The Evolving Faces of the SARS-CoV-2 Genome

Surveillance of the evolving SARS-CoV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis methods. We applied molecular portrayal using self-organizing maps machine learning (SOM portrayal) to characterize the diversity of the virus genomes, their mutual relatedness and development since the beginning of the pandemic. The genetic landscape obtained visualizes the relevant mutations in a lineage-specific fashion and provides developmental paths in genetic state space from early lineages towards the variants of concern alpha, beta, gamma and delta. The different genes of the virus have specific footprints in the landscape reflecting their biological impact. SOM portrayal provides a novel option for ‘bioinformatics surveillance’ of the pandemic, with strong odds regarding visualization, intuitive perception and ‘personalization’ of the mutational patterns of the virus genomes

Identification of useful traits for organic soybean breeding in limiting and changing agro-climatic conditions

Organic farming is practiced on over 72 million hectares of agricultural land worldwide. Soybean (Glycine max) is cultivated organically on 644 323 ha. Each year, the selection of the right soybean varieties for their fields is one of the most challenging management decisions that farmers must undertake. Soybean breeding companies continuously offer varieties from their breeding programs that can meet the various needs of farmers, industry and consumers. The growing demand for soybean varieties suitable for organic farming is fostering breeding activities to better fulfil the specific requirements of the organic value chain participants. Within the ECOBREED project, characterisation of a soybean working collection is carried out across contrasting environments in three countries, i.e. Austria, Romania and Serbia, which will enable the identification of useful traits (variation) and the level of local adaptation of genotypes. The following traits are assessed: yield and yield components, crop growth related traits, grain quality traits

Fostering farmer engagement: ECOBREED participatory trials on organic soybean in Serbia

Farmer Participatory trials (FPTs) promote cooperation and knowledge exchange among farmers and researchers in specific agro-climatic conditions. Farmers who actively participate in field experiments are empowered to share their knowledge and preferences. To test and spread innovations in organic production, farmers actively participate in the decision-making process regarding plant variety selection. Farmer participatory trials for organic soybean production were established in five European countries as part of the ECOBREED project. The goal of these trials was to support farmers in selecting new varieties for their respective pedo-climatic zones and locations. This involves farmers directly in the process of developing new soybean varieties, particularly when it comes to working with breeders to observe cross composite populations (CCPs). FPTs for organic soybean were set up in Serbia (2021-2022). Up to 10 soybean varieties were tested on up to 5 locations for two years period. Trial results have big variations within specific locations and production years. Organic farmers continued with testing some subset of soybean varieties in 2023. FPTs are pathway for increasing the uptake of new and improved soybean varieties for low-input and organic production

Organic soybean: ECOBREED partner contribution

One of the goals of the ECOBREED work package SOYBEAN was to develop soybean genotypes with improved agronomic performance and to offer know-how for cultivation practices tailor-made for low input and organic systems. During the project lifetime, the focus of activities was on henotyping for biotic (weed, pest, diseases) and abiotic (drought and chilling stress) stress tolerance screening, as well as crop and nutritive quality and N fixation efficiency. A marker-assisted selection programme was established to identify genes/QTL of particular importance for organic soybean varieties. In addition, an assessment of the effects of cover crops and inoculation in the process of soybean seed multiplication was performed. Creating and selecting new soybean lines suitable for organic production was a key priority. After the first half of the project and the conduction of different trials and identification of useful traits, cross composite populations (CCPs) and soybean lines were available for further field testing. Chosen soybean lines went through the registration trials (2021-2022) to evaluate their performance and adaptability. The first ECOBREED soybean variety was registered by IFVCNS. NS ECOB is the variety with high protein content (00 maturity group) specifically selected for organic and low input production requirements

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Ökophysiologische Untersuchungen zur Colletotrichum-Welkekrankheit an der Kartoffel

