from Hordeum murinum ssp. glaucum, Hordeum vulgare ssp. spontaneum, Lolium multiflorum and Avena sativa in Iran. A. sativa has only been reported from Iran as a host for R. commune. After cross inoculation, A. sativa was considered as the most resistant host showing the lowest susceptibility to R. commune isolates. Of the grass hosts tested, H. vulgare ssp. spontaneum was the most susceptible. The most aggressive isolate across all tested hosts was isolated from Hordeum murinum ssp. glaucum. Cross-infection of the R. commune isolates from all hosts onto uncultivated grasses and cultivated barley suggests the potential of the uncultivated grasses as inoculum sources for cultivated barley epidemics and pathogen evolution. Thus, management of uncultivated grasses in the vicinity of barley fields should assist in managing the disease on cultivated barley. [ABSTRACT FROM AUTHOR]

Modern cereal cultivars are highly adapted to, and normally bred and trialled under, high input, high soil disturbance conditions. On-farm conditions are often suboptimal for high yield and frequently use minimal soil tillage, sometimes no-tillage, and therefore, cultivars may be differentially adapted to such conditions. We report a series of trials across 10 years comparing multiple cultivars within years and smaller numbers across years to identify stable cultivars showing preferential adaptation to different levels of soil tillage. Cultivars responded differentially to inversion and non-inversion tillage but were not affected by the level of cultivation within each of these tillage types. Yield declined over time but much more so in the non-inversion tillage treatment. Rhynchosporium symptoms were also increasingly suppressed in the non-inversion tillage type. Several cultivars were identified that showed strong adaptation to tillage type, and some of these were consistent across several trial years. These cultivars can be used to identify traits and genotypes associated with tillage adaptation to target breeding for on-farm conditions.

Key message: Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1.Abstract: Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars. [ABSTRACT FROM AUTHOR]

Background: Systemic Epichloë endophytes are common fungal symbionts of many cool-season grasses. They are known for their capability of increasing host plant tolerance against biotic and abiotic stressors, including grass pathogens. However, results on endophyte-mediated disease resistance have been ambiguous, and the underlying mechanisms of disease resistance remain unknown. Aims: We studied how Epichloë endophytes affect naturally occurring pathogen, leaf blotch (Rhynchosporium sp.), infections of wild and cultivated tall fescues (Schedonorus phoenix). Methods: Endophytic and endophyte-free tall fescues were grown in a common garden experiment in southern Finland for eight growing seasons. The experimental plants were subjected to nutrient and water treatments. Results: Our results show that the effects of endophytes on leaf blotch infection incidences varied with plant origins and environmental conditions. Overall, the American cultivar 'Kentucky-31ʹ appeared to have less disease symptoms compared to the Finnish cultivar 'Retu' or the wild grasses. Endophytic wild tall fescues from Gotland Island had lower Rhynchosporium incidences than grasses from Åland Islands or coastal Sweden. Conclusions: These results show that Epichloë endophytes can suppress pathogen Rhynchosporium infections in tall fescues, but pathogen resistance depends on grass origin and environmental conditions. [ABSTRACT FROM AUTHOR]

Rhynchosporium commune is a destructive pathogen of barley, causing leaf scald. Previous microsatellite studies used Syria as a representative of cultivated barley's centre of origin, the Fertile Crescent. These suggested that R. commune and Hordeum vulgare (cultivated barley) did not co‐evolve in the host's centre of origin. The present study compares R. commune populations from Syria with those from Iran, which represents a secondary centre of origin for barley at the eastern edge of the Iranian Plateau. Results from this study also suggest that R. commune and barley did not co‐evolve in the centre of origin of cultivated barley. This was evidenced by the low pathogen genetic diversity in Iran, which was even lower than in Syria, indicating that the pathogen may have been introduced recently into Iran, perhaps through infected barley seed. Hierarchical analyses of molecular variance revealed that most genetic diversity in Iran and Syria is distributed within populations, with only 14% among populations. Analyses of multilocus association, genotype diversity and mating type frequency suggest that Iranian populations reproduce predominantly asexually. The presence of both mating types on barley and uncultivated grasses suggest a potential for sexual reproduction. Rhynchosporium commune was also found on Hordeum murinum subsp. glaucum, H. vulgare subsp. spontaneum, Lolium multiflorum and, for the first time, on Avena sativa. The variety of wild grasses that can be infected with R. commune in Iran raises concerns of these grasses acting as evolutionary breeding grounds and sources of inoculum. [ABSTRACT FROM AUTHOR]

