Functional Variation of Plant-Pathogen Interactions: New Concept and Methods for Virulence Data Analyses

Rare Virulences and Great Pathotype Diversity of a Central European Blumeria hordei Population

Barley is an important crop grown on almost 49 Mha worldwide in 2021 and is particularly significant in Europe where powdery mildew is the most frequent disease on susceptible varieties. The most suitable way to protect crops is by exploiting genetic resistance. However, the causal agent Blumeria hordei is an extremely adaptable pathogen. The aims of this research were to increase our knowledge of the rapidly changing pathogen population and detect rare virulences. Random samples of the pathogen were obtained from the air by means of a mobile spore sampler. Spores were collected by driving across the Czech Republic in 2019, 2021 and 2023, and 299 isolates were analyzed on 121 host varieties. No infection occurred on 35 differentials, rare virulence was recorded on 31 varieties and a higher virulence frequency was found on 55 differentials. A core set of differentials along with four additional varieties distinguishes 295 pathotypes (Simple Index = 0.987) and the virulence complexity of isolates varied from 4 to 19 with an average of 10.39. The detection of new virulences, the increasing frequency of previously rare virulences and high pathotype diversity as well as high virulence complexity confirm that using nonspecific durable resistance is crucial for successfully breeding commercial varieties.

SSR Variability of Stem Rust Pathogen on Spring Bread Wheat in Russia

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, which used to be a harmful disease of winter wheat in the southern part of Russia, has been largely affecting the yield of spring bread wheat in the territories of the temperate climate zone since 2009. In total, 222 P. graminis f. sp. tritici isolates were obtained from samples of susceptible cultivars of spring bread wheat in Central and Volga regions and Omsk and Novosibirsk provinces in 2019. Genotyping of the isolates was carried out at 16 simple-sequence repeat (SSR) loci. Number of alleles, proportion of heterozygotes, and deviation from Hardy-Weinberg equilibrium were determined at each SSR locus. Based on genetic variability of SSR genotypes, it was shown that the P. graminis f. sp. tritici population is subdivided into two large clusters in the territory of the Russian temperate climate zone: the "European" population (the Central region) and the "Asian" one (the Volga region and two main wheat provinces of Western Siberia). Both of the P. graminis f. sp. tritici populations are characterized by a mixed mode of reproduction (sexual and clonal) but different sources of inoculum seem to shape a genotype structure within them. A group of P. graminis f. sp. tritici genotypes with high variability, the inbreeding coefficient closed to zero, and low observed heterozygosity was revealed among samples from Omsk. Moreover, two singular SSR genotypes identified among the Asian samples of P. graminis f. sp. tritici isolates should attract special attention in the monitoring of stem rust in order to disclose unexpected rapid changes of the pathogen in the corresponding regions and to prevent disease outbreak.

Non-Authenticity of Spring Barley Genotypes Revealed in Gene Bank Accessions

Plant research and breeding depends on plant genotypes; therefore, genotype authenticity of accessions is the basic requirement for users of gene banks. Surprisingly, this extremely important topic is rarely reported in the scientific community. Non-authentic are accessions that are mislabelled and undesirable genotypes of heterogeneous accessions. In barley, we try to uncover both named problems on the basis of postulated major powdery mildew resistance genes. These are diverse, environmentally stable and their use is well documented and suitable for genotype characterization. In this contribution, we postulate resistance genes in 15 varieties represented by 157 derived lines of 32 accessions originating from seven foreign gene banks and compare these findings with previous results including those 15 identically labelled varieties from our domestic gene bank. We found that 37.5% of the gene bank accessions investigated herein were heterogeneous, and at least 20.0% were mislabelled. A large-scale molecular characterisation of varieties is now being carried out, and using authentic varieties must be one of the key requirements. Therefore, accessions of each variety from a minimum of three gene banks whose identity has been verified by reliable methods should be compared before starting new experiments. These will involve molecular varietal characterisation to serve as a foundation for future plant science research and effective crop improvement.

Virulence Survey of Puccinia striiformis in Israel Revealed Considerable Changes in the Pathogen Population During the Period 2001 to 2019

A total of 353 urediniospore isolates of Puccinia striiformis f. sp. tritici (Pst) collected in Israel during 2001 to 2019 were analyzed. Pst pathogenicity was studied with a set of 20 differentials (17 Avocet and 3 other lines). Three periods were compared: 2001 to 2007, 2009 to 2016, and 2017 to 2019. No virulence to Yr5 or Yr15 was detected. Virulence frequencies on Yr4, Yr10, Yr24, and YrSp genes rose to the moderate level (0.28 to 0.44) in 2017 to 2019. Virulence frequencies to Yr2 and Yr9 decreased. One Pst phenotype was identified in all three periods, but its frequency drastically decreased from 0.74 in 2001 to 2016 to 0.21 in 2017 to 2019. The most probable scenario of emergence of wheat yellow rust in Israel is wind dissemination of Pst urediniospores from the Horn of Africa. Variability of the Pst population increased amid considerable evolution with two major transformations in 2009 and 2017. The first modification can be attributed to changes in wheat genetic background in Israel due to deployment of new cultivars resistant to yellow rust since 2004. The second shift in 2017 can be primarily explained by intensive deployment of wheat cultivars resistant to the stem rust race Ug99 in the 2010s in the Horn of Africa. This led to changing genetic backgrounds of the cultivated wheats in the donor region and development and long-distance spread of new Pst phenotypes to Israel. Two singular multivirulent Pst phenotypes were identified in 2019, one of them being closely related to the aggressive Warrior race. Such phenotypes may potentially defeat existing resistances.

