SCIENTIFIC PUBLICATIONS
Here you can find all the scientific publications related to the Booster project
Authors: Aakansha Kanojia, Neerakkal Sujeeth, Saurabh Gupta, Saleh Alseekh, Veselin Petrov and Tsanko S. Gechev.
Drought-induced senescence is a major cause of maize yield loss. While biostimulant priming improves stress tolerance, its molecular basis is unclear. Here we demonstrate that priming maize with the plant-derived biostimulant AgriPrime Stimulus (APS) delays drought-induced leaf senescence at reproductive-stage, resulting in improved cob weight and yield. Integrated physiological, transcriptomic, metabolomic, and phytohormone analyses revealed that APS priming preserves source leaf functionality by maintaining key metabolic processes. APS-primed drought-stressed leaves showed enrichment of photosynthesis-related genes and elevated levels of tricarboxylic acid cycle intermediates, indicating maintained carbon metabolism. APS priming also strengthened cell wall through the induction of genes involved in cellulose, hemicellulose, pectin, cutin, and wax biosynthesis, with increased structural metabolites such as xylose, mannose, and galactonic acid. Delayed senescence was further supported by enhanced redox homeostasis, with upregulation of antioxidant-related genes including superoxide dismutase (SOD3), peroxidases (PRXs), glutathione S-transferases (GSTs), and ascorbate-associated genes (BX13), together with increased levels of protective metabolites such as proline, trehalose, and myo-inositol.
Authors: Jacopo Tartaglia, Mario Giorgioni, Luigi Cattivelli and Primetta Faccioli.
Advances in high-throughput DNA sequencing technologies have dramatically reduced the time and cost required to generate genomic data. As sequencing is no longer a limiting factor, increasing attention must be paid to optimizing the analyses of the large-scale datasets produced. Efficient processing of such data is essential to reduce computational time and operational costs. In this context, workflow management systems (WMSs) have become key instruments for orchestrating complex bioinformatic pipelines. Among these systems, Nextflow has emerged as one of the most widely adopted solutions in bioinformatics.
To improve scalability and computational efficiency, we employed Nextflow to re-design an already existing pipeline dedicated to the analysis of MNase‐defined cistrome‐Occupancy (MOA‐seq) data. The re‐engineering process focused on modularizing the workflow and integrating containerization technologies to ensure reproducibility and easier deployment across heterogeneous computing environments.
The resulting workflow, named MOAflow, represents a modernized and fully containerized pipeline for MOA‐seq data analysis. With only Docker and Nextflow required, the pipeline guarantees high portability and reproducibility. The data of the original article was used to benchmark the new pipeline. Its outputs closely match those of the original study with minor variations.
Authors: Lorena Ramirez-Gonzales, Simeo Sumuni, Lea Jäggi and Zerihun Tadele.
Neglected and underutilized crops (NUCs) refer to domesticated plant species that have been used for a long time for their role in food, feed, fiber, oil or medicine, but have lost importance over time. These crops are also known as orphan, abandoned, lost, underused, local, minor, traditional, and alternative crops. Due to multiple dietary benefits and their resilience to extreme environmental conditions, NUCs are considered Crops of the Future. In general, NUCs play a key role in the food and nutrition security of smallholder farmers and consumers in Africa. Due to lack of genetic improvement, the productivity of NUCs is extremely low. For instance, the average productivity of six NUCs consisting of two cereals [fonio (Digitaria spp.), and tef (Eragrostis tef)], two legumes [bambara groundnut (Vigna subterranea) and cowpea (Vigna unguiculata)] and two oil seeds [noug (Guizotia abyssinica)], and sesame (Sesamum indicum)] is below 0.7 t/ha in Africa. Root and tubers such as cassava with high yield are associated with short shelf-life making long-term storage difficult. In general, an agricultural revolution is required to be applied to selected NUCs to boost food production in Africa. This can be made partly by (i) collecting, conserving and utilizing diverse types of germplasms, (ii) applying advanced improvement techniques including speed breeding to improve productivity and quality, (iii) establishing partnerships with relevant stakeholders at the national and international level, and (iv) implementing the right type of strategies which promote research, production and extension. At the same time, emphasis should also be given to major crops such as maize and rice to ensure sustainable food systems in Africa.
Authors: Zerihun Tadele, Lea Jäggi, Lorena Ramirez-Gonzales and Simeo Sumuni.
Neglected and underutilized crops (NUC) refer to domesticated plant species that have been used for long time for their food, feed, fiber, oil, or medicinal properties, but have been reduced in importance over time. These crops are also known as orphan, abandoned, lost, underused, local, minor, traditional, alternative crops. Due to multiple dietary benefits and their resilience to extreme environmental conditions, NUC are considered as crops of the future. In general, NUC plays key role in the food and nutrition security of small-scale farmers and consumers in the developing world.