Bei Colletotrichum coccodes (Wallr.) S. Hughes, dem Erreger der Colletotrichum-Welkekrankheit an der Kartoffel (Solanum tuberosum L.), handelt es sich um ein pilzliches Pathogen, das aufgrund der Klimaerwärmung auch in Österreich an Bedeutung gewinnt. Es führt zur Erkrankung der Kartoffelpflanze und beeinträchtigt die Knollenqualität. Im Rahmen von Feld-, Lager- und Klimakammerversuchen sowie mikroskopischen und biochemischen Analysen sollte die Reaktion der Kartoffel auf den durch C. cocccodes induzierten biotischen Stress und auf abiotische Stressfaktoren gezeigt, sowie die Pilz-Pflanzen-Interaktion untersucht werden. Trotz der Verwendung von gesunden Saatknollen wurden auf Freilandversuchsflächen gering befallene Tochterknollen geerntet. Dabei gab es sortenspezifische Unterschiede. Der Lagerversuch zeigte, dass sich der Befall im Zuge der Lagerung verstärkt und auch an gesunden Knollen ein Befall auftritt. Bei mikroskopischen Analysen konnten zahlreiche Calciumoxalatkristallkomplexe auf den Pflanzenoberflächen, eine Art Hülle um die Fruchtkörper von C. coccodes und aus dem Gewebsinneren hervorbrechende Fruchtkörper beobachtet werden. Der Anbau von infizierten Knollen der Sorte Ditta in der Klimakammer unter verschiedenen Wassermanagements zeigte keine Auswirkungen auf den Befall der Tochterknollen und auf die Vitalität der Pflanzen. Anhand physiologischer Stressparameter konnte kein starker Trockenstress oder Schäden durch einen Wasserüberschuss nachgewiesen werden. Tendenziell war das feuchte Wassermanagement für die Pflanzen günstiger als das trockene und nasse Management. Die Kombination von biotischem und abiotischem Stress hat sich auf bestimmte physiologische Parameter stärker ausgewirkt, wie etwa auf den Glutathion- und Tocopherolhaushalt. Für die Kartoffel scheint besonders das -Tocopherol wichtig zu sein. Hinsichtlich Ascorbinsäure-, Pigment- und Prolingehalt konnten Tendenzen beobachtet werden, die jedoch nicht signifikant waren.Colletotrichum coccodes (Wallr.) S. Hughes is the causative agent of black dot disease on potato (Solanum tuberosum L.). Due to global warming it is gaining in importance in Austria. The fungal pathogen leads to diseased potato plants and impairs their tuber quality. The aim of this master thesis was to examine the reaction of the potato to the biotic stress caused by C. coccodes and abiotic stress factors as well as the fungi-plant-interaction in field, storage and climatic chamber trials along with microscopic and biochemical analyses. After using healthy seed tubers slightly infested daughter tubers could be harvested in field trials. Variety specific differences concerning infestation were detected. The storage trial showed that the infestation strengthened in the course of storage and also on healthy tubers an infestation occurred. In microscopic analysis numerous calcium oxalate crystal complexes on plant surfaces, a kind of shell around the fruiting bodies of C. coccodes and from the inner plant tissue erupting fruiting bodies were observed. The cultivation of infected tubers of the variety Ditta in the climatic chamber under different water managements did not affect the infestation of daughter tubers and the vitality of the plants. Based on physiological stress parameters no strong drought stress or damage because of an excess of water could be detected. The moist water management was more favorable for the plants than the dry and wet managements. The combination of biotic and abiotic stress has had a greater effect on certain physiological stress parameters, such as the glutathione and tocopherol content in the leaf tissue. For the potato especially the -tocopherol appears to be of importance. With respect to ascorbic acid, pigments and proline content trends could be observed, but they were not significant.Maria Elisabeth BernhartAbweichender Titel laut Übersetzung der Verfasserin/des VerfassersZsfassungen in dt. u. engl. SpracheGraz, Univ., Masterarb., 2015(VLID)84174

Morphophysiological and molecular characterization of millet (Panicum miliaceum L.) varieties for crop improvement in Western Europe

Abstract Background Global warming and issues in favour of a more sustainable agriculture suggest a reconsideration of minor cereals in European agrosystems. Compared to other summer crops, proso millet has a remarkable drought resistance and could be used to improve crop rotation and biodiversity. Proso millet is also increasingly sought by industry to produce novel foods such as those designed for coeliac patients. In this study, a thorough characterization of 11, commercially available, proso millet (Panicum miliaceum L.) varieties was carried out as a preliminary step for crop reintroduction and breeding in Western Europe. Methods The cultivars under evaluation were introduced from Austria, Poland, Russia, and the USA (University of Nebraska–Lincoln). Plants were grown at Udine (NE Italy) and Gleisdorf (Styria, Austria), under greenhouse and field conditions, respectively. Yield components and a range of morphophysiological characters were recorded in both locations. In parallel, 85 SSR markers were tested on DNA samples extracted from randomly chosen plants of each variety and the 12 responsive markers used to genotype the whole variety set. Results Morphometric analyses showed that varieties have several diverging phenotypic traits and architectures. In all instances, yields recorded at field level were much lower than potential yields. In this respect, US selections were comparable to earlier developed European varieties, suggesting that breeding for an increased adaptation is the keystone for a stable reintroduction of millet in Western Europe. Molecular analyses uncovered remarkably low genetic differences and heterozygosity levels within cultivars, confirming millet as an essentially autogamous species; in contrast, large genetic distances were noted among cultivars selected in different environments. Results of SSR genotyping combined with those originating from phenotypic analyses indicated possible crosses to source the genetic variability necessary for selection. Conclusions This study enabled the identification of cultivars that could be used to revitalize the crop in Western Europe and to produce genetically variable hybrid progenies exploitable by breeding