Getting ready for the European Health Data Space (EHDS): IDERHA's plan to align with the latest EHDS requirements for the secondary use of health data.

Objective: The European Health Data Space (EHDS) shapes the digital transformation of healthcare in Europe. The EHDS regulation will also accelerate the use of health data for research, innovation, policy-making, and regulatory activities for secondary use of data (known as EHDS2). The Integration of heterogeneous Data and Evidence towards Regulatory and HTA Acceptance (IDERHA) project builds one of the first pan-European health data spaces in alignment with the EHDS2 requirements, addressing lung cancer as a pilot. Methods: In this study, we conducted a comprehensive review of the EHDS regulation, technical requirements for EHDS2, and related projects. We also explored the results of the Joint Action Towards the European Health Data Space (TEHDAS) to identify the framework of IDERHA's alignment with EHDS2. We also conducted an internal webinar and an external workshop with EHDS experts to share expertise on the EHDS requirements and challenges. Results: We identified the lessons learned from the existing projects and the minimum-set of requirements for aligning IDERHA infrastructure with EHDS2, including user journey, concepts, terminologies, and standards. The IDERHA framework (i.e., platform architecture, standardization approaches, documentation, etc.) is being developed accordingly. Discussion: The IDERHA's alignment plan with EHDS2 necessitates the implementation of three categories of standardization for: data discoverability: Data Catalog Vocabulary (DCAT-AP), enabling semantics interoperability: Observational Medical Outcomes Partnership (OMOP), and health data exchange (DICOM and FHIR). The main challenge is that some standards are still being refined, e.g., the extension of the DCAT-AP (HealthDCAT-AP). Additionally, extensions to the Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model (CDM) to represent the patient-generated health data are still needed. Finally, proper mapping between standards (FHIR/OMOP) is a prerequisite for proper data exchange. Conclusions: The IDERHA's plan and our collaboration with other EHDS initiatives/projects are critical in advancing the implementation of EHDS2.

Containment of Fusarium culmorum and Its Mycotoxins in Various Biological Systems by Antagonistic Trichoderma and Clonostachys Strains.

Prevention of fungal diseases caused by Fusarium species, including F. culmorum, and thus the accumulation of mycotoxins in wheat ears, is a constant challenge focused on the development of new, effective crop management solutions. One of the currently most ecologically attractive approaches is biological control using natural antagonistic microorganisms. With this in mind, the antagonistic potential of thirty-three Clonostachys and Trichoderma strains was assessed in this work. Screening tests were carried out in in vitro cultures, and the observed potential of selected Trichoderma and Clonostachys strains was verified in field and semi-field experiments with two forms of wheat: winter cv. Legenda and spring cv. Bombona. Three strains, namely C. rosea AN291, T. atroviride AN240 and T. viride AN430 were reported to be most effective in inhibiting the growth of F. culmorum KF846 and the synthesis of DON, 3AcDON and ZEN under both laboratory and semi-controlled field conditions. Observations of the contact zones of the tested fungi in dual cultures exposed their mycoparasitic abilities against KF846. In addition, studies on liquid cultures have demonstrated the ability of these strains to eliminate F. culmorum toxins. Meanwhile, the strains of T. atroviride AN35 and T. cremeum AN392 used as soil inoculants in the field experiment showed a different effect on the content of toxins in ears (grains and chaffs), while improved wheat yield parameters, mainly grain health in both wheat cultivars. It is concluded that the selected Trichoderma and Clonostachys strains have a high potential to reduce the adverse effects of F. culmorum ear infection; therefore, they can be further considered in the context of potential biocontrol factors and as wheat crop improvers.

High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines.