Integrated Pest Management (IPM) offers a suite of ways by which to reduce the need for pesticide use, thus minimising environmental damage and pathogen resistance build-up in crop production. Farmers and agronomists active in the Scottish spring barley sector were surveyed to determine the extent to which they currently use or are open to implementing three IPM measures – varietal disease resistance, crop rotation, and forecasting disease pressure – in order to control three important fungal diseases. Overall, the survey results demonstrate that farmers and agronomists are open to using the three IPM techniques. However, gaps between actual and perceived recent practice were large: despite over 60% of farmers stating that they sowed varieties highly resistant to Rhynchosporium or Ramularia, less than one third of reportedly sown varieties were highly resistant to these diseases. Similarly, over 80% of farmers indicated that they used crop rotations, yet 66% of farmers also reported sowing consecutive barley often/always. Further research is needed in order to understand why these gaps exist, and how they can be reduced in future in order to increase IPM uptake and optimise pesticide use. [ABSTRACT FROM AUTHOR]

Pathogen-associated molecular patterns ( PAMPs) are detected by plant pattern recognition receptors ( PRRs), which gives rise to PAMP-triggered immunity ( PTI). We characterized a novel fungal PAMP, Cell Death Inducing 1 (Rc CDI1), identified in the Rhynchosporium commune transcriptome sampled at an early stage of barley ( Hordeum vulgare) infection., The ability of Rc CDI1 and its homologues from different fungal species to induce cell death in Nicotiana benthamiana was tested following agroinfiltration or infiltration of recombinant proteins produced by Pichia pastoris. Virus-induced gene silencing ( VIGS) and transient expression of Phytophthora infestans effectors Pi AVR3a and Pex RD2 were used to assess the involvement of known components of PTI in N. benthamiana responses to Rc CDI1., Rc CDI1 was highly upregulated early during barley colonization with R. commune. Rc CDI1 and its homologues from different fungal species, including Zymoseptoria tritici, Magnaporthe oryzae and Neurospora crassa, exhibited PAMP activity, inducing cell death in Solanaceae but not in other families of dicots or monocots. Rc CDI1-triggered cell death was shown to require N. benthamiana Brassinosteroid insensitive 1-Associated Kinase 1 (NbBAK1), N. benthamiana suppressor of BIR1-1 (NbSOBIR1) and N. benthamiana SGT1 (NbSGT1), but was not suppressed by Pi AVR3a or Pex RD2., We report the identification of a novel Ascomycete PAMP, Rc CDI1, recognized by Solanaceae but not by monocots, which activates cell death through a pathway that is distinct from that triggered by the oomycete PAMP INF1. [ABSTRACT FROM AUTHOR]