It is estimated that 85% of globally cultivated crops belong to neglected and underutilized crops. NUC are composed of cereals, pseudo cereals, legumes, vegetables, fruits and nuts, roots and tubers, and spices. NUC cereals are mainly represented by diverse types of millets which are annually cultivated on over 30 million ha of land. Pseudo-cereals which do not belong to the grass family due to their two cotyledons unlike grasses with a single cotyledon but show their closeness to the “true cereals” by their nutritional content especially carbohydrate. Pseudo-cereals include amaranth (Amaranthus spp.), buckwheat (Fagopyrum esculentum) and quinoa (Chenopodium quinoa).
Authors: Christine F. Madden, Brett Williams, Sagadevan Mundree, Sébastien Acket, Eric Ruelland, Henk W. M. Hilhorst and Jill M. Farrant.
Eragrostis nindensis is a resurrection grass capable of surviving near-complete desiccation. We compared non-senescent leaf tissue (NST) and senescent leaf tissue (ST) to investigate the cellular and molecular basis of desiccation tolerance and senescence. NST recovered fully after drying, while ST failed to regain viability. Integrated transcriptomic (using RNA-Seq), lipidomic (using LC-MS), and ultrastructural (Transmission Electron Microscopical) analyses revealed that NST maintain RNA processing, protein folding, and translational activity during desiccation. Lipidomic data and ultrastructure showed preferential accumulation of polyunsaturated triacylglycerols (TAGs) and lipid droplets in NST, supporting membrane protection and energy buffering. In contrast, ST showed cellular collapse, reduced oleosin protein accumulation, and signatures of senescence. These findings highlight the importance of post-transcriptional and post-translational regulation, as well as lipid metabolism, in preserving cellular integrity during desiccation in this species.
Authors: Maximillian R. W. Jones, Worku Kebede, Abel Teshome, Aiswarya Girija, Adanech Teshome, Dejene Girma, James K. M. Brown, Jesus Quiroz-Chavez, Chris S. Jones, Brande B. H. Wulff, Kebebew Assefa, Zerihun Tadele, Luis A. J. Mur, Solomon Chanyalew, Cristobal Uauy & Oluwaseyi Shorinola.
Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free “superfood” with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited “omics” resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1—a transcription factor regulating inflorescence morphology in cereals.
Authors: Julia Engelhorn, Samantha J. Snodgrass, Amelie Kok, Arun S. Seetharam, Michael Schneider, Tatjana Kiwit, Ayush Singh, Michael Banf, Duong Thi Hai Doan, Merritt Khaipho-Burch, Daniel E. Runcie, Victor A. Sánchez-Camargo, Rechien Bader, 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 & Thomas Hartwig.
Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1, ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.
Authors: Lorena Ramirez-Gonzales, Gina Cannarozzi, Abiel Rindisbacher, Lea Jäggi, Regula Schneider, Annett Weichert, Sonia Plaza-Wüthrich, Solomon Chanyalew,Kebebew Assefa and Zerihun Tadele.
The threat to world food security posed by drought is ever increasing. Tef [Eragrostis tef (Zucc.) Trotter] is an allotetraploid cereal crop that is a staple food for a large population in the Horn of Africa. While the grain of tef provides quality food for humans, its straw is the most palatable and nutritious feed for livestock. In addition, the tef plant is resilient to several biotic and abiotic stresses, especially to drought, making it an ideal candidate to study the molecular mechanisms conferring these properties.
The transcriptome expression of tef leaf collected from plants grown under drought conditions was profiled using RNA-Seq and key genes were verified using RT-qPCR. This study revealed that tef exhibits a complex molecular network involving membrane receptors and transcription factors that regulate drought responses. We identified target genes related to hormones like ABA, auxin, and brassinosteroids and genes involved in antioxidant activity. The findings were compared to physiological measurements such as changes in stomatal conductance and contents of proline, chlorophyll and carotenoid. The insights gained from this work could play vital role in enhancing drought tolerance in other economically important cereals such as maize and rice.
Authors: Lorena Y. Ramírez Gonzales, Gina Cannarozzi, Lea Jäggi, Kebebew Assefa, Solomon Chanyalew, Matteo Dell’Acqua and Zerihun Tadele.
Tef research has little benefited from omics due to neglect of the crop by the global scientific community. However, the few utilized tools showed promising results. Chromosome-scale assembly of the genome reveals the evolution of tef. The whole-genome sequencing of drought-resurrecting Eragrostis nindensis and desiccation-sensitive Eragrostis curvula shows genes that play key roles in drought responses. A few studies using omics tools have revealed differentially expressed genes, proteins, and metabolites in tef plants exposed to drought. Molecular markers have deciphered diversity in tef germplasm collected from diverse agroecologies in Ethiopia. The application of targeting induced local lesions in genomes resulted in mutant tef lines with a semidwarf stature, which were later bred to locally adapted and high-yielding varieties. Genome editing using ‘Green Revolution’ genes resulted in a semidwarf and lodging-tolerant tef plant.
Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef’s diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.
Authors: Nicolás Manosalva Pérez, Camilla Ferrari, Julia Engelhorn, Thomas Depuydt, Hilde Nelissen, Thomas Hartwig and Klaas Vandepoele.
Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF–target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.