Editorial
FROM GENES TO GROWTH: Enhancing drought tolerance in maize and teff through advanced genetic analysis
TOWARDS DROUGHT RESILIENT CROPS: Genomic comparisons across maize, teff, and E. nindensis
BOOSTING CROP DROUGHT TOLERANCE: The role of biostimulants in maize and teff resilience
MOLECULAR PRIMING AND MICROBIAL SOLUTIONS: Innovative dual approaches for drought-resilient crops
Collaborations with sister projects
BOOSTER's scientific articles
Upcoming BOOSTER events
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FROM GENES TO GROWTH: Enhancing drought tolerance in maize and teff through advanced genetic analysis
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Work Package 1 (WP1) titled 'Genome-wide identification of maize and teff CREs and genes associated with drought tolerance' aims to revolutionize the identification and utilization of natural genetic variability associated with drought tolerance in European maize and Ethiopian teff germplasm. By project's end, this approach is poised to significantly enhance the effectiveness of classical and biotechnological breeding programs for developing resilient maize and teff genotypes.
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The strategy hinges on employing MNase-defined cistrome-Occupancy Analysis (MOA), integrated with next-generation sequencing. This methodology enables comprehensive, high-resolution mapping of functional genetic variations within cis-regulatory elements (CREs). Identified candidate CREs are then correlated with gene expression data to determine their role in conferring drought tolerance. Given that a substantial portion of genetic diversity influencing quantitative traits resides in non-coding regions, particularly within transcription factor binding sites, adopting MOA promises to markedly elevate the efficiency of genetic variation exploitation for breeding initiatives.
For a visual depiction, refer to the accompanying figure illustrating the MOA strategy.
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The initial steps of the MOA strategy involved identifying maize and teff populations that represent a broad range of genetic variability within Europe and Ethiopia. Following this, trials were conducted to optimize plant growth conditions and drought stress treatments. Samples were then collected to prepare MOA/mRNA-seq libraries.
Bioinformatic analysis of the sequencing data allows for a genome-wide identification of transcription factor (TF) binding sites and their correlation with gene expression regulated by these TFs. The analysis also examines how TF binding and expression vary based on genetic diversity in each genotype and the different treatment conditions, such as well-watered versus drought-stressed plants. As TF binding can also be influenced by cytosine methylation, methylome data were generated to differentiate between changes in TF binding due to methylation patterns or genetic variation.
The next phase will focus on integrating all these data to pinpoint potential genetic variants in cis-regulatory elements, particularly those located within known drought-related quantitative trait loci (QTLs).
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TOWARDS DROUGHT RESILIENT CROPS: Genomic comparisons across maize, teff, and E. nindensis
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Work Package 2 (WP2) titled 'Comparative genomics of drought CREs and genes in three different grasses and validation of maize and teff drought CREs genome-wide data' aims to conduct a comparative genomic analysis of drought-responsive cis-regulatory elements and genes across three grass species—maize, teff, and E. nindensis—with the goal of validating these regulatory elements in maize and teff.
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The first step involved obtaining the drought cistrome of E. nindensis, which will be compared with those from maize and teff. To understand the remarkable drought tolerance of E. nindensis, the WP2 teams are focusing on analyzing variations in transcription factor (TF) binding and the transcriptome. These analyses aim to uncover the molecular mechanisms that enable E. nindensis to survive extreme drought conditions. The UCT team collected seeds from E. nindensis plants grown in South Africa, germinated and maintained them under controlled growth conditions. The plants were subjected to various drought stress levels, followed by rehydration, with leaf samples collected at multiple stages: well-watered, mild drought stress, severe drought stress, and post-rehydration (24h and 48h).
The CREA team optimized the MOA/mRNA-seq protocol and bioinformatic pipeline to sequence the cistrome of E. nindensis using the samples from UCT. Meanwhile, the UDUS team is developing strategies for comparative genome analysis to identify similarities and differences in drought and desiccation responses across maize, teff, and E. nindensis. The VIB team is focusing on optimizing genome-editing tools to precisely edit these drought-responsive cis-regulatory elements in the maize genome.