BACKGROUND: High temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues for plant performance under various environmental stimuli is the crown. However, the molecular characterization of this region remains poorly investigated. Gibberellins play a fundamental role in whole-plant stature formation. This study identified plant stature modifications and crown-specific transcriptome re-modeling in gibberellin-deficient barley sdw1.a (BW827) and sdw1.d (BW828) mutants exposed to increased temperature. RESULTS: The deletion around the sdw1 gene in BW827 was found to encompass at least 13 genes with primarily regulatory functions. A bigger genetic polymorphism of BW828 than of BW827 in relation to wild type was revealed. Transcriptome-wide sequencing (RNA-seq) revealed several differentially expressed genes involved in gibberellin metabolism and heat response located outside of introgression regions. It was found that HvGA20ox4, a paralogue of the HvGA20ox2 gene, was upregulated in BW828 relative to other genotypes, which manifested as basal internode elongation. The transcriptome response to elevated temperature differed in the crown of sdw1.a and sdw1.d mutants; it was most contrasting for HvHsf genes upregulated under elevated temperature in BW828, whereas those specific to BW827 were downregulated. In-depth examination of sdw1 mutants revealed also some differences in their phenotypes and physiology. CONCLUSIONS: We concluded that despite the studied sdw1 mutants being genetically related, their heat response seemed to be genotype-specific and observed differences resulted from genetic background diversity rather than single gene mutation, multiple gene deletion, or allele-specific expression of the HvGA20ox2 gene. Differences in the expressional reaction of genes to heat in different sdw1 mutants, found to be independent of the polymorphism, could be further explained by in-depth studies of the regulatory factors acting in the studied system. Our findings are particularly important in genetic research area since molecular response of crown tissue has been marginally investigated, and can be useful for wide genetic research of crops since barley has become a model plant for them.

Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume.

The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.

Image Phenotyping of Spring Barley (Hordeum vulgare L.) RIL Population Under Drought: Selection of Traits and Biological Interpretation.

Image-based phenotyping is a non-invasive method that permits the dynamic evaluation of plant features during growth, which is especially important for understanding plant adaptation and temporal dynamics of responses to environmental cues such as water deficit or drought. The aim of the present study was to use high-throughput imaging in order to assess the variation and dynamics of growth and development during drought in a spring barley population and to investigate associations between traits measured in time and yield-related traits measured after harvesting. Plant material covered recombinant inbred line population derived from a cross between European and Syrian cultivars. After placing the plants on the platform (28th day after sowing), drought stress was applied for 2 weeks. Top and side cameras were used to capture images daily that covered the visible range of the light spectrum, fluorescence signals, and the near infrared spectrum. The image processing provided 376 traits that were subjected to analysis. After 32 days of image phenotyping, the plants were cultivated in the greenhouse under optimal watering conditions until ripening, when several architecture and yield-related traits were measured. The applied data analysis approach, based on the clustering of image-derived traits into groups according to time profiles of statistical and genetic parameters, permitted to select traits representative for inference from the experiment. In particular, drought effects for 27 traits related to convex hull geometry, texture, proportion of brown pixels and chlorophyll intensity were found to be highly correlated with drought effects for spike traits and thousand grain weight.

Marker assisted selection of new high oleic and low linolenic winter oilseed rape (Brassica napus L.) inbred lines revealing good agricultural value.

Development of oilseed rape (Brassica napus L.) breeding lines producing oil characterized by high oleic and low linolenic acid content is an important goal of rapeseed breeding programs worldwide. Such kind of oil is ideal for deep frying and can also be used as a raw material for biodiesel production. By performing chemical mutagenesis using ethyl methanesulfonate, we obtained mutant winter rapeseed breeding lines that can produce oil with a high content of oleic acid (C18:1, more than 75%) and a low content of linolenic acid (C18:3, less than 3%). However, the mutant lines revealed low agricultural value as they were characterized by low seed yield, low wintering, and high content of glucosinolates in seed meal. The aim of this work was to improve the mutant lines and develop high-oleic and low-linolenic recombinants exhibiting both good oil quality and high agronomic value. The plant materials used in this study included high-oleic and low-linolenic mutant breeding lines and high-yielding domestic canola-type breeding lines of good agricultural value with high oleic acid content and extremely low glucosinolates content. Field trials were conducted in four environments, in a randomized complete block design. Phenotyping was performed for wintering, yield of seed and oil, and seed quality traits. Genotype × environment interaction was investigated with respect to the content of C18:1 and C18:3 acids in seed oil. Genotyping was done for the selection of homozygous high oleic and low linolenic lines using allele-specific CAPS markers and SNaPshot assay, respectively. Finally, new high oleic and low linolenic winter rapeseed recombinant lines were obtained for use as a starting material for the development of new varieties that may be of high value on the oil crop market.

