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The conservation of biodiversity and the improvement of agricultural productivity stand as imperative pursuits within the context of sustainable development, wherein gene banks assume a central role. These repositories safeguard a diverse array of plant genetic resources, constituting indispensable assets for both conservation and prospective breeding endeavors. Improving technologies for gene banks are crucial for the preservation and utilization of global biodiversity. Automation plays a pivotal role in advancing gene banks, streamlining critical processes, and bolstering the efficiency of genetic resource management. Automated technologies, such as robotic systems for seed handling and germination testing, significantly accelerate the pace at which plant genetic resources can be collected, processed, and cataloged. This not only optimizes the use of human resources but also minimizes the risk of errors and contamination. Automation in data management ensures accurate record-keeping and facilitates the swift retrieval of information, aiding researchers in identifying valuable traits and making informed decisions for crop improvement. Furthermore, the integration of artificial intelligence, plant phenotyping, and novel kinds of sensors in gene banks enhances the characterization of vast collections of plant genetic resources, enabling the rapid identification of novel genetic traits and the development of more resilient and adaptive crop varieties. In essence, improving technologies for gene banks not only enhance operational efficiency but also amplify the impact of genetic resources in addressing global challenges related to food security and environmental sustainability.

SEB Conference Prague 2024

Innovating Gene Banks: Unleashing Automation and Advanced Technologies for Global Biodiversity Conservation and Agricultural Innovation

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SEB’s Annual Conference is celebrated for creating the perfect composition of research, new discoveries and collaborative connections. Be creative and innovative by exchanging ideas and knowledge with masters of biology from all over the world.

One of the many steps towards reaching the UK’s goal of tripling its tree planting figures to 30,000 hectares a year is increasing the current tree production output. Threats such as ash dieback disease shed light on the need to maintain certain genetic features, calls for the development of complementary clonal propagation protocols. Stem cuttings are simple propagules that, upon successful development of adventitious roots, may provide high numbers of individuals with the desired features for the future woodlands. Cuttings from broadleaved tree species such as oak and ash are often considered recalcitrant to rooting, especially as they age. Auxin-containing powders and solutions are the main rooting enhancer treatment used in nurseries, though often unsuccessfully in hard-to-root cuttings. With the role of auxin being knowingly dependent on time, a single application might not provide the target tissues with adequate auxin levels. In this project, we are monitoring the responses to different auxin formulations along time and correlating it to rooting-related physiological parameters. Early results evidence the low rooting rates of oak and ash cuttings, higher callus formation rates in warmer seasons, and a strong seasonality factor, with the few rooting events taking place in cuttings collected in late summer-early autumn. Observation from the next, larger experiments will be used to build a working model for how different physiological parameters affect rooting outcomes in UK tree cuttings, paving the way for improved, data-driven propagation protocols.

Propagation of broadleaved UK tree species by cuttings: gauging physiological responses to different auxin formulations

Rice (Oryza sativa L.) is one of the ancient, cultivated crops which is consumed by over half of the world’s population. Globally the percentage of soil affected by salinity is increasing, with irrigated areas of particular concern. Rice is highly salt sensitive crop that may lose 50% of its yield at a soil electrical conductivity (EC) value of only ~6 dsm−1. About 150 genotypes from Bengal and Assam Aus Population (BAAP) was used for this experiment having four replications with three different salt treatments i.e. control (0 dsm−1), 2 dsm−1 and 4 dsm−1. The seeds were sown in a 38 cm long tubes whose bottom was closed with a fine mash to pass water but not soil. The tubes were placed in a box whereas each box contained 15 tubes with 15 different genotypes. Sea water collected from Cox’s Bazar was diluted up to the desired level by adding ground water. All the traits showed significant treatments effect. Salt injury score (SIS), stomatal conductivity, grain biomass had significant genotype and treatment effects whereas SIS had highly significant (p<0.001) negative correlation with grain biomass (-0.55). Plant height, shoot biomass, stomatal conductivity and SIS showed normal frequency distribution in three of the treatments. Salt tolerant accessions have been identified. Genome Wide Association mapping will be presented to identify to identify QTLs and candidate genes responsible for salt tolerance from those genotypes of BAAP.