Together, these efforts aim to identify key elements that drive drought tolerance in maize, teff, and E. nindensis, validate these findings in maize and teff, and explore the potential of transferring drought-tolerant features from E. nindensis and teff to maize.
To experience a piece of Ethiopian culture, the VIB team visited an Ethiopian restaurant for the first time and enjoyed injera, a traditional dish made from teff (see picture).
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Together, these efforts aim to identify key elements that drive drought tolerance in maize, teff, and E. nindensis, validate these findings in maize and teff, and explore the potential of transferring drought-tolerant features from E. nindensis and teff to maize.
To experience a piece of Ethiopian culture, the VIB team visited an Ethiopian restaurant for the first time and enjoyed injera, a traditional dish made from teff (see picture).
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BOOSTING CROP DROUGHT TOLERANCE: The role of biostimulants in maize and teff resilience
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Work Package 3 (WP3) titled 'Development and characterization of new SWE and microbial biostimulants for improving maize and teff drought tolerance' focuses on developing natural biostimulants as eco-friendly, bio-based solutions to enhance drought resilience in semi-arid regions with water scarcity. Two complementary biostimulants are being explored: plant growth-promoting rhizobacteria (PGPR) from drought-prone areas and seaweed extracts (SWEs). The goal is to identify the most effective microbial strains and SWE candidates that boost drought tolerance in maize and teff without compromising crop yield.
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In the PGPR studies, soil samples enriched with plant roots and rhizosphere material have been collected from regions with a history of drought in Europe and Africa. These samples were gathered from 22 maize-growing sites in Europe, four locations in Ethiopia (teff and wild relative Eragrostis pilosa), and 14 sites in South Africa (where drought-resilient E. nindensis grows in the wild).
Collected soil samples were used to grow maize and teff in greenhouses in Europe and Ethiopia, both under well-watered and drought-stressed conditions, to identify bacterial strains that enhance drought resilience in these crops.
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Sample collections from drought prone areas in Ethiopia (left) and South Africa (right)
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The greenhouse studies led to the identification of 200 promising bacterial strains from maize samples in Europe, 24 strains from E. nindensis in South Africa, and 78 strains from teff and E. pilosa in Ethiopia. These strains are now being prepared for whole-genome sequencing to further investigate their potential.
In parallel, eight SWE extracts produced by BioAtlantis have been used for seed and leaf priming applications. Both single and combined applications were tested on maize and teff under drought conditions. The effectiveness of SWEs in promoting drought tolerance is assessed by evaluating the performance of the crops in terms of grain yield and other key parameters.
The next step will involve a deeper investigation into the modes of action of the best-performing microbial and SWE biostimulants. This will include meta-transcriptomics and root colonization studies for the PGPRs, along with metabolomics analysis for the SWEs. Finally, large-scale field trials in drought-prone regions of Europe (for maize) and Ethiopia (for teff) will be conducted by WP4 partners to validate the effectiveness of the selected biostimulants.
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MOLECULAR PRIMING AND MICROBIAL SOLUTIONS: Innovative dual approaches for drought-resilient crops
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Work Package 4 (WP4) titled 'Production of the best performing SWE and microbial biostimulants and evaluation of their performance in improving maize and teff drought tolerance through field trials' aims to develop and validate seaweed-based and microbial-based biostimulant technologies that enhance drought tolerance in maize and teff by delivering bespoke formulations enriched with bioactive compounds proven to prime crop resilience.
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BioAtlantis has been focusing on the development of proprietary ‘Molecular Priming’ formulations aimed at enhancing stress resilience, growth, and productivity in maize. Currently, the formulations are being tested in controlled growth room trials at BioAtlantis' R&D department to evaluate their potential under stress conditions. Alongside these trials, scientists from the CPSBB in Bulgaria and Universität Bern in Switzerland are also screening the formulations to assess their broader effectiveness. These initial steps are critical for understanding how these novel molecular priming agents can improve crop performance under extreme environmental stress, particularly drought.
