@article{2-s2.0-85201389758,

title = {Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana},

author = { B. Wójcikowska and K. Chwiałkowska and K. Nowak and S. Citerne and J. Morończyk and A.M. Wójcik and A. Kiwior-Wesołowska and J. Francikowski and M. Kwaśniewski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85201389758&doi=10.1186%2fs12864-024-10623-5&partnerID=40&md5=610b94d9150b69d42cedfa57e0bee734},

doi = {10.1186/s12864-024-10623-5},

year  = {2024},

date = {2024-01-01},

journal = {BMC Genomics},

volume = {25},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. Results: To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2;4-dichlorophenoxyacetic acid; 2;4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. Conclusion: The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants. © The Author(s) 2024.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85203646112,

title = {miR156-SPL and miR169-NF-YA Modules Regulate the Induction of Somatic Embryogenesis in Arabidopsis via LEC- and Auxin-Related Pathways},

author = { K. Nowak and A.M. Wójcik and K. Konopka and A. Jarosz and K. Dombert and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85203646112&doi=10.3390%2fijms25179217&partnerID=40&md5=795e29b568cf2506ff073245689df897},

doi = {10.3390/ijms25179217},

year  = {2024},

date = {2024-01-01},

journal = {International Journal of Molecular Sciences},

volume = {25},

number = {17},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

abstract = {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. © 2024 by the authors.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85176574335,

title = {The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A},

author = { K. Nowak and B. Wójcikowska and M. Gajecka and A. Elżbieciak and J. Morończyk and A.M. Wójcik and P. Żemła and S. Citerne and A. Kiwior-Wesołowska and J. Zbieszczyk and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85176574335&doi=10.1007%2fs13353-023-00800-9&partnerID=40&md5=aba91f468acebb6e7ac6030f68dc49f7},

doi = {10.1007/s13353-023-00800-9},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Applied Genetics},

volume = {65},

number = {1},

pages = {13-30},

publisher = {Springer Science and Business Media Deutschland GmbH},

abstract = {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. © 2023, The Author(s).},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85126018562,

title = {Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis},

author = { J. Morończyk and A.J. Brąszewska-Zalewska and B. Wójcikowska and K. Chwiałkowska and K. Nowak and A.M. Wójcik and M. Kwaśniewski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85126018562&doi=10.3390%2fcells11050863&partnerID=40&md5=b2d79e5ee5e0aad3ef0629dc7393c322},

doi = {10.3390/cells11050863},

issn = {20734409},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {5},

publisher = {MDPI},

abstract = {Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryo-genic 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 pro-cesses, 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. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85124973159,

title = {miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2},

author = { K. Nowak and J. Morończyk and M. Grzyb and A. Szczygieł-Sommer and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124973159&doi=10.3390%2fcells11040718&partnerID=40&md5=ba09056c3ca26cd08825a4f03a93afcc},

doi = {10.3390/cells11040718},

issn = {20734409},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {4},

publisher = {MDPI},

abstract = {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. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85140796333,

title = {Polish Contribution to Global Research on Somatic Embryogenesis},

author = { A. Mikuła and M.D. Gaj and M. Grzyb and T. Hazubska-Przybył and E. Kȩpczyńska and J. Kȩpczyński and J.J. Rybczyński and K. Tomiczak and A.M. Wójcik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140796333&doi=10.5586%2fasbp.9115&partnerID=40&md5=7ea17dc93b91bd67a0f5aef943cfa327},

doi = {10.5586/asbp.9115},

issn = {00016977},

year  = {2022},

date = {2022-01-01},

journal = {Acta Societatis Botanicorum Poloniae},

volume = {91},

publisher = {Polish Botanical Society},

abstract = {Somatic embryogenesis (SE) is a complex process that begins with regaining totipotency in some somatic cells, proceeds through embryo development and maturation, and ends with the formation of a whole plant. Since the first publications on SE in 1958, this regeneration process has been applied to the in vitro propagation of many plant species and has led to the development of some specific model systems. SE has been used to expand our understanding of the cytomorphological, physiological, biochemical, and genetic processes that govern the earliest developmental events in the life of plants. This paper summarizes the achievements of Polish research groups working on SE systems established for several plants (gentians; the tree fern Cyathea delgadii Sternb.; and conifers) and three model species (Arabidopsis thaliana; Medicago sativa; and M. truncatula). SE systems have used a broad spectrum of experimental approaches involving genomic tools (transcriptomics; proteomics; and chromatin analyses), physiological methods which focus on phytohormones, and cytological techniques. Studies on the experimental models of A. thaliana and Medicago spp. have resulted in the identification of new genetic and epigenetic elements of the complex regulatory network controlling embryogenic induction in plant somatic cells. The protocol developed for ferns has provided a unique and simple system for cytological analysis of early SE events that occur in a single cell of initial explants. Gentian embryogenic suspension cultures have successfully been used in broad biotechnological applications, including plant transformation, protoplast isolation, culture, and fusion. Systems described for coniferous species effectively produced many vigorous somatic seedlings and cost-efficient storage of genotypes during clonal field-testing. The research undertaken by Polish scientists has resulted in developing experimental systems that have enabled significant advances in SE knowledge. © The Author(s) 2022.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85091104919,

title = {Hypermethylation of auxin-responsive motifs in the promoters of the transcription factor genes accompanies the somatic embryogenesis induction in arabidopsis},

author = { D. Grzybkowska and K. Nowak and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091104919&doi=10.3390%2fijms21186849&partnerID=40&md5=264ea62fcf6e3760a051dca840ab2c4a},

doi = {10.3390/ijms21186849},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-22},

publisher = {MDPI AG},

abstract = {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. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85082731253,

title = {Epigenetic regulation of auxin-induced somatic embryogenesis in plants},

author = { B. Wójcikowska and A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082731253&doi=10.3390%2fijms21072307&partnerID=40&md5=ab1fc9ddb6bd291d0c7e177c7d8313d0},

doi = {10.3390/ijms21072307},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {7},

publisher = {MDPI AG},

abstract = {Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted. © 2020, MDPI AG. All rights reserved.},

