The most important achievements

of Institute of Plant Genetics PAS in 2024

Regulation of Gene Expression Team

Using ChIP-seq, we identified sites in the genome of cultivated potato species, Solanum tuberosum cv. Desiree, to which StBBX20 protein binds during the light and dark phases of the circadian cycle. We identified 4971 DNA peaks in the dark and 4598 in the light for which protein-DNA interactions were detected. We identified 55 DNA regions which statistically significantly differed between the light and dark phases. The most probable 3 conserved cis-regulatory motifs for each experimental condition tested, were generated (1) for darkness: AYCYACGGDCCGTRG, CCGACTGCTCCTTTY, CTGKAACTTTVGGCG, (2) for light: AHCYACGGRCCGTRG, ABTCGGCGAHTCGC, CGCCYAAWGTTMCAG, (3) differentiating the dark and light phases: CTTCTTCWTCT, ACYATGTGCCCACAT, CTAAGCCAAACATCG, which were subjected to comparative analysis and GO annotation.

Plant Physiology Team

Four BnaHB6 gene homeologs in Brassica napus have been shown to exhibit functional diversity under conditions of water deficit, salinity, and circadian rhythm. Only two of these are molecular components regulating the expression of some BnaABF2 and BnaDREB2 paralogs under stress conditions. The results confirmed that BnaHB6 genes are part of a complex regulatory network in oilseed rape which allows plants to adapt to adverse environmental conditions.

Żyła N., Cieśla A., Szała L., Babula-Skowrońska D. (2024) Functional and regulatory diversity of homeobox-leucine zipper transcription factors BnaHB6 under dehydration and salt stress in Brassica napus L. Plant Molecular Biology 114 (3): 59. DOI: 10.1007/s11103-024-01465-6.

Biometry and Bioinformatics Team

ATAC-seq (assay for transposase-accessible chromatin) was used for the first time  to identify open chromatin regions in the crown of barley plants exposed to elevated temperatures. Prolonged exposure increased chromatin accessibility, including genes involved in stress signaling and tolerance. Loss of chromatin accessibility in response to heat was shown to downregulate the expression of genes involved in gibberellin signaling.

Kiełbowicz-Matuk A., Smaczniak C., Mikołajczak K., Kuczyńska A., Xu X., Braeuning C., Krajewski P. (2024) Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare). Plant Molecular Biology 114 (6): 115. DOI: 10.1007/s11103-024-01509-x.

Cereal Phenomics Team

Based on GWAS analysis, which identified SNP in genes associated with barley phenotype and yield, CAPS markers were developed for selected genes, e.g., HORVU.MOREX.r3. 7HG0658720 (plant height) and HORVU.MOREX.r3.3HG0234500 and HORVU.MOREX.r3.3HG0234660 (number of grains per spike). Their use may facilitate the selection of genotypes for desired breeding traits.

Kempa M., Kuczyńska K., Mikołajczak K., Ogrodowicz P., Michałek M., Mokrzycka M. Unveiling Barley Genetic Sequences through CAPS Technique: Implications for Breeding and Cultivation. Global Challenges for Crop Improvement, XXII EUCARPIA General Congress, Lipsk, Niemcy, 18-23 sierpnia 2024; plakat.

Plant Biotechnology Team

Based on selected chlorophyll fluorescence parameters and biometric traits, cold stress tolerance and sensitivity markers were developed, which enabled the selection of two forms from a collection of 18 Miscanthus sinensis genotypes which differ significantly in their stress response, the so-called Low/High Cold Tolerant, i.e. LCT – Ms12 and HCT – Ms16, used in detailed studies on the genetic, physiological and biochemical aspects of stress response, including changes in the cell wall.

Sobańska K., Mokrzycka M., Przewoźnik M., Pniewski T., Głowacka K. Exploring Chilling Stress and Recovery Dynamics in C4 perennial grass of Miscanthus sinensis. PLoS ONE, DOI:10. 1371/journal.pone.0308162 (praca przyjęta do druku).

Pathogen Genetics and Plant Resistance Team

In the collaboration with the Plant Breeding and Acclimatization Institute – National Research Institute, Poznań, we have developed unique forms of winter rapeseed with high oleic acid content (≥ 72%, HO), low linolenic acid content (< 5%, LL), and resistance to specific pathotypes of Plasmodiophora brassicae (clubroot). The HOLL-CR forms we have obtained are the first valuable rapeseed genotypes with these parameters described in the literature. The plant material is the property of the Plant Breeding and Acclimatization Institute – National Research Institute.

Spasibionek S., Mikołajczyk K., Matuszczak M., Kaczmarek J., Ramzi N., Jędryczka M. (2024) HO-CR and HOLL-CR: new forms of winter oilseed rape (Brassica napus L.) with altered fatty acid composition and resistance to selected pathotypes of Plasmodiophora brassicae (clubroot). Journal of Applied Genetics 65 (3): 439 - 452. DOI: 10.1007/s13353-024-00867-y.

Plant - Pathogen Interaction Team

An enhanced protective effect of the co-culture of Pseudomonas protegens and Trichoderma koningiopsis strains in limiting the infection of wheat plants by Fusarium cerealis was demonstrated, as well as increased growth of treated plants compared to control plants.