The results to date on BioAtlantis’ molecular priming formulations in BOOSTER are promising, and show significant benefits in both maize and teff. These promising molecular priming agents will soon undergo large-scale field trials across diverse locations in Europe and Ethiopia. This broader testing will provide valuable data on their performance in varying environmental conditions. Advanced analytical techniques, including transcriptomics and metabolomics, will be employed to uncover the mechanisms behind the formulations' effectiveness. The insights gained from these studies will play a key role in optimizing maize growth and yield under climatic challenges, ensuring stability in agricultural production despite the increasing threat of drought and other climate-related stressors. The ultimate goal is to provide sustainable solutions that improve maize and teff productivity while mitigating the impacts of climate change.
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Aphea.Bio is combining greenhouse experiments with extensive field trials to identify and develop effective microbial biostimulants aimed at improving drought resilience in crops. The company initiated its work with a large-scale soil collection effort, gathering 22 samples from regions in Europe with a history of drought, which provided a diverse pool of microbial isolates. These isolates, about 200 in total, were screened using Aphea.Bio’s advanced greenhouse program, where maize plants were first grown under optimal conditions before being subjected to drought stress. The plants were then allowed to recover, and their biomass was measured to assess the effects of the microbial treatments on drought tolerance.
So far, the results have been promising, with some microbial isolates significantly increasing dry biomass compared to untreated seeds, while others showed little effect or even negative results. This process has led to the development of both a drought screening protocol and a seed coating protocol for applying microbial strains. In parallel, Aphea.Bio has been working on producing high-quality microbial biostimulants, which have shown proven efficacy in enhancing drought resistance in controlled conditions. These biostimulants, along with patentable seed coating formulations, will be tested in field trials across drought-prone regions in the Mediterranean and South/East Europe. The next phase will involve scaling up production to create batches of microbial biostimulants for both maize and teff, ensuring the most promising candidates are tested in real-world agricultural conditions.
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Collaborations with sister projects
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BOOSTER aims to establish connections with projects and individuals engaged in research on drought tolerance in maize and teff, in order to promote awareness and potential application of BOOSTER’s work, while also gaining insights into the methods employed by other projects and experts.
Within the framework of Networking with EU Initiatives, close collaboration has been fostered with sister projects such as HeLEx and TOLERATE. At the 2024 First Annual Meeting, representatives from these projects participated in a mapping activity presentation, which successfully identified promising opportunities for future partnership and joint research.
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HelEx
Use of extremophile Helianthus species to mitigate climate change impact on feedstock and ecosystem services provided by sunflower (Grant Agreement ID: 101081974).
HelEx aims to produce knowledge and tools to accelerate the breeding of sunflower varieties adapted to extreme drought and heat stresses and evaluate their environmental impact and economic outputs.
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Tolerate
Adaptation to climate change in the rhizosphere across the millennia (Grant agreement ID: 101082049).
TOLERATE studies ancient Arctic soil and sediment samples to analyze NaDNA, aiming to understand how root (rhizosphere) zone biodiversity has responded to climate changes and extreme events over millions of years.
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Scientific Advisory Board (SAB)
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The BOOSTER project's Scientific Advisory Board, comprised of leading external experts, provides independent guidance on the project's scientific strategy, rigorously evaluating progress and ensuring alignment with state-of-the-art research. It also fosters collaboration, advises on the effective dissemination and exploitation of results, and plays a critical role in maximizing the project's impact within the EU research landscape.
Meet the BOOSTER SAB experts:
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Dorothea Bartels
Professor at University of Bonn, Germany
Dorothea Bartels initiated early studies of resurrection plants. After her PhD in Botany at the University of Hannover, she worked for several years as a postdoc at the Plant Breeding Institute in Cambridge, then started to work on resurrection plants when she became a group leader at the Max Planck Institute for Plant Breeding in Cologne. She now leads research on plant physiology and biochemistry at the University of Bonn. She chose to work on Craterostigma plantagineum as model plant for desiccation tolerance. She is the editor in chief for the journal Planta and she has been involved with editorial work in several other journals.