Genome Wide Association Genetics of Rice for Salinity Tolerance at Maturity Stage under Field Condition

Nowadays, the threat of drought to crop production is increasing due to ongoing climate change and a growing world population, which poses a challenge to food security. To solve the problem of plant susceptibility to drought, one potential solution is to study new varieties that are more resistant and investigate key regulators of plant responses to unfavorable environmental conditions. In our research, we examined the effect of exogenous abscisic acid (ABA) treatment, a plant hormone crucial for the response to drought, on barley mutants carrying mutations in the genes encoding the CBC complex, an important component of ABA-related signaling pathways, as well as on the parental cultivar Sebastian. Using the TILLING technique, we created mutants in the genes (hvcbp20.ab and hvcbp80.b) encoding both subunits of the CBC complex and we also generated a double mutant (hvcbp20.ab/hvcbp80) carrying mutations in both genes simultaneously. We subjected these mutants and the parent variety to drought stress, ABA-only treatment, and ABA pretreatment followed by drought stress. Our studies showed that these mutations significantly affected photosynthetic parameters, especially after ABA treatment. Additionally, transcriptome sequencing enabled the observation of changes in biological processes within the analyzed genotypes and the identification of key genes that may cause the observed changes. In conclusion, we have shown that mutations in the genes encoding the CBC complex can increase plant resistance to drought conditions, providing valuable information for improving crop sustainability in the face of climate challenges.

Impact of abscisic acid treatment for better adaptation of spring barley CBC mutants to drought stress

Enhancing photosynthesis is widely acknowledged as an underutilized strategy for increasing crop productivity. For crops like maize (Zea mays L.), even small improvements in yield can have significant implications for global food security. Although maize is a C4 species, which is considered to be more efficient than C3 photosynthesis, there is substantial evidence that there is potential for further improvement.
Improving photosynthetic efficiency via targeted manipulation of non-photochemical quenching has focused on a limited set of genes that are known to be important determinants of the NPQ response in C3 plants. The C4 pathway may alter NPQ responses but only relatively few studies have explored genetic variation in NPQ kinetics in species that perform C4 photosynthesis. Here we apply high-definition phenotyping of NPQ responses and photosynthetic efficiency and quantitative trait locus (QTL) mapping using a field-grown maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which combines the allelic diversity of eight contrasting inbred founder lines. We find substantial and consistent variation for dynamic NPQ and PSII efficiency for two consecutive field season experiments in which over 300 Recombinant Inbred Lines (RILs) were characterized. The exploration of candidate genes within three major QTL regions identified a strong impact of allelic variation in expression of the minor PSII antenna protein CP24 (LHCB6) on a major QTL for NPQ and efficiency of PSII photochemistry on chromosome 10.


The Genetic Basis of Dynamic Non-photochemical Quenching and Photosystem II Efficiency in Fluctuating Light Reveals Novel Molecular Targets for Maize (Zea mays L.) Improvement