Powdery Mildew Resistance Genes in European Barley Cultivars Registered in the Czech Republic from 2016 to 2020

Barley is an important crop grown annually on about 55 Mha and intensively cultivated in Europe. In central and north-western Europe, spring and winter barley can be grown in similar environments which creates suitable conditions for the development of barley pathogens, including Blumeria graminis f. sp. hordei, the causal agent of powdery mildew. Apart from pesticide application, it can be controlled by inexpensive and environmentally-friendly genetic resistance. In this contribution, results of the resistance gene identification in 58 barley cultivars to powdery mildew are presented. In 56 of them their resistances were postulated and in two hybrid cultivars a recently developed method of gene identification was used. In total, 18 known resistance genes were found and several unknown genes were detected. In spring barley, a gene of durable resistance mlo is still predominant. MlVe found in winter SU Celly was the only new resistance gene recorded in barley cultivars registered in the Czech Republic in this time span. Since 2001 eight new genes of specific resistance have been identified in cultivars registered in the country and their response under field conditions is discussed, including the corresponding responses of the pathogen population due to directional selection. Different strategies for breeding spring and winter barley are recommended.

Postulation of Specific Disease Resistance Genes in Cereals: A Widely Used Method and Its Detailed Description

Cultivation of resistant varieties is an environmentally friendly and inexpensive method of crop protection. Numerous alleles of specific disease resistance occur in cereals and other crops, and knowledge of their presence in individual varieties has wide utilization in research and practice. Postulation based on phenotyping host-pathogen interactions and the gene-for-gene model is a common way of identifying these genes. The same technique and design of tests are used for postulating virulence when pathogen populations are studied. Powdery mildews caused by different formae speciales of Blumeria graminis (Bg) are important cereal diseases. In this contribution, experimental methods are described that use a model organism Bg f. sp. hordei, which can be employed for other cereal mildews and possibly rusts. It includes illustrations and a summary of our long-term practical experience. It also critically evaluates the benefits of leaf segment tests compared with screening whole plants.

In-depth evaluation of root infection systems using the vascular fungus Verticillium longisporum as soil-borne model pathogen

BACKGROUND

While leaves are far more accessible for analysing plant defences, roots are hidden in the soil, leading to difficulties in studying soil-borne interactions. Inoculation strategies for infecting model plants with model root pathogens are described in the literature, but it remains demanding to obtain a methodological overview. To address this challenge, this study uses the model root pathogen Verticillium longisporum on Arabidopsis thaliana host plants and provides recommendations for selecting appropriate infection systems to investigate how plants cope with root pathogens.

RESULTS

A novel root infection system is introduced, while two existing ones are precisely described and optimized. Step-by-step protocols are presented and accompanied by pathogenicity tests, transcriptional analyses of indole-glucosinolate marker genes and independent confirmations using reporter constructs. Advantages and disadvantages of each infection system are assessed. Overall, the results validate the importance of indole-glucosinolates as secondary metabolites that limit the Verticillium propagation in its host plant.

CONCLUSION

Detailed assistances on studying host defence strategies and responses against V. longisporum is provided. Furthermore, other soil-borne microorganisms (e.g., V. dahliae) or model plants, such as economically important oilseed rape and tomato, can be introduced in the infection systems described. Hence, these proven manuals can support finding a root infection system for your specific research questions to further decipher root-microbe interactions.

Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement

Towards the identification of entophytic fungal taxa with potential for crop improvement, we characterized and compared fungal endophyte communities (FECs) from domesticated bread wheat and two wheat ancestors, Aegilopssharonensis and Triticumdicoccoides. Data generated by next generation sequencing identified a total of 1666 taxa. The FECs in the three plant species contained high proportions of random taxa with low abundance. At plant species level, the majority of abundant taxa were common to all host plants, and the collective FECs of each of the three plant species had similar diversity. However, FECs from the wild plants in specific sites were more diverse and had greater richness than wheat FECs from corresponding specific fields. The wild plants also had higher numbers of differentially abundant fungal taxa than wheat, with Alternaria infectoria being the most abundant species in wild plants and Candida sake the most abundant in wheat. Network analysis on co-occurrence association revealed a small number of taxa with a relatively high number of co-occurrence associations, which might be important in community assembly. Our results show that the actual endophytic cargo in cultivated wheat plants is limited relative to wild plants, and highlight putative functional and hub fungal taxa with potential for wheat improvement.

Significant host- and environment-dependent differentiation among highly sporadic fungal endophyte communities in cereal crops-related wild grasses

Endophytic fungi compose a significant part of plant microbiomes. However, while a small number of fungal taxa have proven beneficial impact, the vast majority of fungal endophytes remain uncharacterized, and the drivers of fungal endophyte community (FEC) assembly are not well understood. Here, we analysed FECs in three cereal crops-related wild grasses - Avena sterilis, Hordeum spontaneum and Aegilops peregrina - that grow in mixed populations in natural habitats. Taxa in Ascomycota class Dothideomycetes, particularly the genera Alternaria and Cladosporium, were the most abundant and prevalent across all populations, but there was also high incidence of basidiomyceteous yeasts of the class Tremellomycetes. The fungal community was shaped to large extent by stochastic processes, as indicated by high level of variation even between individuals from local populations of the same plant species, and confirmed by the neutral community model and Raup-Crick index. Nevertheless, we still found strong determinism in FEC assembly with both incidence and abundance data sets. Substantial differences in community composition across host species and locations were revealed. Our research demonstrated that assembly of FECs is affected by stochastic as well as deterministic processes and suggests strong effects of environment heterogeneity and plant species on community composition. In addition, a small number of taxa had high incidence and abundance in all of the 15 populations. These taxa represent an important part of the core FEC and might be of general functional importance.