note = {30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079636159,

title = {Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants},

author = { A.M. Wójcik and B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079636159&doi=10.3390%2fijms21041333&partnerID=40&md5=280c4b8858da9a30c603d1009ec24500},

doi = {10.3390/ijms21041333},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {4},

publisher = {MDPI AG},

abstract = {Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo-and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2;4-dichlorophenoxyacetic acid; which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down-and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85090863996,

title = {AGL15 controls the embryogenic reprogramming of somatic cells in arabidopsis through the histone acetylation-mediated repression of the mirna biogenesis genes},

author = { K. Nowak and J. Morończyk and A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090863996&doi=10.3390%2fijms21186733&partnerID=40&md5=63d2df1c0f8e6e068cb818919a3e59ae},

doi = {10.3390/ijms21186733},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-20},

publisher = {MDPI AG},

abstract = {The embryogenic transition of somatic cells requires an extensive reprogramming of the cell transcriptome. Relevantly, the extensive modulation of the genes that have a regulatory function, in particular the genes encoding the transcription factors (TFs) and miRNAs, have been indicated as controlling somatic embryogenesis (SE) that is induced in vitro in the somatic cells of plants. Identifying the regulatory relationships between the TFs and miRNAs during SE induction is of central importance for understanding the complex regulatory interplay that fine-tunes a cell transcriptome during the embryogenic transition. Hence, here, we analysed the regulatory relationships between AGL15 (AGAMOUS-LIKE 15) TF and miR156 in an embryogenic culture of Arabidopsis. Both AGL15 and miR156 control SE induction and AGL15 has been reported to target the MIR156 genes in planta. The results showed that AGL15 contributes to the regulation of miR156 in an embryogenic culture at two levels that involve the activation of the MIR156 transcription and the containment of the abundance of mature miR156 by repressing the miRNA biogenesis genes DCL1 (DICER-LIKE1), SERRATE and HEN1 (HUA-ENHANCER1). To repress the miRNA biogenesis genes AGL15 seems to co-operate with the TOPLESS co-repressors (TPL and TPR1-4), which are components of the SIN3/HDAC silencing complex. The impact of TSA (trichostatin A), an inhibitor of the HDAC histone deacetylases, on the expression of the miRNA biogenesis genes together with the ChIP results implies that histone deacetylation is involved in the AGL15-mediated repression of miRNA processing. The results indicate that HDAC6 and HDAC19 histone deacetylases might co-operate with AGL15 in silencing the complex that controls the abundance of miR156 during embryogenic induction. This study provides new evidence about the histone acetylation-mediated control of the miRNA pathways during the embryogenic reprogramming of plant somatic cells and the essential role of AGL15 in this regulatory mechanism. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85073735587,

title = {The miR396–GRF regulatory module controls the embryogenic response in Arabidopsis via an auxin-related pathway},

author = { A. Szczygieł-Sommer and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85073735587&doi=10.3390%2fijms20205221&partnerID=40&md5=631115d0d4d20b3b080dc69c708204ad},

doi = {10.3390/ijms20205221},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {20},

publisher = {MDPI AG},

abstract = {In plants, microRNAs have been indicated to control various developmental processes, including somatic embryogenesis (SE), which is triggered in the in vitro cultured somatic cells of plants. Although a transcriptomic analysis has indicated that numerous MIRNAs are differentially expressed in the SE of different plants, the role of specific miRNAs in the embryogenic reprogramming of the somatic cell transcriptome is still poorly understood. In this study, we focused on performing a functional analysis of miR396 in SE given that the transcripts of MIR396 genes and the mature molecules of miR396 were found to be increased during an SE culture of Arabidopsis. In terms of miR396 in embryogenic induction, we observed the SE-associated expression pattern of MIR396b in explants of the β-glucuronidase (GUS) reporter line. In order to gain insight into the miR396-controlled mechanism that is involved in SE induction, the embryogenic response of mir396 mutants and the 35S:MIR396b overexpressor line to media with different 2,4-Dichlorophenoxyacetic acid (2;4-D) concentrations was evaluated. The results suggested that miR396 might contribute to SE induction by controlling the sensitivity of tissues to auxin treatment. Within the targets of miR396 that are associated with SE induction, we identified genes encoding the GROWTH-REGULATING FACTOR (GRF) transcription factors, including GRF1, GRF4, GRF7, GRF8, and GRF9. Moreover, the study suggested a regulatory relationship between miR396, GRF, and the PLETHORA (PLT1 and PLT2) genes during SE induction. A complex regulatory relationship within the miR396–GRF1/4/8/9–PLT1/2 module that involves the negative and positive control of GRFs and PLT (respectively) by miR396 might be assumed. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85069637860,

title = {Glutathione (GSH) induces embryogenic response in in vitro cultured explants of Arabidopsis thaliana via auxin-related mechanism},

author = { K. Kudełko and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85069637860&doi=10.1007%2fs10725-019-00514-1&partnerID=40&md5=8497bc7716ab4fc029a942e2cbc4e3a7},

doi = {10.1007/s10725-019-00514-1},

issn = {01676903},

year  = {2019},

date = {2019-01-01},

journal = {Plant Growth Regulation},

volume = {89},

number = {1},

pages = {25-36},

publisher = {Springer Netherlands},

abstract = {To gain insight into the relationship between oxidative stress and somatic embryogenesis (SE) induction, we analysed the effects of a reduced glutathione (GSH) of antioxidant activity on the embryogenic potential of in vitro cultured explants of the model plant Arabidopsis. The results showed that the GSH treatment resulted in SE induction in the explants that had been cultured on an auxin-depleted medium. The GSH-induced SE was shown to be associated with auxin biosynthesis and the accumulation of both the YUCCA transcripts (YUC10/11) and the indolic compounds that are indicative for IAA. Inversely, 2,4-D treatment was found to increase the GSH level in the cultured explants and thus, complex interactions between the auxin and oxidative stress were assumed to control SE induction. The genetic regulators of auxin-induced SE, the LEC1 and LEC2 genes, were also up-regulated in the GSH-triggered SE. In contrast, the expression profiles of BBM and MYB118 were distinctly different in the GSH- than in 2,4-D-induced SE, which suggests differences in the genetic regulation of these alternative embryogenic pathways. Collectively, the study provides evidence that the GSH-imposed changes in the oxidative stress level affect auxin production, which triggers embryogenic development in the cultured explants. © 2019, The Author(s).},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054500845,