Abscisic acid (ABA) serves as a pivotal phytohormone enabling plant adaptation to unfavorable conditions and seed germination regulation. The negative regulators of the ABA signaling, such as CBP20 (Cap-Binding Protein 20) and CBP80 encode CBC (Cap-Binding Complex) subunits, crucial for RNA metabolism and alternative splicing. However, the role of CBC in ABA signaling during seed germination in crops like barley (Hordeum vulgare) remains unclear. We conducted experiments using a hvcbp20.ab/hvcbp80.b double mutant with single hvcbp20.ab and hvcbp80.b, identified within our TILLING population, and its parent cv. ‘Sebastian’. After the exposure to exogenous ABA at the seed germination stage, we performed physiological, high-throughput transcriptomics (RNA-seq), and metabolome analyses of genotypes tested. Our results showed that in the presence of ABA, hvcbp20.ab and hvcbp80.b exhibited sensitivity to ABA. Unexpectedly, the hvcbp20.ab/cbp80.b appeared to be ABA-insensitive, similarly to the WT. Identification of differentially expressed genes (DEG), differentially expressed transcripts (DET) and differentially alternatively spliced genes (DAS) combined with metabolome results allow us to link the hvcbp20.ab/hvcbp80.b phenotype in response to ABA with the altered alternative splicing regulation and with changes in brassinosteroid signaling and biosynthesis. This highlights the importance of delving deeper into the relevance of the double mutation in hvcbp20.ab/hvcbp80.b, as it offers valuable insights into the pivotal role of CBC in ABA signaling and adaptation to ongoing environmental changes.
This work was supported by the National Science Center, Poland project SONATA BIS10 ‘(QUEST) Quest for climate-smart barley–the multilayered genomic study of CBC function in ABA signaling’ (2020/38/E/NZ9/00346).

The role of Cap-Binding Complex (CBC) in ABA-dependent seed germination in barley

European Hazelnut (Corylus avellana L.) is a high-value, understudied crop. Commercial production is based on a small number of varieties that are grown globally and exhibit a large diversity of traits with a substantial influence of environment. Genetic improvement of hazelnut requires a deeper understanding of its extant agrobiodiversity and of its relationship with agronomic and quality traits. Here, we use a genotyping-by-sequencing approach to characterise the diversity of a global collection of hazelnut varieties and to identify loci associated to traits of interest. We describe the diversity of 141 non-redundant accessions with 16,378 high-quality single-nucleotide polymorphisms (SNPs). We use population genetics analyses to reveal the existence of three to five cryptic genetic clusters, with Asian varieties being more distinct, while populations in Europe and in the United States are more admixed. Concurrently, we measured kernel diversity and main agronomic traits in the collection. A Genome-Wide Association Study (GWAS) revealed 3 significant associations between SNPs and seed size, an important trait for industrial exploitation of hazelnut. 5 SNPs could also be associated with aromatic components measured with gas chromatography-ion mobility spectrometry (GC-IMS). These findings set the foundation for a genomics-driven exploration of hazelnut germplasm, promoting hazelnut research for industrial and conservation purposes.


European Hazelnut (Corylus avellana L.) in the genomic era: deciphering the genetic diversity and providing insights into agronomic traits

This study addresses the challenge of detecting grain spikes in images for crop yield assessment. Grain spikes are crucial but difficult to discern due to their minimal presence and similarity to surrounding leaves, posing a challenge even for advanced deep-learning networks. We enhance detection by refining the Faster R-CNN (FRCNN) architecture, simplifying feature extraction layers, and adding a global attention module. Testing on diverse European wheat varieties, including complex bushy types, our modified FRCNN (FRCNN-A) outperforms the standard model, achieving a mean Average Precision (mAP) increase from 76.0% to 81.0%. Compared to the Swin Transformer's 83.0% mAP, our model shows competitive performance. We also tested Yolov8 and Yolov4 models, achieving 0.79 and 0.78 mAP, respectively. The model was deployed on the PlantScreenTM system to extract phenotypes such as awn detection and spike count in late reproductive stage plants.


