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Povzetek: Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.
Ključne besede: potato, Solanum tuberosum, abiotic stress responses, heat, drought, waterlogging, multi-omics, integrative omics, adaptomics, panomics
Objavljeno v DiRROS: 14.04.2025; Ogledov: 164; Prenosov: 128
Celotno besedilo (2,89 MB)
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Povzetek: The ELIXIR Plant Sciences Community is an interdisciplinary group of researchers with diverse backgrounds from computer science to different fields of plant biology. We answer the needs of both bioinformaticians and plant biologists. The Community objective is to develop services supporting the integration and linking of phenotypic, genotypic, omics (e.g. expression, metabolomics, etc.), environmental, and bibliographic data. The underlying scientific use cases encompass fundamental and applied plant sciences, including genetics, system biology and omics approaches, within the broader context of climate change, agroecology, food security, and sustainable agriculture. To meet the current challenges in agriculture, the ELIXIR Community promotes tools, databases, standards, and best practices for plant research while developing joint initiatives such as international projects and events in collaboration with European infrastructures (EMPHASIS, AnaEE-ERIC, Euro-Bioimaging, METROFOOD-RI). The ELIXIR Community also supports the establishment of links to structuring national projects and initiatives such as NFDI in Germany, or the french Agroecology and ICT program. Despite ongoing efforts, challenges remain, such as the continued scattering of plant molecular and cellular data, which hampers efficient data integration and reuse. Additionally, progressing toward a comprehensive agriculture data space is essential to address the interdisciplinary challenges that modern agriculture faces. Strengthening engagement with related research communities, such as those working on plant pathogens, is also a priority to ensure a holistic approach to plant science and agricultural research. Finally the Plant Sciences Community links with other ELIXIR Communities and Focus Groups, in particular to contribute to the objectives and priority of the Biodiversity, Food Security and Pathogens and of the Cellular and Molecular Research scientific priority areas.
Ključne besede: system biology, genotyping, plant
Objavljeno v DiRROS: 04.04.2025; Ogledov: 205; Prenosov: 55
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Ključne besede: odprti podatki, odprta znanost, delo z delotoki, projekt Spoznaj, okolje Galaxy, raziskovalni podatki, uporabljanje podatkov
Objavljeno v DiRROS: 12.03.2025; Ogledov: 252; Prenosov: 84
Celotno besedilo (13,57 MB)
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Povzetek: Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
Ključne besede: Stress knowledge map, knowledge graph, knowledge network, entry point, plant digital twin, plant stress responses, plant signaling, systems biology
Objavljeno v DiRROS: 11.06.2024; Ogledov: 961; Prenosov: 430
Celotno besedilo (1,35 MB)
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