title = {Trichostatin a triggers an embryogenic transition in arabidopsis explants via an auxin-related pathway},

author = { B. Wójcikowska and M. Botor and J. Morończyk and A.M. Wójcik and T. Nodzyński and J. Karcz and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054500845&doi=10.3389%2ffpls.2018.01353&partnerID=40&md5=cbe7e1e0677493466506c918a06e7cf0},

doi = {10.3389/fpls.2018.01353},

issn = {1664462X},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Plant Science},

volume = {9},

publisher = {Frontiers Media S.A.},

abstract = {Auxin is an important regulator of plant ontogenies including embryo development and the exogenous application of this phytohormone has been found to be necessary for the induction of the embryogenic response in plant explants that have been cultured in vitro. However, in the present study, we show that treatment of Arabidopsis explants with trichostatin A (TSA), which is a chemical inhibitor of histone deacetylases, induces somatic embryogenesis (SE) without the exogenous application of auxin. We found that the TSA-treated explants generated somatic embryos that developed efficiently on the adaxial side of the cotyledons, which are the parts of an explant that are involved in auxin-induced SE. A substantial reduction in the activity of histone deacetylase (HDAC) was observed in the TSA-treated explants, thus confirming a histone acetylation-related mechanism of the TSA-promoted embryogenic response. Unexpectedly, the embryogenic effect of TSA was lower on the auxin-supplemented media and this finding further suggests an auxin-related mechanism of TSA-induced SE. Congruently, we found a significantly increased content of indolic compounds, which is indicative of IAA and an enhanced DR5::GUS signal in the TSA-treated explants. In line with these results, two of the YUCCA genes (YUC1 and YUC10), which are involved in auxin biosynthesis, were found to be distinctly up-regulated during TSA-induced SE and their expression was colocalised with the explant sites that are involved in SE. Beside auxin, ROS were extensively accumulated in response to TSA, thereby indicating that a stress-response is involved in TSA-triggered SE. Relevantly, we showed that the genes encoding the transcription factors (TFs) that have a regulatory function in auxin biosynthesis including LEC1, LEC2, BBM, and stress responses (MYB118) were highly up-regulated in the TSA-treated explants. Collectively, the results provide several pieces of evidence about the similarities between the molecular pathways of SE induction that are triggered by TSA and 2,4-D that involve the activation of the auxin-responsive TF genes that have a regulatory function in auxin biosynthesis and stress responses. The study suggests the involvement of histone acetylation in the auxin-mediated release of the embryogenic program of development in the somatic cells of Arabidopsis. © 2018 Wójcikowska, Botor, Morończyk, Wójcik, Nodzyński, Karcz and Gaj.},

note = {36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054553781,

title = {Whole mount in situ localization of mirnas and mrnas during somatic embryogenesis in arabidopsis},

author = { A.M. Wójcik and M. Mosiolek and J. Karcz and M.D. Nodine and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054553781&doi=10.3389%2ffpls.2018.01277&partnerID=40&md5=45983ecce8697f5aad654572bc8a0228},

doi = {10.3389/fpls.2018.01277},

issn = {1664462X},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Plant Science},

volume = {9},

publisher = {Frontiers Media S.A.},

abstract = {Somatic embryogenesis (SE) results from the transition of differentiated plant somatic cells into embryogenic cells that requires the extensive reprogramming of the somatic cell transcriptome. Commonly, the SE-involved genes are identified by analyzing the heterogeneous population of explant cells and thus, it is necessary to validate the expression of the candidate genes in the cells that are competent for embryogenic transition. Here, we optimized and implemented the whole mount in situ hybridization (WISH) method (Bleckmann and Dresselhaus; 2016; Dastidar et al.; 2016) in order to analyze the spatiotemporal localization of miRNAs (miR156; miR166; miR390; miR167) and mRNAs such as WOX5 and PHABULOSA-target of miR165/166 during the SE that is induced in Arabidopsis explants. This study presents a detailed step-by-step description of the WISH procedure in which DIG-labeled LNA and RNA probes were used to detect miRNAs and mRNAs, respectively. The usefulness of the WISH in the functional analysis of the SE-involved regulatory pathways is demonstrated and the advantages of this method are highlighted: (i) the ability to analyze intact non-sectioned plant tissue; (ii) the specificity of transcript detection; (iii) the detection of miRNA; and (iv) a semi-quantitative assessment of the RNA abundance. © 2018 Wójcik, Mosiolek, Karcz, Nodine and Gaj.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85044541795,

title = {Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis},

author = { D. Grzybkowska and J. Morończyk and B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044541795&doi=10.1007%2fs10725-018-0389-1&partnerID=40&md5=1bb66f4e3178174a22c61d3a216b5eec},

doi = {10.1007/s10725-018-0389-1},

issn = {01676903},

year  = {2018},

date = {2018-01-01},

journal = {Plant Growth Regulation},

volume = {85},

number = {2},

pages = {243-256},

publisher = {Springer Netherlands},

abstract = {Epigenetic processes including DNA methylation play a pivotal role in regulating the genes that control plant development. In contrast to in planta development, the contribution of DNA methylation to the morphogenic processes that are induced in vitro are much less recognised. Hence, in the present study, we analysed the impact of DNA methylation on somatic embryogenesis (SE) that was induced in Arabidopsis. The results demonstrated a decrease in the global DNA methylation level during SE that contrasted with the up-regulation of MET1 and CMT3 DNA methylases and the down-regulation of DNA demethylases (ROS1; DME and DML2). Hence, the global DNA methylation level appears not to correlate with the transcriptional activity of the genes encoding DNA methylases/demethylases, thereby implying the complexity of the regulatory mechanism that controls the DNA methylation status of the SE-epigenome. Moreover, distinct changes in the expression level of the SE-regulatory genes were indicated in the 5-AzaC-treated and DNA methylase mutant cultures. Accordingly, a significant repression of the LEC2, LEC1 and BBM genes was found in the 5-AzaC-treated culture that was incapable of SE induction. In contrast, the distinct up-regulation of these genes was observed in the drm1drm2 and drm1drm2cmt3 mutant cultures with an improved embryogenic response. The modulated expression of DNA methylase genes and the significantly modified embryogenic response of the met1 and drm mutants imply that both the maintenance and the de novo pathway of DNA methylation are engaged in the regulation of SE in Arabidopsis. © 2018, The Author(s).},