BACKGROUND Rhynchosporium commune is a major fungal pathogen of barley crops, and the application of fungicides, such as quinone outside inhibitors ( QoIs), plays an important role in crop disease control. The genetic mechanisms linked to QoI resistance have been identified in the cytochrome b gene, with QoI resistance conferred by the G143A substitution. The objective of this study was to develop a high-throughput molecular assay to detect and identify mutations associated with QoI resistance within the Irish R. commune population. RESULTS Leaf lesions of R. commune sampled from 74 sites during 2009-2014 and isolates from 2006 and 2007 were screened for non-synonymous mutations of the cytochrome b gene using 454 targeted sequencing. The presence of the G143A substitution was confirmed in R. commune samples at one site in 2013 and at four sites in 2014; however, the frequency of the substitution in these samples was low (2-18%). The 454 sequencing results were confirmed by PCR-RFLP and Sanger sequencing. CONCLUSION The molecular assay that has been applied to this monitoring programme has shown that the application of 454 next-generation sequencing offers the potential for high throughput and accurate characterisation of non-synonymous mutations associated with fungicide resistance in a crop pathogen. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Evolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene ( CYP51) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CYP51 mutations and the mechanisms leading to CYP51-independent resistance are poorly understood. We used whole-genome sequencing and genome-wide association studies ( GWAS) to perform an unbiased screen of azole resistance loci in Rhynchosporium commune, the causal agent of the barley scald disease. We assayed cyproconazole resistance in 120 isolates collected from nine populations worldwide. We found that mutations in highly conserved genes encoding the vacuolar cation channel YVC1, a transcription activator, and a saccharopine dehydrogenase made significant contributions to fungicide resistance. These three genes were not previously known to confer resistance in plant pathogens. However, YVC1 is involved in a conserved stress response pathway known to respond to azoles in human pathogenic fungi. We also performed GWAS to identify genetic polymorphism linked to fungal growth rates. We found that loci conferring increased fungicide resistance were negatively impacting growth rates, suggesting that fungicide resistance evolution imposed costs. Analyses of population structure showed that resistance mutations were likely introduced into local populations through gene flow. Multilocus resistance evolution to fungicides shows how pathogen populations can evolve a complex genetic architecture for an important phenotypic trait within a short time span. [ABSTRACT FROM AUTHOR]

Background: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts. Results: The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type. Conclusion: Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition. [ABSTRACT FROM AUTHOR]

Barley scald caused by Rhynchosporium commune is known as one of the most deleterious diseases on barley all over the world, especially in the Middle East including Iran. Barley genotypes screening against this disease is an efficient way to find the more tolerant pedigrees. For this purpose, a field experiment was designed at Ghamlou station in the Kurdistan province of Iran during 2013 and 2014, and reaction of twenty four lines and commercial cultivars were evaluated under natural inoculums of R. commune. Based on our results, the genotypes had different reactions compared with each other during both years of experiment. Disease severity rate in 2013 was higher than in 2014, while reactions of some genotypes showed a positive correlation. All genotypes in 2014 had higher yield than in 2013. It appears that different reaction of the genotypes during these both years was in association with meteorological fluctuations such as rainfall rate. Finding resistant or tolerant genotypes to scald disease and compatible to specific areas along with their extensive cultivation lead to obtain the most adapted and yielding cultivars. [ABSTRACT FROM AUTHOR]

Rhynchosporium commune (formerly known as Rhynchosporium secalis), the causal agent of scald disease on barley, is known to spread asexually by splash dispersed conidia. However, there are multiple lines of evidence for the possibility of a clandestine sexual cycle occurrence in this species including extensive genotypic diversity, equal distribution of mating type alleles across the world and expression of mating type genes. In the current study, the potential for the occurrence of a sexual cycle amongst the Iranian population of R. commune was assessed by analyzing distribution and frequency of the mating type alleles at both micro and macrospatial scales. A total of 95 single-conidial R. commune isolates were obtained from different barley fields in Kurdistan province. Previously designed primers were applied in a multiplex PCR assay to study distribution and frequency of the mating type alleles within and between populations. Totally, 67 isolates were determined as MAT1-1 and the remaining 28 isolates as MAT1-2 throughout the sampling counties. The results obtained at a macro-spatial scale revealed that unlike Kamyaran county (both MAT1-1 and MAT1-2 at an equal ratio), an unequal distribution of mating type genes was dominant among R. commune isolates in both Mariwan and Dehgolan counties. Our findings support a predominantly asexual reproduction for Mariwan and Dehgolan counties and the possibility of sexual stage occurrence in Kamyarna county. [ABSTRACT FROM AUTHOR]

Background: The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. Results: The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Conclusions: Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains. [ABSTRACT FROM AUTHOR]

