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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]

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]

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]

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]

Mycochaetophora gentianae, the causal agent of brown leaf spot on gentian ( Gentiana scabra), is characterized by its hyaline besom-like sporophore, although its conidiogenesis and phylogenetic position have so far remained unknown. We isolated the causal fungus from a new host, G. triflora, in Iwate, Japan. Both the G. triflora isolate and the ex-type M. gentianae isolate produced symptoms on G. triflora but not on G. scabra. Microscopic observations of the diseased leaves indicated that conidiogenesis was blastic from short conidiophores, and schizolytic secession of conidia left unthickened and inconspicuous conidial scars on the conidiogenous cells. Conidia were catenate, in branched acropetalous chains; secondary conidia were blastically produced from the first or second cell at the base of primary conidium. The G. triflora isolate was identified as M. gentianae because of its identity to the ex-type in characteristics of culture, pathogenicity, and conidia. Phylogenetic analyses using three ribosomal DNA (rDNA) sequences combined [small subunit (SSU) + large subunit (LSU) + 5.8S rDNA] indicated that both isolates clustered with Rhexocercosporidium carotae, and the cluster was placed within Helotiales–Rhytismatales. Additional analyses using internal transcribed spacers including 5.8S rDNA sequences revealed that both isolates were monophyletic and that they were closely related to three helotialean Pseudocercosporella-like hyphomycetous genera: Helgardia, Rhexocercosporidium and Rhynchosporium. [ABSTRACT FROM AUTHOR]

The study of population genetics attempts to investigate evolutionary forces such as mutation, migration, genetic drift, selection and recombination, and how gene frequencies change in populations to shape their genetic structure. These evolutionary forces and the interaction among them are particularly important in plant pathogens where, combined with the pathogen's life history characteristics, they determine the pathogen's evolutionary potential. Advances in DNA sequencing and analytical approaches have significantly improved the accuracy of population genetic parameter estimates. In particular, coalescent-based approaches are a powerful extension of classical population genetics because it is a collection of mathematical models that can accommodate biological phenomena as reflected in molecular data. In a comparison of migration estimates of Rhynchosporium secalis, which were either derived from FSTestimates, or estimated with a coalescent method, reveals that the latter are more reliable, are less dependent on population sizes being stable, are not affected by asymmetrical migration between populations, and are affected less by populations with small sample sizes. Improved analyses and their usefulness in determining the phylogeography and demography of R. secalisare discussed. [ABSTRACT FROM AUTHOR]

Surveys of incidence and severity of foliar diseases in a total of 127 barley (Hordeum vulgare) crops throughout Victoria were carried out during 2007 and 2008. In each crop, 100 tillers were assessed for disease symptoms on the top four leaves. Spot form of net blotch caused by Pyrenophora teresf. maculatahad the highest incidence, being present in more than 90% of crops surveyed, with severity ranging from 0 to 42%. Scald caused by Rhynchosporium secalishad the second highest incidence, being found in 13 and 23% of crops in 2007 and 2008, respectively, with severity ranging from 0 to 16%. Leaf rust caused by Puccinia hordeiwas present in 13 and 18% of crops in 2007 and 2008, respectively, with severity of up to 3%. Powdery mildew caused by Erysiphe graminiswas present in 11 and 9% of crops in 2007 and 2008, respectively, with severity below 0.1%. No other diseases, such as the net form of net blotch caused by P. teresf. tereswere detected. The high incidence of spot form of net blotch, which can cause up to 44% grain yield loss, suggests that resistance traits need to be made a priority and targeted by barley breeding programs in Victoria for control of this important disease. [ABSTRACT FROM AUTHOR]

Two barley populations, i.e. 135 doubled haploid (DH) lines of the cross ‘Igri’ ( rrs1) × ‘Triton’ ( Rrs1) (I × T) and 76 DH lines of the cross ‘Post’ × ‘Vixen’ (both rrs1) (P × V), were analysed to identify QTL for Rhynchosporium secalis resistance independent of the Rrs1 locus by using the single spore R. secalis isolate 271 ( Rrs1-virulent). A major QTL with its positive allele derived from cv. ‘Triton’ was detected in the I × T population on chromosome 2HS explaining almost 80% of the phenotypic variance. Thus, it can be considered as an R-gene corresponding to the already described Rrs15CI8288 on chromosome 2HS. In addition, two minor QTL were identified, one in the centromeric region of 6H in a highly polymorphic region with already several mapped R-genes and a second one at the end of the short arm of chromosome 7H which may be an allele of Rrs2 because of its chromosomal position. Regarding the DH population P × V different minor QTL were identified on chromosomes 6H and 7H. The first one is corresponding to the genomic region of the Rrs13 gene whereas the QTL on chromosome 7H maps in a genomic region where several R-genes against different pathogens have been localized. A comparison of both QTL analyses reveals no R. secalis isolate 271-specific resistance locus but leads to the hypothesis that two of the identified QTL may be alleles of the R-genes Rrs15CI8288 and Rrs2. [ABSTRACT FROM AUTHOR]