note = {37},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85038354165,

title = {MiR160 and miR166/165 contribute to the LEC2-mediated auxin response involved in the somatic embryogenesis induction in arabidopsis},

author = { A.M. Wójcik and M.D. Nodine and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038354165&doi=10.3389%2ffpls.2017.02024&partnerID=40&md5=02bb61c60417ea8910b696b718c48421},

doi = {10.3389/fpls.2017.02024},

issn = {1664462X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Plant Science},

volume = {8},

publisher = {Frontiers Media S.A.},

abstract = {MicroRNAs are non-coding small RNA molecules that are involved in the post-transcriptional regulation of the genes that control various developmental processes in plants, including zygotic embryogenesis (ZE). miRNAs are also believed to regulate somatic embryogenesis (SE), a counterpart of the ZE that is induced in vitro in plant somatic cells. However, the roles of specific miRNAs in the regulation of the genes involved in SE, in particular those encoding transcription factors (TFs) with an essential function during SE including LEAFY COTYLEDON2 (LEC2), remain mostly unknown. The aim of the study was to reveal the function of miR165/166 and miR160 in the LEC2-controlled pathway of SE that is induced in in vitro cultured Arabidopsis explants.In ZE, miR165/166 controls the PHABULOSA/PHAVOLUTA (PHB/PHV) genes, which are the positive regulators of LEC2, while miR160 targets the AUXIN RESPONSE FACTORS (ARF10, ARF16, ARF17) that control the auxin signaling pathway, which plays key role in LEC2-mediated SE. We found that a deregulated expression/function of miR165/166 and miR160 resulted in a significant accumulation of auxin in the cultured explants and the spontaneous formation of somatic embryos. Our results show that miR165/166 might contribute to SE induction via targeting PHB, a positive regulator of LEC2 that controls embryogenic induction via activation of auxin biosynthesis pathway (Wójcikowska et al., 2013). Similar to miR165/166, miR160 was indicated to control SE induction through auxin-related pathways and the negative impact of miR160 on ARF10/ARF16/ARF17 was shown in an embryogenic culture. Altogether, the results suggest that the miR165/166- and miR160-node contribute to the LEC2-mediated auxin-related pathway of embryogenic transition that is induced in the somatic cells of Arabidopsis. A model summarizing the suggested regulatory interactions between the miR165/166-PHB and miR160-ARF10/ARF16/ARF17 nodes that control SE induction in Arabidopsis was proposed. © 2017 Wójcik, Nodine and Gaj.},

note = {44},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85014060247,

title = {Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis},

author = { B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014060247&doi=10.1007%2fs00299-017-2114-3&partnerID=40&md5=964d2525fd57bcaaf03c35f7ce9b8080},

doi = {10.1007/s00299-017-2114-3},

issn = {07217714},

year  = {2017},

date = {2017-01-01},

journal = {Plant Cell Reports},

volume = {36},

number = {6},

pages = {843-858},

publisher = {Springer Verlag},

abstract = {Key message: Extensive modulation of numerous ARF transcripts in the embryogenic culture of Arabidopsis indicates a substantial role of auxin signaling in the mechanism of somatic embryogenesis induction. Abstract: Somatic embryogenesis (SE) is induced by auxin in plants and auxin signaling is considered to play a key role in the molecular mechanism that controls the embryogenic transition of plant somatic cells. Accordingly, the expression of AUXIN RESPONSE FACTOR (ARF) genes in embryogenic culture of Arabidopsis was analyzed. The study revealed that 14 of the 22 ARFs were transcribed during SE in Arabidopsis. RT-qPCR analysis indicated that the expression of six ARFs (ARF5; ARF6; ARF8; ARF10; ARF16; and ARF17) was significantly up-regulated, whereas five other genes (ARF1; ARF2; ARF3; ARF11; and ARF18) were substantially down-regulated in the SE-induced explants. The activity of ARFs during SE was also monitored with GFP reporter lines and the ARFs that were expressed in areas of the explants engaged in SE induction were detected. A functional test of ARFs transcribed during SE was performed and the embryogenic potential of the arf mutants and overexpressor lines was evaluated. ARFs with a significantly modulated expression during SE coupled with an impaired embryogenic response of the relevant mutant and/or overexpressor line, including ARF1, ARF2, ARF3, ARF5, ARF6, ARF8, and ARF11 were indicated as possibly being involved in SE induction. The study provides evidence that embryogenic induction strongly depends on ARFs, which are key regulators of the auxin signaling. Some clues on the possible functions of the candidate ARFs, especially ARF5, in the mechanism of embryogenic transition are discussed. The results provide guidelines for further research on the auxin-related functional genomics of SE and the developmental plasticity of somatic cells. © 2017, The Author(s).},

note = {73},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85010888075,

title = {MicroRNAs are intensively regulated during induction of somatic embryogenesis in arabidopsis},

author = { K.P. Szyrajew and D. Bielewicz and J. Dolata and A.M. Wójcik and K. Nowak and A. Szczygieł-Sommer and Z. Szweykowska-Kulinska and A. Jarmolowski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010888075&doi=10.3389%2ffpls.2017.00018&partnerID=40&md5=d8db68bd8366253f2074f2b48d23b4ca},

doi = {10.3389/fpls.2017.00018},

issn = {1664462X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Plant Science},

