Katarzyna Nowak

During its lifetime, the plant undergoes transitions between critical developmental stages, such as seed-to-seedling and adult-to-flowering stages. The changes between stages are strictly controlled by genetic and epigenetic factors that act together during the transition. The developmental transition involves repressing active genes in the first stage and activating genes in the next stage. Thus, repression appears to be essential for terminating the previous developmental program, and among the repressors, the VAL genes play a central role. The VALs are B3-domain DNA-binding proteins that regulate LAFL genes during the seed-to-seedling transition, during which VALs downregulate LAFL expression, thereby terminating the embryogenic program in seedlings. Moreover, the VAL also affects the expression of MIR156C, FLC, or FT in the regulation of flowering. These proteins interact with numerous chromatin remodeling factors, such as PRC1, PRC2, and HDAC, which perform distinct histone modifications, ubiquitination, methylation, or deacetylation to negatively regulate the expression of target genes. This review examines the recent advances in studies on the VALs genetic network, which is involved in the developmental transition via diverse epigenetic mechanisms. Moreover, a future perspective on studies of these essential regulators was discussed.

The genus Fagopyrum includes economically important species such as F. esculentum and F. tataricum, which are valued for their nutritional and bioactive properties, as well as their wild relative F. homotropicum, which is understudied in tissue culture systems. While callus cultures of Fagopyrum species are essential for breeding and biotechnology applications, their growth and metabolic dynamics are poorly characterised, particularly regarding phenolic compound accumulation, which can influence callus proliferation and regeneration. This study aims to provide a comparative analysis of callus growth kinetics, phenolic metabolism, and gene expression in F. esculentum, F. tataricum, and F. homotropicum. Callus growth varied significantly among the three species, with F. esculentum exhibiting the highest proliferation rate, with an increase of 11.4-fold of its initial mass, followed by F. tataricum with a 4.7-fold increase and F. homotropicum with a 3.5-fold increase. Phenolic profiling revealed distinct metabolic specialisations: F. homotropicum exhibited the highest total phenolic content, primarily dominated by flavan-3-ols, such as (+)-catechin (3207.98 µg/g). In contrast, F. tataricum predominantly accumulated rutin (1331.63 µg/g), while F. esculentum displayed the minimal total phenolics content. Corresponding gene expression patterns aligned with these trends, as F. homotropicum strongly upregulated dihydroflavonol 4-reductase (proanthocyanidin synthesis), whereas F. tataricum favoured flavonol synthase expression, consistent with its rutin-rich profile. This study establishes a foundation for optimising Fagopyrum tissue culture systems and elucidates species-specific metabolic adaptations, advancing their potential use in biotechnology and breeding programs. Graphical abstract

Background: Fagopyrum tataricum (Tartary buckwheat) is known for its high phenolic content, particularly rutin. High concentrations of these compounds secreted in the tissue culture medium can lead to its darkening and the eventual death of explants in in vitro cultures. This study aims to enhance the morphogenesis of F. tataricum callus cultures by utilising phenylalanine ammonia-lyase (PAL) inhibitors and polyvinylpyrrolidone (PVP) to mitigate oxidative browning and improve tissue viability. Results: We analysed the response of protoplasts isolated from morphogenic callus to media supplemented with varying concentrations of PAL inhibitors (AIP, AOPP, OBHA) and PVP. The flow cytometry results revealed that 10 µM AIP and 1% PVP yielded exclusively diploid plants, whereas higher concentrations (100 µM AIP and 3% PVP) failed to regenerate plants. Moreover, AOPP and OBHA addition resulted in the regeneration of tetraploid plants. Further analysis of proembryogenic cell complexes (PECCs) isolated from Tartary buckwheat morphogenic calli responses to AIP and PVP indicated that 100 µM AIP was most effective for plant regeneration. Metabolomic analysis showed that AIP treatments reduced phenolic compounds, notably rutin, and increased the GSH/GSSG ratio, indicating reduced oxidative stress. Gene expression analysis highlighted elevated expression of somatic embryogenesis-related genes (LEC2, BBM) and WUSCHEL in AIP-treated callus. Conclusions: This study demonstrates that AIP enhances the regeneration potential of F. tataricum callus cultures, offering valuable insights for optimising tissue culture techniques for industrial crops. Additionally, we have detailed the metabolomic changes in calli treated with PVP and AIP, highlighting their impact on metabolism. Graphical