A partial genetic linkage map was constructed on 71 doubled-haploid lines derived from a cross between the barley lines Tadmor and WI2291 with 181 molecular markers. The segregating population was used to detect markers linked to the geneMlg conferring resistance to powdery mildew (Erysiphe graminis f. sp. hordei) and to genes for quantitative resistance to scald (Rhynchosporium secalis). The gene Mlg on chromosome 4H was flanked by two AFLP markers at a distance of 2.0 and 2.4 cM, respectively. QTLs for resistance to scald were detected on chromosomes 2H and 3H. This association of molecular markers with qualitative and quantitative disease resistance loci represents a valuable starting-point for marker-assisted selection. [ABSTRACT FROM AUTHOR]

summary. the interactions between hordeum vulgare (barley) and two fungal necrotrophs, rhynchosporium secalis and pyrenophora teres (causal agents of barley leaf scald and net blotch), were investigated in a detached-leaf system. an early oxidative burst specific to epidermal cells was observed in both the susceptible and resistant responses to r. secalis, and later on, a second susceptible-specific burst was observed. time points of the first and the second burst correlated closely with pathogen contact to the plasma membrane and subsequent cell death, respectively. ho2•/o2- levels in resistant and susceptible responses to p. teres were limited in comparison. during later stages, ho2•/o2- was only detected in 2 to 3 epidermal cells immediately adjacent to phenolic browning and cell death observed during the susceptible response. however, h2o2 was detected in the majority of mesophyll cells adjacent to the observed lesion caused by p. teres. in contrast to observations during challenge with r. secalis, no direct contact between p. teres and the plasma membrane at sites of reactive oxygen species production was evident. preinfiltration of leaves with antioxidants prior to challenge with either pathogen had no effect on resistance responses but did limit the growth of the pathogens and inhibit the extent of cell death during susceptible responses. these results suggest a possible role for reactive oxygen species in the induction of cell death during the challenge of a susceptible plant cell with a necrotrophic fungal leaf pathogen. [ABSTRACT FROM AUTHOR]

With the increasing population it is important to increase the total yield of most crops, importantly the staple cereal crops. Whilst modern elite barley varieties are high yielding and responsive to high levels of agronomic inputs they have plateau in 'on farm yield', with little evidence of an overall increase in abiotic and biotic stress tolerance due to the low priority in breeding for increased stress, low input or marginal environments. A potential source of viable resilience and resource use efficiency traits are landraces local to areas of marginal land, such as the Scots Bere from the Highlands and Islands of Scotland. The Bere are a deeply historically rooted landrace of barley which has been grown on predominately marginal land for the last half millennia; allowing them to yield well un-der marginal conditions with impoverished soils. By introgressing them into elite cultivar backgrounds they may contribute biotic and abiotic stress-tolerance genes and nutritional genes that enable them to efficiently and resiliently yield under low input and stress-prone environments. The overall aim of the proposed project is to assess and genetically characterise these traits thereby improving low-input performance and yield stability in elite barley. Screening for biotic stress resistance to pathogens such as Rhynchosporium commune & Puccinia hordei, abiotic stress resistance to stresses such as Mn defeciency & salt toxicity, and a combination of one abiotic and one biotic stress to assess the interaction within the genotype. [ABSTRACT FROM AUTHOR]

Leaf scald caused by Rhynchosporium commune (formerly R. secalis) is an important fungal disease in barley (Hordeum vulgare) in western Canada. Pyramiding multiple scald resistance qualitative trait loci (QTL) is considered an effective strategy for breeding durable scald resistance into barley. The objective of this study was to map QTLs with restriction site-associated (RAD) markers and identify single nucleotide polymorphism (SNP) markers for scald resistance. Two recombinant inbred line (RIL) populations (crosses Harrington/Seebe and Seebe/Shyri) with good resistance to local scald isolates were genotyped by RAD sequencing (RADseq). A total of 4203 SNPs were obtained from the RADseq analysis of 162 F7 RILs. Inclusive composite interval mapping identified multiple major QTLs for scald resistance on chromosomes 3H, 4H, and 5H in Shyri, and 2H and 6H in Seebe. SNP markers from Shyri were located in the same region as the previously reported 3H QTL Rrs1. Several SNP markers from Seebe clustered on chromosome 6H near a major scald resistance QTL. The 6H QTL appeared effective for both adult plant resistance and seedling resistance, and explained up to 70.9% of the phenotypic variation among the sequenced lines. A tightly linked SNP for the major 6H QTL was converted into an allele specific PCR marker. The QTLs and their genetic markers found in this study will be useful in barley breeding for the selection of resistance to barley leaf scald. [ABSTRACT FROM AUTHOR]