volume = {8},

publisher = {Frontiers Media S.A.},

abstract = {Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction. © 2017 Szyrajew, Bielewicz, Dolata, Wójcik, Nowak, Szczygieł-Sommer, Szweykowska-Kulinska, Jarmolowski and Gaj.},

note = {42},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84962159759,

title = {miR393 contributes to the embryogenic transition induced in vitro in Arabidopsis via the modification of the tissue sensitivity to auxin treatment},

author = { A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84962159759&doi=10.1007%2fs00425-016-2505-7&partnerID=40&md5=4feaadd4e14ac53a53e2c2835f7c1a3e},

doi = {10.1007/s00425-016-2505-7},

issn = {00320935},

year  = {2016},

date = {2016-01-01},

journal = {Planta},

volume = {244},

number = {1},

pages = {231-243},

publisher = {Springer Verlag},

abstract = {Main conclusion: miR393 was found to control embryogenic transition in somatic cells in Arabidopsis via control of theTIR1andAFB2auxin receptors genes of the F-box family. miR393 molecules are believed to regulate the expression of the auxin receptors of the TAAR clade. Considering the central role of auxin in the induction of somatic embryogenesis (SE) in plant explants cultured in vitro, the involvement of miR393 in the embryogenic transition of somatic cells has been hypothesised. To verify this assumption, the reporter, overexpressor and mutant lines in genes encoded MIR393 and TIR1/AFB proteins of the F-box family were analysed during SE in Arabidopsis. Expression profiling of MIR393a and MIR393b, mature miR393 and the target genes (TIR1; AFB1; AFB2; AFB3) were investigated in explants undergoing SE. In addition, the embryogenic potential of various genotypes with a modified activity of the MIR393 and TIR1/AFB targets was evaluated. The distinct increase in the accumulation of miR393 that was coupled with a notable down-regulation of TIR1 and AFB2 targets was observed at the early phase of SE induction. Relevant to this observation, the GUS/GFP monitored expression of MIR393, TIR1 and AFB2 transcripts was localised in explant tissue undergoing SE induction. The results suggest the miR393-mediated regulation of TIR1 and AFB2 during embryogenic transition induced in Arabidopsis and a modification of the explant sensitivity to auxin treatment is proposed as underlying this regulatory pathway. © 2016, The Author(s).},

note = {49},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84960158396,

title = {Stress-related function of bHLH109 in somatic embryo induction in Arabidopsis},

author = { K. Nowak and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84960158396&doi=10.1016%2fj.jplph.2016.02.012&partnerID=40&md5=e493e62a7f2ecf7ef319aa1cc887db65},

doi = {10.1016/j.jplph.2016.02.012},

issn = {01761617},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Plant Physiology},

volume = {193},

pages = {119-126},

publisher = {Elsevier GmbH},

abstract = {The bHLH109 gene of the bHLH family was identified among the transcription factor encoding genes that were differentially expressed in an embryogenic culture of Arabidopsis. A strong activation of bHLH109 expression was found to be associated with somatic embryogenesis (SE) induction. Several pieces of evidence suggested the involvement of bHLH109 in SE, including the high stimulation of the gene expression in SE-induced explants, which contrasts to the drastically lower level of the gene transcripts in the non-embryogenic callus and in tissue that is induced towards shoot regeneration via organogenesis. Moreover, in contrast to the overexpression of bHLH109, which has been indicated to enhance SE induction in a culture, the bhlh109 knock-out mutation was found to impair the embryogenic potential of explants. In order to identify the genes interacting with the bHLH109, the candidate co-expressed genes were identified in a yeast one hybrid assay. The in vitro regulatory interactions that were identified were verified through mutant and expression analysis. The results suggest that in SE bHLH109 acts as an activator of ECP63, a member of the LEA (LATE EMBRYOGENESIS ABUNDANT) family. Among the potential regulators of bHLH109, three candidates (At5g61620; bZIP4 and bZIP43) were indicated to possibly control bHLH109. The functions of all of the genes that are assumed to interact with bHLH109 are annotated to stress responses.Collectively, the results of the study provide new evidence that cell responses to stress that is imposed under in vitro conditions underlies the promotion of SE. bHLH109 may play a central role in the stress-related mechanism of SE induction via an increased accumulation of the LEA protein (ECP63), which results in the enhanced tolerance of the cells to stress. © 2016 Elsevier GmbH.},

note = {17},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84925493018,

title = {ERF022 impacts the induction of somatic embryogenesis in Arabidopsis through the ethylene-related pathway},

author = { K. Nowak and B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925493018&doi=10.1007%2fs00425-014-2225-9&partnerID=40&md5=484ed96fbd6cd5bdc8273abcabee016a},

doi = {10.1007/s00425-014-2225-9},

issn = {00320935},

year  = {2015},

date = {2015-01-01},

journal = {Planta},

volume = {241},

number = {4},

pages = {967-985},

publisher = {Springer Verlag},

abstract = {Main conclusion: TheERF022gene was found to affect embryogenic transition in somatic cells in Arabidopsis via the ethylene-related pathway. The study provides evidence thatERF022-LEC2interaction is involved in the auxin–ethylene crosstalk that operates in somatic embryogenesis induction.The ERF022 gene of the ERF family was previously identified among the transcription factor genes that were differentially expressed in an embryogenic culture of Arabidopsis. A strong inhibition of the gene was found to be associated with the induction of somatic embryogenesis (SE) and an erf022 mutant was indicated to display a substantially impaired capacity for SE. Therefore, the molecular function of ERF022 in the induction of SE was studied in the present work. A phenotype of an erf022 mutant was indicated as being related to an increased content of ethylene. The results further suggest that the ERF022 controls the genes that are involved in both the biosynthesis (ACS7) and signalling (ERF1; ETR1) of ethylene and indicate that the ERF022 is a new regulatory element in ethylene-related responses that negatively control the ethylene content and perception. It is proposed that the negative impact of ethylene on the induction of SE may result from a modulation of the auxin-related genes that control the embryogenic transition in somatic cells. Among them, the LEC2, which is a key regulator of the induction of SE through the stimulation of auxin synthesis, was possibly related to ERF022. The results of the study provide new hormone-related clues to define the genetic network that governs SE. A putative model of the regulatory pathway is proposed that is involved in the induction of SE in which the auxin–ethylene interactions are controlled by ERF022 and LEC2 and their targets. © 2014, The Author(s).},