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

Semantic concept schema of the linear mixed model of experimental observations.

In the information age, smart data modelling and data management can be carried out to address the wealth of data produced in scientific experiments. In this paper, we propose a semantic model for the statistical analysis of datasets by linear mixed models. We tie together disparate statistical concepts in an interdisciplinary context through the application of ontologies, in particular the Statistics Ontology (STATO), to produce FAIR data summaries. We hope to improve the general understanding of statistical modelling and thus contribute to a better description of the statistical conclusions from data analysis, allowing their efficient exploration and automated processing.

Mapping of quantitative trait loci for traits linked to fusarium head blight in barley.

Fusarium head blight (FHB) is a devastating disease occurring in small grain cereals worldwide. The disease results in the reduction of grain yield, and mycotoxins accumulated in grain are also harmful to both humans and animals. It has been reported that response to pathogen infection may be associated with the morphological and developmental traits of the host plant, e.g. earliness and plant height. Despite many studies, effective markers for selection of barley genotypes with increased resistance to FHB have not been developed. In the present study, we investigated 100 recombinant inbred lines (RIL) of spring barley. Plants were examined in field conditions (three locations) in a completely randomized design with three replications. Barley genotypes were artificially infected with spores of Fusarium culmorum before heading. Apart from the main phenotypic traits (plant height, spike characteristic, grain yield), infected kernels were visually scored and the content of deoxynivalenol (DON) mycotoxin was investigated. A set of 70 Quantitative Trait Loci (QTLs) were detected through phenotyping of the mapping population in field conditions and genotyping using a barley Ilumina 9K iSelect platform. Six loci were detected for the FHB index on chromosomes 2H, 3H, 5H, and 7H. A region on the short arm of chromosome 2H was detected in which many QTLs associated with FHB- and yield-related traits were found. This study confirms that agromorphological traits are tightly related to FHB and should be taken into consideration when breeding barley plants for FHB resistance.

Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids.

BACKGROUND: Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns. Here we studied these issues in allotetraploid Festuca pratensis × Lolium perenne hybrids. RESULTS: Cytogenetic procedures, including fluorescent in situ hybridization, genomic in situ hybridization, and molecular markers - inter-simple sequence repeats (ISSR) were exploited. This cytogenetic approach indicated the dynamics in the number and distribution of ribosomal RNA genes and structural rearrangements for both parental genomes (Festuca and Lolium) in hybrid karyotypes. The separate analysis of F. pratensis and L. perenne chromosomes in hybrid plants (F2-F3 generations of F. pratensis × L. perenne) revealed the asymmetrical level of rearrangements. Recognized structural changes were mainly located in the distal part of chromosome arms, and in chromosomes bearing ribosomal DNA, they were more frequently mapped in arms without this sequence. Based on the ISSR markers distribution, we found that the tetrasomic type of inheritance was characteristic for the majority of ISSR loci, but the disomic type was also observed. Nonetheless, no preference in the transmission of either Festuca or Lolium alleles to the following generations of allotetraploid F. pratensis × L. perenne hybrid was observed. CONCLUSION: Our study reports cytogenetic and molecular genotyping of the F. pratensis × L. perenne hybrid and its following F2-F3 progenies. The analysis of 137 allotetraploid F. pratensis × L. perenne hybrids revealed the higher level of recombination in chromosomes derived from F. pratensis genome. The results of ISSR markers indicated a mixed model of inheritance, which may be characteristic for these hybrids.