CYP51 encodes the target site of the azole class of fungicides widely used in plant protection. Some ascomycete pathogens carry two CYP51 paralogs called CYP51A and CYP51B. A recent analysis of CYP51 sequences in 14 European isolates of the barley scald pathogen Rhynchosporium commune revealed three CYP51 paralogs, CYP51A, CYP51B, and a pseudogene called CYP51A-p. The same analysis showed that CYP51A exhibits a presence/absence polymorphism, with lower sensitivity to azole fungicides associated with the presence of a functional CYP51A. We analyzed a global collection of nearly 400 R. commune isolates to determine if these findings could be extended beyond Europe. Our results strongly support the hypothesis that CYP51A played a key role in the emergence of azole resistance globally and provide new evidence that the CYP51A gene in R. commune has further evolved, presumably in response to azole exposure. We also present evidence for recent longdistance movement of evolved CYP5IA alleles, highlighting the risk associated with movement of fungicide resistance alleles among international trading partners. [ABSTRACT FROM AUTHOR]

A family of putative PECTIN ESTERASE INHIBITOR (PEI) genes, which were detected in the genomic region co-segregating with the resistance gene Rrs2 against scald caused by Rhynchosporium commune in barley, were characterized and tested for their possible involvement in mediating resistance to the pathogen by complementation and overexpression analysis. The sequences of the respective genes were derived from two BAC contigs originating from the susceptible cultivar ‘Morex’. For the genes HvPEI2, HvPEI3, HvPEI4 and HvPEI6, specific haplotypes for 18 resistant and 23 susceptible cultivars were detected after PCR-amplification and haplotype-specific CAPS-markers were developed. None of the tested candidate genes HvPEI2, HvPEI3 and HvPEI4 alone conferred a high resistance level in transgenic over-expression plants, though an improvement of the resistance level was observed especially with OE-lines for gene HvPEI4. These results do not confirm but also do not exclude an involvement of the PEI gene family in the response to the pathogen. A candidate for the resistance gene Rrs2 could not be identified yet. It is possible that Rrs2 is a PEI gene or another type of gene which has not been detected in the susceptible cultivar ‘Morex’ or the full resistance reaction requires the presence of several PEI genes. [ABSTRACT FROM AUTHOR]

Seedling reactions of 25 advanced barley lines and 5 barley cultivars to one virulent isolate of Rhychosporium commune were determined under greenhouse conditions. Cultivar Avcı 2002 was found highly resistant and cvs Kalaycı 97 and Bülbül 89 were found susceptible. Barley cultivars Karatay 94 and Efes 3 exhibited a highly susceptible reaction to R. commune. Among the advanced lines, 9 was the most resistant genotype. Barley lines 3, 7, and 11 showed a moderately resistant reaction to the isolate. Genotypes 1, 2, 4, 6, 10, 13, 16, 18, 19, 20, 24, and 25 were susceptible and genotypes 5, 8, 12, 14, 15, 17, 21, 22, and 23 were highly susceptible to the R. commune isolate. Cultivar Avcı 2002 and advanced barley lines 3, 7, 9, and 11 could be used as resistance sources. [ABSTRACT FROM AUTHOR]