note = {43},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84925341356,

title = {LEAFY COTYLEDON2-mediated control of the endogenous hormone content: implications for the induction of somatic embryogenesis in Arabidopsis},

author = { B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925341356&doi=10.1007%2fs11240-014-0689-8&partnerID=40&md5=80f9d7825c98b430bac8911bfabe70fb},

doi = {10.1007/s11240-014-0689-8},

issn = {01676857},

year  = {2015},

date = {2015-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {121},

number = {1},

pages = {255-258},

publisher = {Kluwer Academic Publishers},

abstract = {The overexpression of LEAFY COTYLEDON2 (LEC2) in Arabidopsis, results in the induction of somatic embryogenesis (SE) in an auxin-free environment and the stimulation of auxin biosynthesis was postulated as being involved in this response. To gain further insight into the hormone-related functions of LEC2 in SE, the effect of LEC2 overexpression on the hormone content in Arabidopsis plants and in vitro cultured explants was analysed. In addition to indole-3-acetic acid (IAA) and cytokinins (CKs), which are hormones that play a key role in plant development, the stress-related hormones, abscisic acid (ABA) and salicylic acid (SA), which are involved in the stress response that is related to SE-induction, were analysed. Together with the observations that LEC2 activity can compensate for the auxin treatment required for SE induction (Ledwoń and Gaj in Plant Tissue Cell Org Cult 28:1677–1688; 2009) and LEC2 may control auxin biosynthesis pathway during SE induction (Wójcikowska et al. in Planta 238:425–440; 2013), a significant increase in the IAA content in response to LEC2 overexpression found in the present study supply further evidence that LEC2-controlled auxin biosynthesis may be involved in the mechanism that triggers embryogenic development in somatic cells. Moreover, LEC2-controlled SE induction was shown to be associated with a decrease in the total content of CKs and an accumulation of some specific CK types, including isopentenyl-adenin and cis-zeatin. Additionally, an increase in SA and a decrease in ABA content were also found to be related to LEC2 activity in embryogenically induced tissue. The obtained results provide further proof of the close link between LEC2 and the establishment of the hormonal environment that is required for the promotion of SE. © 2014, The Author(s).},

note = {15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84880397137,

title = {Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana},

author = { M. Gliwicka and K. Nowak and S. Balazadeh and B. Mueller-Roeber and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880397137&doi=10.1371%2fjournal.pone.0069261&partnerID=40&md5=ac729d4b4a424a526a64c9ea1ffdee18},

doi = {10.1371/journal.pone.0069261},

issn = {19326203},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {7},

abstract = {Molecular mechanisms controlling plant totipotency are largely unknown and studies on somatic embryogenesis (SE), the process through which already differentiated cells reverse their developmental program and become embryogenic, provide a unique means for deciphering molecular mechanisms controlling developmental plasticity of somatic cells. Among various factors essential for embryogenic transition of somatic cells transcription factors (TFs), crucial regulators of genetic programs, are believed to play a central role. Herein, we used quantitative real-time polymerase chain reaction (qRT-PCR) to identify TF genes affected during SE induced by in vitro culture in Arabidopsis thaliana. Expression profiles of 1,880 TFs were evaluated in the highly embryogenic Col-0 accession and the non-embryogenic tanmei/emb2757 mutant. Our study revealed 729 TFs whose expression changes during the 10-days incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. The embryo-induction stage of SE occurring during the first 5 days of culture was associated with a robust and dramatic change of the TF transcriptome characterized by the drastic up-regulation of the expression of a great majority (over 80%) of the TFs active during embryogenic culture. In contrast to SE induction, the advanced stage of embryo formation showed attenuation and stabilization of transcript levels of many TFs. In total, 519 of the SE-modulated TFs were functionally annotated and transcripts related with plant development, phytohormones and stress responses were found to be most abundant. The involvement of selected TFs in SE was verified using T-DNA insertion lines and a significantly reduced embryogenic response was found for the majority of them. This study provides comprehensive data focused on the expression of TF genes during SE and suggests directions for further research on functional genomics of SE. © 2013 Gliwicka et al.},

note = {84},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84882990244,

title = {LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis},

author = { B. Wójcikowska and K. Jaskóła and P. Gąsiorek and M. Meus and K. Nowak and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84882990244&doi=10.1007%2fs00425-013-1892-2&partnerID=40&md5=b86ad3f6b078c67f6368504f82397b4b},

doi = {10.1007/s00425-013-1892-2},

issn = {00320935},

year  = {2013},

date = {2013-01-01},

journal = {Planta},

volume = {238},

number = {3},

pages = {425-440},

publisher = {Springer Verlag},

abstract = {The LEAFY COTYLEDON2 (LEC2) transcription factor with a plant-specific B3 domain plays a central role in zygotic and somatic embryogenesis (SE). LEC2 overexpression induced in planta leads to spontaneous somatic embryo formation, but impairs the embryogenic response of explants cultured in vitro under auxin treatment. The auxin-related functions of LEC2 appear during SE induction, and the aim of the present study was to gain further insights into this phenomenon. To this end, the effect of LEC2 overexpression on the morphogenic responses of Arabidopsis explants cultured in vitro under different auxin treatments was evaluated. The expression profiles of the auxin biosynthesis genes were analysed in embryogenic cultures with respect to LEC2 activity. The results showed that LEC2 overexpression severely modifies the requirement of cultured explants for an exogenous auxin concentration at a level that is effective in SE induction and suggested an increase in the auxin content in 35S::LEC2-GR transgenic explants. The assumption of an LEC2 promoted increase in endogenous auxin in cultured explants was further supported by the expression profiling of the genes involved in auxin biosynthesis. The analysis indicated that YUCCAs and TAA1, working in the IPA-YUC auxin biosynthesis pathway, are associated with SE induction, and that the expression of three YUCCA genes (YUC1; YUC4 and YUC10) is associated with LEC2 activity. The results also suggest that the IAOx-mediated auxin biosynthesis pathway involving ATR1/MYB34 and CYP79B2 does not seem to be involved in SE induction. We conclude that de novo auxin production via the tryptophan-dependent IPA-YUC auxin biosynthesis pathway is implicated in SE induction, and that LEC2 plays a key role in this mechanism. © 2013 The Author(s).},

