Czechia

Nitrogen (N) is essential for agriculture and its excessive use causes severe environmental damage. Improving nitrogen use efficiency (NUE) is crucial for achieving more productive crops under conditions of limited N availability. To the best of our knowledge, this is the first study aiming to integrate the morphophysiological responses, transcriptomics and proteomic profiles of leaves and roots of popcorn to understand NUE. For this, two NUE-contrasting inbred lines P2 (high NUE) L80 (low NUE), were cultivated under high (100% of N supply) and low (10% of N supply) N conditions. Morphological and physiological traits such as photochemical quenching (qP), non-photochemical quenching (NPQ), quantum yield of photosystem II (ΦPSII), and potential photosynthesis (Apot) were evaluated. P2 showed more pronounced vegetative growth under low N, as well as higher values of qP, NPQ, ΦPSII and Apot. Comparative transcriptomics and proteomics analysis revealed that more than 215 differentially accumulated proteins (DAPs) and 430 differentially expressed genes (DEGs) were involved in the response to low N in both lines. In leaves, DAPs and DEGs involved in the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, the mechanisms of nitrate transport, ammonium assimilation, and amino acid metabolism seem to have contributed to the improved NUE in P2. This study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.

SEB Conference Prague 2024

Combined transcriptomics and proteomics profiling reveals mechanisms underlying nitrogen use efficiency in popcorn (Zea mays var. everta)

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High tomato (Solanum lycopersicum) sugar content, redness of color, and firm texture are associated with a prominence of rich flavor, directly influencing consumer preferences. One major challenge of tomato improvement is to deliver superior flavor in the context of high yield and long postharvest shelf-life. TAM-SP18-157 line is extraordinarily firm resulting in long shelf-life fruit that conserves quality characterized by lack of locule gel caused by a single recessive gene mapped to chromosome 10. As opposed to long shelf-life tomatoes with impaired ripening hormone emissions, ethylene production is high in TAM-SP18-157. Tomato line TAM-SP18-157 was crossed with locule gel carrying line TAM-SP18-501. Fruits from TAM-SP18-157 lacking locule gel were 43.75% and 9.41% more firm than fruits having gel from TAM-SP18-501 and F1, respectively. Furthermore, fruits lacking locule gel were still very firm up to for 21 days (0.8 KgF), while fruits with gel were softer at that time point (0.6 KgF). Similar trend was observed for Brix, were fruits lacking gel had higher soluble solid content than fruit with gel with intermediate levels in the F1 hybrid. Fruit acidity content was lower in fruits lacking locule gel, while fruits from the F1 cross had higher acidity content as compared with the two parental lines. Together, result indicate that locule gel plays an important role in postharvest life and quality. Therefore, tomato line TAM-SP18-157 can be used to improve those characteristics by breeding for locule gel content in tomato fruits.

Lack of locule gel increases post-harvest shelf-life and quality in tomato

Drought represents one of the main threats to global food security. As a response, plants have adapted their metabolism to cope with stress factors like water scarcity. Among these adaptations, polyamine (PA) metabolism plays a crucial role in regulating plant growth, development, and resilience to stress. Under stress factors, plants adjust their endogenous levels of PAs through de novo synthesis and catabolism. In Arabidopsis thaliana, a model plant species, five polyamine oxidase enzymes (AtPAO1 to 5) have been identified, which participate actively in the catabolism of superior PAs like spermidine, spermine, and thermospermine.

This research focused on the impact of water deficit (WD), defined as 20 to 30% substrate moisture, on five single Atpao mutant lines over three weeks. By using plant phenotyping approaches (non-invasive sensors), we assessed the effects of drought on various aspects of growth and photosynthetic performance for each mutant line.

Our findings revealed that WD significantly reduced water status (<RWC), biomass, rosette size, and photosynthesis across all mutant lines compared to the wild-type. Furthermore, stressed plants significantly increased foliar temperature, which adversely affected leaf transpiration rates. Interestingly, the study uncovered a variable response among the mutant lines in terms of photosynthesis capacity and leaf energy dissipation when subjected to stress, highlighting the significant contribution of PA catabolism to plant drought tolerance. Future studies addressing the biochemical and molecular profile will further elucidate the mechanism involved and the specific role of each AtPAO gene in plant adaptation to water scarcity.

Plant phenotyping approaches to understand the polyamine catabolism role in Arabidopsis plants under water deficit

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.

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

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.


Combined transcriptomics and proteomics profiling reveals mechanisms underlying nitrogen use efficiency in popcorn (Zea mays var. everta)

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Lack of locule gel increases post-harvest shelf-life and quality in tomato

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