Enhancing Spike Detection in Greenhouse-Grown Grain Crops Using Attention-Based Deep Learning Models

GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) is a histone acetyltransferase in Arabidopsis thaliana involved in numerous biological processes, including flower development. Previous studies have demonstrated GCN5's interaction with the CLAVATA (CLV) pathway, influencing gynoecium development potentially through modulating auxin and cytokinin dynamics and regulating WUSCHEL (WUS) expression. In clv1gcn5 double mutants, noticeable phenotypic alterations include reduced or absent valves, an enlarged stigma, and an elongated gynophore, indicative of disruptions in both apical-basal and mediolateral axes of the gynoecium. SPATULA (SPT), a bHLH transcription factor, is a pivotal regulator in gynoecium development. Intriguingly, this work demonstrates that SPT mutations partially alleviate clv1gcn5 phenotypes; specifically, they restore the formation of valves in the ovary. Transcriptomic analysis of gynoecium mutants, including spt, clv1, gcn5 and the various genetic combinations, reveals their significant impact on apical-basal, mediolateral, and adaxial-abaxial polarity axes. Genes such as STY1/2, PID, and TCP15 governing apical-basal polarity were misexpressed in clv1gcn5 mutants and showed either complete or partial restoration of their levels in sptclv1gcn5 gynoecia. Similarly, mediolateral genes, including CUC2, FIL, YAB3, and JAG, downregulated in clv1gcn5, were reinstated in sptclv1gcn5 mutants. Notably, adaxial-abaxial factors like REV, ATHB4, and AS1 follow a similar pattern, suggesting that GCN5, CLV1 and SPT are essential players in the proper determination of polarity axes in the Arabidopsis gynoecium.
This study unveils the intricate interplay among GCN5, CLV1, and SPT, underscoring their pivotal roles in orchestrating gene expression and polarity determination during Arabidopsis thaliana gynoecium development.

Transcription factor SPT interacts with CLAVATA signaling and GCN5 acetyltransferase to affect polarity axes in Arabidopsis thaliana gynoecium

The evolution of the mitochondrion enabled multicellularity and diversity of life histories that necessitated not merely a large, but in many cases, a variable supply of energy. With that, individual organisms also need a means to precisely regulate energy to match life’s demands. Over the past 15 years, a growing number of researchers have delved into evaluating mitochondrial respiratory function to understand evolutionary adaption and constraints on energetic capacity. Within these data, we have seen many examples suggesting that the energetic capacity of mitochondria is not fixed within individuals and can vary with genotype, leakiness of the mitochondria’s inner membrane, and oxidative damage. Yet, these do not appear to be the only means by which animals can adjust their capacity for oxidative phosphorylation. With this presentation, I will review evidence from my lab and others suggesting that changes in mitochondrial morphology and mitochondrial dynamics (most notably fission and fusion) play an essential role in up and down-regulating oxidative phosphorylation and mitigating oxidative damage. I will propose that these processes are vital to the diversity of energetic ability observed throughout Animalia.



Remodelling the powerhouse: Mitochondria morphology and dynamics in ecological and evolutionary processes

Cowpea is a promising crop for future Food Security in Sub-Sahra Africa (SSA) due to its nutritional value and resilience to extreme weather conditions like high temperatures and severe drought. However, projected climate changes threaten its production in SSA by exacerbating these weather conditions. While efforts have been made to improve cowpea yields by increasing the above-ground biomass, little attention has been given to enhancing its photosynthetic efficiency, which directly impacts harvest index and yield. This study investigates how heatwaves during the vegetative and reproductive stages independently affect cowpea photosynthesis and biomass using two genotypes with varying tolerance to heat. Heatwaves significantly reduced cowpea net photosynthesis and the number of grains per plant, with greater impact during the reproductive stage although the impact on photosynthesis and grain number are not directly correlated. The impact of heat on net photosynthesis could be associated with limited biochemical capacity of cowpeas during heatwave. These findings will contribute to understanding the factors of cowpea photosynthesis that need more focus for improving its photosynthetic efficiency and resilience. These insights are crucial for developing strategies to sustain cowpea productivity amidst changing climate conditions in SSA.

Innovating Gene Banks: Unleashing Automation and Advanced Technologies for Global Biodiversity Conservation and Agricultural Innovation

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Propagation of broadleaved UK tree species by cuttings: gauging physiological responses to different auxin formulations

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