note = {97},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84859873413,

title = {Evaluation of different embryogenic systems for production of true somatic embryos in Arabidopsis},

author = { K. Nowak and B. Wójcikowska and K.P. Szyrajew and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859873413&doi=10.1007%2fs10535-012-0063-9&partnerID=40&md5=5a3da4545127c05ea9df9d0597eb6ad3},

doi = {10.1007/s10535-012-0063-9},

issn = {00063134},

year  = {2012},

date = {2012-01-01},

journal = {Biologia Plantarum},

volume = {56},

number = {3},

pages = {401-408},

abstract = {Somatic embryogenesis (SE) in Arabidopsis was induced using various systems, including auxin treatment of in vitro cultured explants (immature zygotic embryos; IZEs) and transgenic plants overexpressing embryogenesis-related transcription factors, e. g. LEC2 together with the GUS reporter gene under control of the auxin-induced DR5 promoter. The study indicated that the SE-systems used gave different embryogenic capacities for the production of true embryos. The highest ratio of true embryos (75 %) was found among embryo-like structures in transgenic seedlings overexpressing LEC2. Analysis of in vitro induced SE systems indicated that in somatic embryos produced in response to exogenous auxin treatment the formation of root poles is frequently disturbed. A lack of a properly formed root meristem was observed in 35-80 % of in vitro induced somatic embryos, in dependence on auxin concentration and duration of treatment. © 2012 Springer Science+Business Media B.V.},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84859431559,

title = {Expression of seed storage product genes (CRA1 and OLEO4) in embryogenic cultures of somatic tissues of Arabidopsis},

author = { M. Gliwicka and K. Nowak and E. Cieśla and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859431559&doi=10.1007%2fs11240-011-0089-2&partnerID=40&md5=3ca1c154c6f2ff92ae14f16ba58c124e},

doi = {10.1007/s11240-011-0089-2},

issn = {01676857},

year  = {2012},

date = {2012-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {109},

number = {2},

pages = {235-245},

abstract = {In Arabidopsis, immature zygotic embryos (IZEs) at the late cotyledon stage provide the only explants that can be used to induce in vitro somatic embryogenesis (SE) with high efficiency. The most conspicuous characteristic of SE-competent IZEs is the accumulation of seed storage reserves (SSR), as proteins and lipids. In order to elucidate an assumed role of these compounds in the mechanisms involved in tissue capacity for SE, the genes encoding the main seed storage protein, cruciferin (CRUCIFERIN1; CRA1) and the lipid body-related protein oleosin (OLEOSIN4; OLEO4), were studied. Significantly higher transcriptional activity of both genes, CRA1 and OLEO4, in embryogenic than in non-embryogenic cultures, were indicated. However, their activity under in vitro culture were found not to be induced by auxin treatment or LEC2 expression, and were unspecific for SE induction. In addition, the results on mutants severely impaired in SE response indicated that high activity of SSR genes in explant tissue is not sufficient for SE induction. On the other hand, the cra1 and oleo4 insertional mutants were found to be defective in their capacity for SE. In addition, it was found that the mutants displayed lower tolerance to high salinity and osmotic stress. Altogether, the results suggest an indirect influence of SSR genes on the embryogenic capacity of cultured tissues possibly via improvement of cell response to stress imposed in vitro. © 2011 The Author(s).},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84856920216,

title = {Immature zygotic embryo cultures of Arabidopsis. Amodel system for molecular studies on morphogenic pathways induced in vitro},

author = { M. Kraut and B. Wójcikowska and A. Ledwoń and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856920216&doi=10.2478%2fv10182-011-0028-x&partnerID=40&md5=c1b1164c7aa0b0ac58fd4ed7cbf5b22b},

doi = {10.2478/v10182-011-0028-x},

issn = {00015296},

year  = {2011},

date = {2011-01-01},

journal = {Acta Biologica Cracoviensia Series Botanica},

volume = {53},

number = {2},

pages = {59-67},

abstract = {To understand the molecular mechanism controlling in vitro plant morphogenesis, a culture system enabling induction of alternative morphogenic pathways (somatic embryogenesis; SE; shoot organogenesis; ORG) in a well defined population of somatic cells is needed. Arabidopsis is the most useful model plant for genomic studies, but a system in which SE or ORG can be induced alternatively in the same type of explant has not been proposed. Immature zygotic embryos (IZEs) of Arabidopsis provide the only explants with embryogenic potential, and have been recommended for studying mechanisms of SE induced in vitro. This study was aimed at defining culture conditions promoting induction of alternative morphogenic pathways: shoot ORG in IZE explants. The established protocol involves pretreatment of IZE explants with liquid auxin-rich callus induction (CIM) medium, followed by subculture on solid cytokinin-rich shoot induction medium (SIM). The method enables efficient shoot induction in Columbia (Col-0) and Wassilewskija (Ws), genotypes commonly used in molecular studies. During 3 weeks of culture up to 90% of Col-0 and 70% of Ws explants regenerated shoots via an indirect morphogenic pathway. We analyzed the qRT-PCR expression patterns of the LEC (LEC1; LEC2 and FUS3) genes, the key regulators of Arabidopsis embryogenesis, in the IZE explants induced to promote shoot ORG. The sharp decline of LEC expression on SIM medium confirmed that culture of Arabidopsis IZE explants enables experimental manipulation of the morphogenic response of somatic cells. A scheme illustrating various in vitro morphogenic responses of IZEs in relation to hormonal treatment is presented. © Polish Academy of Sciences and Jagiellonian University, Cracow 2011.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-80052479450,

title = {LEAFY COTYLEDON1, FUSCA3 expression and auxin treatment in relation to somatic embryogenesis induction in Arabidopsis},

