Czechia

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.


SEB Conference 2024

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

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poster

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

Plasticity enables organisms to extend their tolerance limits, but the physiological basis of plastic responses is not well characterized. Here, we demonstrate that Drosophila melanogaster embryos undergo rapid thermal acclimation, on the timescale of hours, that extends their upper thermal limit. Because early development is coordinated by changes in chromatin state and gene activation, we set out to characterize the molecular basis of embryonic thermal plasticity by performing single nuclei multiome ATAC and RNA sequencing. We found coordinated changes in chromatin state and the transcriptome in response to thermal acclimation. Cool-acclimated embryos exhibited thermal compensation through increased chromatin accessibility of transcription factor binding motifs of global transcriptional activators and higher expression of genes encoding ribosomal proteins and enzymes involved in oxidative phosphorylation. Although most of these shifts were common to all cell types, many changes were cell type specific. For example, cold-acclimated embryos had higher overall gene expression in tracheal primordial cells, presumably to prepare for increased gas exchange to support a higher metabolic rate. On the other hand, we observed modestly higher expression of genes involved in cell migration and cell adhesion in warm-acclimated embryos, particularly in ventral nerve cord primordia, suggesting a potential role for locomotor and sensory development in embryonic heat tolerance. Our results indicate that thermal plasticity is largely mediated by shifts in the epigenome and transcriptome that regulate the speed of development and that may impose metabolic costs that constrain upper thermal limits.

Single nuclei multiome ATAC and RNA sequencing reveals the molecular basis of thermal acclimation in Drosophila melanogaster embryos

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

Both adaptation and plasticity are critical for species persistence during rapid anthropogenic global change. However, we know little about how these mechanisms of resilience interact, particularly the role of epigenetic variation in long-term adaptation. We used a 25-generation selection experiment simulating future acidification, warming, and their combination to reveal how epigenetic and genetic mechanisms interact to promote resilience in a foundational copepod at the base of the marine food web. Epigenetic divergence was positively linked to gene expression divergence, indicating that epigenetic changes may facilitate phenotypic change. In contrast, genetic and epigenetic changes were negatively related, where genomic regions experiencing significant epigenetic changes had lower genetic divergence than those without. Thus, evolutionary and epigenetic changes acted in different regions of the genome during adaptation to global change conditions, due to either local inhibition of one another or distinct functional targets of selection. These results suggest that both genetic and epigenetic mechanisms underlie resilience to global change but have unique contributions.

Epigenetic and genetic mechanisms uniquely contribute to evolutionary rescue from global change

Climate change is increasing the frequency and severity of heatwaves, posing a significant threat to aquatic organisms globally. During an extended heatwave, aquatic organisms, like fish, may use phenotypic plasticity to help offset the effects of increased temperatures and associated low oxygen. The ability of a population to use plasticity to cope with heatwaves could be key for predicting species responses to climate change, especially in species of conservation concern like white sturgeon. We assessed the tolerance of juvenile white sturgeon from an endangered population to heatwave conditions and the effects of heatwave acclimation on subsequent stressors. We measured both thermal and hypoxia performance paired with underlying epigenetic and transcriptional mechanisms to assess the resilience of white sturgeon to heatwaves. Sturgeon exposed to simulated heatwave conditions had increased thermal tolerance and showed complete compensation for the effects of acute hypoxia. These changes were associated with increases in mRNA levels of genes associated with thermal and hypoxic stress. Global DNA methylation was sensitive to heatwave acclimation, changing in the gill and heart over the course of the heatwave exposure. Additionally, we observed rapid changes in DNA methylation during stressor trials over the course of an hour. These data demonstrate tremendous resilience in juvenile white sturgeon to heatwaves which was associated with improved cross-tolerance and responses in epigenetic and transcriptional mechanisms.

From the epigenome to performance: heatwave resilience through impressive thermal plasticity in white sturgeon

Balancing the control that is possible with lab studies with the real-world applicability of field work is a challenge in all experimental work. Using the example of the relationship between temperature, metabolic potential and social behaviour in fish, I will explore ways to incorporate more field relevance into lab studies and take lab-based theory to the field. As ectotherms, temperature has been called the “master factor” for fish; playing a large role in setting metabolic potential which in turn influences many aspects of behaviour and physiology. For example, changes in temperature have the potential to shift the cost-benefit analysis fish must conduct to balance the benefits of remaining in a group with the costs of increased competition. However, when considering the complexities of the natural world this relationship becomes less straight forward.

Taking our understanding of thermal influences on social behaviour from the lab to the field

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.

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

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