The Szum is a right-side tributary of the Tanew River crossing the southern escarpment zone of the Central Roztocze region (SE Poland). Downstream of the strict river break in a section between the 10th and 12th km of the river course in the Szum valley, meadow and peatbog complexes have developed, associated with semi-hydrogenic and marshy soils. In an area of approx. 13 ha of the most valuable non-forest habitats, a variety of plant communities have been identified, including habitats of the Natura 2000 network and habitats that are protected under the Regulation of the Minister of the Environment (2001). These are, for instance, meadow associations Lysimachio vulgaris-Filipenduletum, Lythro-Filipenduletum, Filipendulo ulmariae-Menthetum longifoliae, Angelico-Cirsietum oleracei, and Cirsietum rivularis. The moss-sedge and sphagnum bog communities comprise noteworthy associations Caricetum limosae, Rhynchosporetum albae, Caricetum lasiocarpae, Caricetum paniceo-lepidocarpae, Caricetum davallianae, and Sphagnetum magellanici. These communities are composed of ca. 160 vascular plant species and 40 moss and liverwort species. In 1999-2014, the greatest changes occurred within macroforb meadows, i.e. small Angelico-Cirsietum oleracei and Cirsietum rivularis patches have been transformed into Lysimachio vulgaris-Filipenduletum, while some patches of the latter association have been transformed into a Caricetum acutiformis rush. Several patches of bog-spring associations Caricetum paniceo-lepidocarpae and Carici canescentis-Agrostietum caninae have been irretrievably destroyed. Sphagnetum magellanici appears to be the least stable community among the preserved peatbogs. The changes of meadow and peatbog vegetation observed for the last 15 years are a consequence of natural processes that take place in the river valley and to a large extent human activity connected with the so-called small-scale water retention as well as the presence of a beaver colony in the area and later the abandonment of this area by beavers. Despite the multidirectional changes, the peatbogs of the Szum valley have retained their high species and phytocoenotic diversity, which indicates a substantial degree of naturalness. [ABSTRACT FROM AUTHOR]

The genetic basis of resistance to Rhynchosporium commune was investigated in a winter barley mapping population derived from a cross between cultivars Saffron (moderately susceptible) and Retriever (moderately resistant). Resistance was assessed in field trials through total infection (measured using qPCR), and visible disease symptoms. Phenotypic correlations between both methods of assessing disease severity were high. QTL mapping from three years of field trials identified five significant QTL effects. One QTL effect on chromosome 2H confirms a previously reported resistance from a population derived from the spring cultivar Cocktail and a winter parent derived from the cultivars Pearl and Cocktail. Another QTL effect on 3H corresponds to the reported position of major resistance gene Rrs1. An effect was detected at the mapped position of the semi-dwarfing gene sdw- 1 despite the fact that neither parent has the semi-dwarf phenotype. Of the remaining two QTL effects, one on 6H may represent a previously reported rhynchosporium resistance (QTLRrs6H), whilst the final QTL, represents a novel resistance. In addition, interactions during early infection stages in the parental lines were studied by confocal microscopy of detached leaves inoculated with a GFP-expressing R. commune isolate. This approach identified a number of major differences in fungal growth morphology between the resistant and susceptible parent. [ABSTRACT FROM AUTHOR]

Leaf blotch is a globally important disease of barley crops and other grasses that is caused by at least five host-specialized species in the fungal genus Rhynchosporium. The pathogen R. commune (specialized to barley, brome-grass and Italian ryegrass) has long been considered to reproduce only by asexual means, but there has been accumulating evidence for recombination and gene flow from population genetic studies and the detection of complementary MAT1 -1 and MAT 1-2 isolates in a c. 1:1 ratio in the field. Here, it is demonstrated that 28 isolates of the closely related species R. agropyri (on couch-grass) and R. secalis (on rye and triticale), collected from Europe, were also either of MAT 1-1 or MAT 1-2 genotype and that the distribution of mating types did not deviate significantly from a 1:1 ratio. Evidence is then provided for MAT 1-1-1 and MAT 1-2-1 gene expression during mycelial growth for all three species. By contrast, 27 isolates of the more distantly related R. orthosporum (on cocksfoot) and R. lolii (on Italian and perennial ryegrasses) from Europe were exclusively of the MAT 1-1 genotype, and expression of the MAT 1-1-1 gene could not be detected during mycelial growth. These data suggest that cryptic sexual cycles are more likely to exist for R. commune, R. agropyri and R. secalis than for either R. orthosporum or R. lolii. A phylogenetic analysis of partial MAT 1-1 idiomorph sequences resolved these five species into two distinct groups ( R. commune, R. agropyri and R. secalis versus R. orthosporum and R. lolii) but provided only limited resolution within each group. [ABSTRACT FROM AUTHOR]

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55–0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits. [ABSTRACT FROM AUTHOR]

Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51, and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R. commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B, but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by horizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation. [ABSTRACT FROM PUBLISHER]