Ajijah N., Fiodor A., Kazimierczuk K., Urbaniak M., Enow E.A. Stasiuk R., Stępień Ł., Dziewit Ł., Pranaw K. (2024) Pseudomonas protegens ML15 and Trichoderma koningiopsis Tr21 co-culture: a potent strategy for suppressing Fusarium cerealis infections in wheat through augmented antifungal metabolite production. Biological Control 198: 105621. DOI: 10.1016/j.biocontrol.2024.105621.

Plant Microbiomics Team

The transmission pathways of wheat endophytic fungi have been determined. Using classical methods and those which do not require fungal isolation (high-throughput methods), it has been documented that some endophytic fungal species have the capacity for horizontal transmission between generations of wheat plants via seeds.

Legume Genomics Team

A collection of white lupin (>2000 pure SSD lines) has been developed, utilizing the global genetic resources of this species. This collection has been characterized in detail in experiments conducted over several years in various locations (controlled conditions) using a phenotyping protocol (Kroc et al. 2021, Bellucci et al. 2021). It currently represents the largest and best-characterized collection of white lupin in the world, and the demonstrated lines variability has the potential to significantly increase the utilization of the gene pool in breeding programs for this species.

Submitted paper::

Tanwar U., Tomaszewska M., Czepiel K., Neji M., Jamil H., Rocchetti L., Pieri A., Bitocchi E., Bellucci E., Pipan B., Meglič V., Kroc M., Papa R., Susek K. “Genetic and phenotypic characterization of global Lupinus albus genetic resources for the development of a CORE collection”. BioRxiv 2024.09.25.614894; doi: https://doi.org/10.1101/2024.09.25.614894.

Gene Structure and Function Team

In a pool of 262 white lupin genotypes from 19 countries and different climate zones, genomic association mapping of PCR and DArT-seq markers identified a significant association with flowering date and vernalization response for four deletions from the promoter region of LalbFTc1 gene, which is a homolog of Flowering locus T gene in A. thaliana. These deletions are 2388 bp and 2126 bp in the 5' region of the promoter, 264 bp in the middle, and 28 bp in the 3' region.

Rychel-Bielska S., Bielski W., Surma A., Annicchiarico P., Belter J., Kozak B., Galek R., Harzic N., Książkiewicz M. (2024). A GWAS study highlights significant associations between a series of indels in a FLOWERING LOCUS T gene promoter and flowering time in white lupin (Lupinus albus L.). BMC Plant Biology 24(1): DOI: 10.1186/s12870-024-05438-1.

Integrative Plant Biology Team

The systemic nature of phloem-mediated reprogramming in the coordination of physiological and developmental processes in rapeseed plants infected with clubroot, was described.

To understand the role of the phloem in mediating the interaction between the underground, infested by Plasmodiophora brassicae, and aboveground parts of the plant, gene expression profiling was performed in laser-dissected cells of this tissue. Phloem was found to play a key role in coordinating the distribution of carbon, nitrogen, and cytokinins between the upper and lower parts of the plant. The systemic nature of the plant response to P. brassicae infection was demonstrated, which is crucial for understanding disease progression.

Blicharz S., Stefanowicz K., Truman W., Basińska-Barczak A., Singh D., Kasprzewska A., de Diego N., Vrobel O., Ćavar Zeljković S., Tarkowski P., Malinowski R. (2025) Laser dissection-assisted phloem transcriptomics highlights the metabolic and physiological changes accompanying clubroot disease progression in oilseed rape. Plant Journal 121: DOI: 10.1111/tpj.17156.

Plant Biology and Nanotechnology Team

Despite the pharmacological value, annotated complete genome sequence data are not yet publicly available for any of the Hypericum species. We have published the single-molecule real-time sequencing (SMRT) data sets of H. perforatum plantlets and cell suspension cultures. SMRT sequencing yielded over 33,000 high-quality transcripts from cell cultures and 55,000 from plantlets of H. perforatum. The data not only fill crucial gaps in our understanding of secondary metabolite biosynthesis, but also provide a fundamental resource for comparative transcriptomic analyses of the large genus Hypericum, which comprises more than 500 species.

Selvakesavan R.K., Nuc M., Kolarčik V., Krajewski P., Franklin G. (2024) Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures, Scientific Data 11 (1): 42. DOI: 10.1038/s41597-023-02878-6.

Plant Nanotechnology Team

Understanding the Effect of Ionic Liquid–Mediated Solvent Engineering on the Kinetics and Thermodynamic Stability of Phenylalanine Ammonia-Lyase: phenylalanine ammonia-lyase (PAL) plays a central role in the phenylpropanoid pathway and in the treatment of phenylketonuria. However, the integration of PAL into sustainable industrial biocatalysis is hampered by its instability under harsh conditions. This study demonstrates that ionic liquid (IL)–assisted solvent (Tris-HCl buffer) engineering enables improvement of the reaction kinetics and thermodynamic stability of Rhodotorula glutinisPAL (RgPAL) under various stresses. Under optimized conditions, a 66.2% higher K_cat value, >60% remaining activity after 5 weeks of storage at room temperature, and >80% activity of RgPAL after incubation at 60 °C for 1 h were obtained in the [Ch][Ac]-blended Tris-HCl solvent compared to pristine Tris-HCl. Overall, IL-mediated solvent engineering alters the microenvironment of RgPAL and allows the development of a robust PAL-based biocatalytic system.