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Adriana Silva Hemerly
Full professor and Researcher at the Medical Biochemistry Institute (Coordinator of the Laboratory of Plant Molecular Biology), at Federal University of Rio de Janeiro, Brazil
Dr. Adriana Hemerly is Full Professor and Researcher at the Federal University of Rio de Janeiro (UFRJ, Brazil). She coordinates the Laboratory of Plant Molecular Biology since 1997, identifying regulatory networks that integrate environmental signaling with plant development, focusing on plant cell cycle regulation and plant association with beneficial bacteria. The research aims to develop biotechnological tools to increase plant productivity and adaptation to environmental changes. She has a Bachelor in Genetics at UFRJ (Brazil), a PhD in Biotechnology at UGent (Belgium) and a Post-Doctorate in Molecular and Cellular Biology at Cold Spring Harbor Laboratory (NY, USA). She has been Coordinator of all the Biotechnology Graduate Programs in Brazil at CAPES (2014 – 2022).
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Randall J. Wisser
Research Director at INRAE (National Research Institute for Agriculture, Food and Environment), France
Dr. Wisser joined INRAE as a research director in 2020 where he currently leads a project on the integration of ecophysiology and quantitative genetics for maize adaptation to climate change. He obtained his PhD in Plant Breeding and Genetics at Cornell University (New York, USA) and was a USDA-AFRI postdoctoral fellow in quantitative genetics and plant pathology at North Carolina State University (North Carolina, USA). Dr. Wisser spent a decade leading a research and teaching program at the University of Delaware, where he now holds a joint appointment. His research spans biological scales to investigate genetic diversity, crop adaptation, experimental evolution, and disease resistance, in addition to pedagogical contributions for active learning.
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Curious about BOOSTER’s innovative objectives and strategic approach? Click here for a detailed insight into our vision and plans.
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BOOSTER Scientific Publications
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To date, BOOSTER partners have published three scientific papers in recognized journals, focusing on research related to tef, transcription factor binding in maize, and gene regulatory networks in plants:
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Transcriptomic profile of tef (Eragrostis tef) in response to drought
Authors: Lorena Ramirez-Gonzales, Gina Cannarozzi, Abiel Rindisbacher, Lea Jäggi, Regula Schneider, Annett Weichert, Sonia Plaza-Wüthrich, Solomon Chanyalew,Kebebew Assefa and Zerihun Tadele.
Journal: Plants MDPI
November 2024, 13(21), 3086. Special Issue: Crop Breeding for Food and Nutrition Security
DOI: https://doi.org/10.3390/plants13213086
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The role of omics in improving the orphan crop tef
Authors: Lorena Y. Ramírez Gonzales, Gina Cannarozzi, Lea Jäggi, Kebebew Assefa, Solomon Chanyalew, Matteo Dell’Acqua and Zerihun Tadele
Journal: Trends in Genetics
Volume 40, Issue 5, May 2024, Pages 449-461
DOI: https://doi.org/10.1016/j.tig.2024.03.003
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Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
Authors: Julia Engelhorn, Samantha J. Snodgrass, Amelie Kok, Arun S. Seetharam, Michael Schneider, Tatjana Kiwit, Ayush Singh, Michael Banf, Merritt Khaipho-Burch, Daniel E. Runcie, Victor A. Sanchez-Camargo, J. Vladimir Torres-Rodriguez, Guangchao Sun, Maike Stam, Fabio Fiorani, Sebastian Beier, James C. Schnable, Hank W. Bass, Matthew B. Hufford, Benjamin Stich, Wolf B. Frommer, Jeffrey Ross-Ibarra and Thomas Hartwig
Journal: Cold Spring Harbor Laboratory
Genomics, April 2024
DOI: https://doi.org/10.1101/2023.08.08.551183
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MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles
Authors: Nicolás Manosalva Pérez, Camilla Ferrari, Julia Engelhorn, Thomas Depuydt, Hilde Nelissen, Thomas Hartwig and Klaas Vandepoele
Journal: The Plant Journal
Volume 117, Issue 1, January 2024, Pages 280-301
DOI: https://doi.org/10.1111/tpj.16483
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In the coming months, we’ll highlight key conferences and workshops that focus on innovative research and advancements in the field. Stay tuned!
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