Detailed knowledge of the evolutionary genetics of virulence is needed to understand and predict host-pathogen dynamics. This study used a virulence assay based on digital image analysis and treated virulence as a quantitative rather than a binary trait. Such quantitative data may better reflect the genetic underpinning of virulence in many pathogen systems and provide better resolution in statistical investigations. A greenhouse experiment based on a common garden design was conducted to measure virulence (% of leaf area covered by lesions) of 126 genetically distinct isolates of the barley scald pathogen, Rhynchosporium commune, originating from nine field populations around the world. Virulence in this pathosystem was found to be a quantitative trait with a continuous distribution in all populations. By comparing population genetic differentiation for virulence and neutral microsatellite markers (i.e. a QST/ GST comparison), evidence that virulence is under stabilizing selection across populations was found. Heritability values were high and ranged from 0·52 to 0·96 with a mean heritability of 0·84. Virulence was positively correlated with spore production as predicted by the trade-off theory of virulence evolution. Furthermore, an association analysis between virulence and sequence haplotypes of three known necrosis-inducing effector genes ( NIP1, NIP2 and NIP3) revealed a significant effect of NIP2 haplotypes and NIP1 deletions. Overall, the results support a quantitative model for virulence in the R. commune-barley pathosystem and very high evolutionary potential for this trait. [ABSTRACT FROM AUTHOR]

Highlights: [•] We report the complete mitochondrial genomes of four closely related fungal species. [•] Three mitochondrial genomes significantly expanded as result of intron invasion. [•] The mitochondrial mutation rate was 77 times higher than the nuclear mutation rate. [•] Our study revealed a very dynamic mitochondrial genome evolution. [Copyright &y& Elsevier]

The fungal genus Rhynchosporium (causative agent of leaf blotch) contains several host-specialised species, including R. commune (colonising barley and brome-grass), R. agropyri (couch-grass), R. secalis (rye and triticale) and the more distantly related R. orthosporum (cocksfoot). This study used molecular fingerprinting, multilocus DNA sequence data, conidial morphology, host range tests and scanning electron microscopy to investigate the relationship between Rhynchosporium species on ryegrasses, both economically important forage grasses and common wild grasses in many cereal growing areas, and other plant species. Two different types of Rhynchosporium were found on ryegrasses in the UK. Firstly, there were isolates of R. commune that were pathogenic to both barley and Italian ryegrass. Secondly, there were isolates of a new species, here named R. lolii, that were pathogenic only to ryegrass species. R. lolii was most closely related to R. orthosporum, but exhibited clear molecular, morphological and host range differences. The species was estimated to have diverged from R. orthosporum ca. 5735 years before the present. The colonisation strategy of all of the different Rhynchosporium species involved extensive hyphal growth in the sub-cuticular regions of the leaves. Finally, new species-specific PCR diagnostic tests were developed that could distinguish between these five closely related Rhynchosporium species. [ABSTRACT FROM AUTHOR]

Diseases of rye (Secale cereale), an important crop in Latvia, might be a risk factor for rye production. The aim of the study was to determine features of rye leaf diseases, to estimate the risk of rye diseases under conditions of Latvia, and to compare various schemes of fungicide treatment that possibly might be useful for integrated disease control. Field trials were carried out from 2009 to 2012 in two locations in Latvia -- State Stende Cereals Breeding Institute and State Priekuļi Plant Breeding Institute. Sixteen trials (two cultivars each year, two sites, and four years) were established during the investigations. Each trial was one-factor design with three variants of fungicide treatment: control (without fungicides), standard treatment during heading (GS 51-55), and DSS (Decision support system). Leaf scald caused by Rhynchosporium secalis and brown rust, caused by Puccinia recondita, were found to be the most important rye diseases during the study. Average additional yield achieved by fungicide application was 8%. Number of rainy days (more than seven, starting from GS 31) was not a sufficient threshold for the control of rye diseases. It was necessary to make assessment of the disease development in the the field. Fungicide application might be necessary if symptoms of leaf scald appear on the youngest leaves after beginning of stem elongation (GS 31-32). [ABSTRACT FROM AUTHOR]