Background: Due to the totipotency of plant cells, which allows them to reprogram from a differentiated to a dedifferentiated state, plants exhibit a remarkable regenerative capacity, including under in vitro culture conditions. When exposed to plant hormones, primarily auxins and cytokinins, explant cells cultured in vitro can undergo differentiation through callus formation. Protoplast culture serves as a valuable research model for studying these processes in detail. This knowledge is particularly relevant for improving common and Tartary buckwheat species. To gain deeper insights into the stages of cell development from protoplasts—such as cell division, cell colony formation, and microcalli development—we focused on analyzing proteomes, cell wall composition, and changes in the expression profiles of selected genes in Fagopyrum protoplast cultures. Results: The results demonstrate a significant accumulation of somatic embryogenesis-related proteins like late embryogenesis abundant proteins (embryogenic protein-DC-8-like, seed biotin-containing protein) and endochitinases during the developmental path of protoplast-derived cultures. Additionally, we noted an extensive increase in seed storage proteins like vicilin, oleosins, and seed biotin-containing proteins during the culture. Investigation of somatic embryogenesis-associated transcription factors revealed massive up-regulation of LEAFY COTYLEDON1 for the 50th day of F. tataricum protoplast-derived cultures. However, for BABY BOOM, the transcription factor was noted to be down-regulated during the development of cell colonies. Furthermore, we demonstrated the variable distribution of cell wall components like pectin side chains, arabinogalactan proteins (AGPs) and extensins (EXTs), indicating the reorganisation of cell wall composition during the culture period. Conclusions: This study revealed changes correlating with regaining embryogenic competence during the development of Fagopyrum protoplast-derived cell colonies. Our findings revealed variable expression levels of genes and proteins associated with somatic embryogenesis. This analysis identified an increase in seed storage proteins that play a significant role in the somatic somatic embryogenesis pathway of regeneration. Furthermore, the relationship between transcription factors and these processes seems to be connected with regaining somatic cells’ totipotency and promoting embryogenic competence of protoplast-derived cell colonies. Additionally, we observed dynamic changes in cell wall composition during the development of the protoplast-derived cultures. Clinical trial number: Not applicable.

The embryogenic transition of plant somatic cells to produce somatic embryos requires extensive reprogramming of the cell transcriptome. The prominent role of transcription factors (TFs) and miRNAs in controlling somatic embryogenesis (SE) induction in plants was documented. The profiling of MIRNA expression in the embryogenic culture of Arabidopsis implied the contribution of the miR156 and miR169 to the embryogenic induction. In the present study, the function of miR156 and miR169 and the candidate targets, SPL and NF-YA genes, were investigated in Arabidopsis SE. The results showed that misexpression of MIRNA156 and candidate SPL target genes (SPL2, 3, 4, 5, 9, 10, 11, 13, 15) negatively affected the embryogenic potential of transgenic explants, suggesting that specific fine-tuning of the miR156 and target genes expression levels seems essential for efficient SE induction. The results revealed that SPL11 under the control of miR156 might contribute to SE induction by regulating the master regulators of SE, the LEC (LEAFY COTYLEDON) genes (LEC1, LEC2, FUS3). Moreover, the role of miR169 and its candidate NF-YA targets in SE induction was demonstrated. The results showed that several miR169 targets, including NF-YA1, 3, 5, 8, and 10, positively regulated SE. We found, that miR169 via NF-YA5 seems to modulate the expression of a master SE regulator LEC1/NF-YA and other auxin-related genes: YUCCA (YUC4, 10) and PIN1 in SE induction. The study provided new insights into miR156-SPL and miR169-NF-YA functions in the auxin-related and LEC-controlled regulatory network of SE.

Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including “Golden Promise,” a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.

Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryogenic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental processes, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin- and TSA-induced SE.

In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.

The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.