author = { A. Ledwoń and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052479450&doi=10.1007%2fs10725-011-9585-y&partnerID=40&md5=ed47668a4973990babc84c80d0348d9a},

doi = {10.1007/s10725-011-9585-y},

issn = {01676903},

year  = {2011},

date = {2011-01-01},

journal = {Plant Growth Regulation},

volume = {65},

number = {1},

pages = {157-167},

abstract = {The expression pattern of the LEC1 and FUS3 genes during somatic embryogenesis in Arabidopsis explants (immature zygotic embryos) induced in vitro was analysed, using Real-time quantitative PCR (qRT-PCR). The analysis revealed differential expression of LEC1 but not FUS3 within a 30 day time course of somatic embryo development, and a significant auxin-dependent upregulation of LEC1 was found over the time course. In contrast to embryogenic culture, the level of LEC1 and FUS3 expression was noticeably lower in non-embryogenic callus of Col-0 and hormonal mutants (cbp20 and axr4-1) with low SE-efficiency. In addition, the expression profile of LEC1 and FUS3 was followed in the embryogenic culture derived from 35S::LEC2-GR explants. A significant increase of LEC1 but not FUS3 activity was observed under LEC2 overexpression induced in auxin-treated explants. The work provides further experimental evidence on LEC gene involvement in the embryogenic response in Arabidopsis somatic cells, and also implicates LEC1 function in more advanced stages of SE culture in relation to somatic embryo differentiation and development. © 2011 The Author(s).},

note = {40},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-76149136359,

title = {Arabidopsis tanmei/emb2757 embryo mutant is defective for in vitro plant morphogenesis},

author = { P. Baster and A. Ledwoń and M. Gliwicka and A. Trojanowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-76149136359&doi=10.1007%2fs11240-009-9605-z&partnerID=40&md5=36798c1b348250751436727ada94fb5d},

doi = {10.1007/s11240-009-9605-z},

issn = {01676857},

year  = {2009},

date = {2009-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {99},

number = {3},

pages = {305-312},

abstract = {A mutation in the Arabidopsis TANMEI/EMB2757 (TAN) gene with an embryo defective phenotype was analysed for its effect on the morphogenic potential of somatic tissue cultured under in vitro conditions. The capacity for in vitro morphogenesis was evaluated using cultures of immature zygotic embryos, and seedling explants of the tan mutant and the parental Col-0 genotype. The explants were cultured on media supplemented with different plant growth regulators, and the capacity for two alternative pathways of morphogenesis, somatic embryogenesis (SE) and shoot organogenesis, was evaluated. Reporter genes (GUS; GFP) were used to monitor auxin and LEC2 and FUS3 gene activity in the tan explants. Moreover, the expression pattern of the TAN gene was analyzed during SE and in callus tissue of Col-0. It was indicated that the tan mutation resulted in a total lost of embryogenic and organogenic capacity of cultured tissues, suggesting the involvement of the TAN gene in basic cellular processes related to cell growth and differentiation. However, differential expression of the TAN gene during SE, and its increased activity at advanced stages of embryogenesis, implicate a specific role for the gene in the development of somatic embryos. © 2009 Springer Science+Business Media B.V.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-77950356166,

title = {LEAFY COTYLEDON2 gene expression and auxin treatment in relation to embryogenic capacity of Arabidopsis somatic cells.},

author = { A. Ledwoń and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77950356166&doi=10.1007%2fs00299-009-0767-2&partnerID=40&md5=7bd3138cb025243ffc8fab2e690d37b8},

doi = {10.1007/s00299-009-0767-2},

issn = {1432203X},

year  = {2009},

date = {2009-01-01},

journal = {Plant cell reports},

volume = {28},

number = {11},

pages = {1677-1688},

abstract = {The expression pattern of the LEC2 gene during somatic embryogenesis (SE) in Arabidopsis explants (immature zygotic embryos) induced in vitro was followed, using real-time quantitative PCR (qRT-PCR). The analysis revealed differential expression of LEC2 transcripts within a 30 days time course of somatic embryo development. A significant auxin-dependent upregulation of the LEC2 gene was found to be associated with the induction phase of SE. In contrast to embryogenic culture the level of LEC2 expression was noticeably lower in non-embryogenic callus of Col-0 and hormonal mutants (cbp20 and axr4-1) with low SE-efficiency. The study with 35S::LEC2-GR transgenic plants showed that overexpression of LEC2 can compensate for the auxin requirement, and that transgenic explants formed somatic embryos when cultured in vitro under auxin-free conditions. However, unlike in auxin-induced SE, intense callus formation preceded the embryogenic response triggered via LEC2 overexpression, suggesting an indirect pathway of morphogenesis. Moreover, a negative interaction between auxin treatment and LEC2 overexpression in terms of SE efficiency was observed, as transgenic explants cultured on auxin medium displayed a significantly reduced level of embryogenic potential. The study provides further experimental evidence that in the determination of the embryogenic response in Arabidopsis somatic cells, a close link exists between auxin and the LEC2 activity.},

note = {56},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-34447121906,

title = {Histological analysis of direct somatic embryogenesis in Arabidopsis thaliana (L.) Heynh},

author = { E.U. Kurczyńska and M.D. Gaj and A. Ujczak and E. Mazur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34447121906&doi=10.1007%2fs00425-007-0510-6&partnerID=40&md5=3d00a2a2cebccc7fda9ee11b0da3e024},

doi = {10.1007/s00425-007-0510-6},

issn = {00320935},

year  = {2007},

date = {2007-01-01},

journal = {Planta},

volume = {226},

number = {3},

pages = {619-628},

abstract = {In Arabidopsis the in vitro culture of immature zygotic embryos (IZEs) at a late stage of development, on the solid medium containing synthetic auxin, leads to formation of somatic embryos via direct somatic embryogenesis (DSE). The presented results provide evidence that in IZE cells competent for DSE are located in the protodermis and subprotodermis of the adaxial side of cotyledons and somatic embryos displayed a single- or multicellular origin. Transgenic Arabidopsis lines expressing the GUS reporter gene, driven by the DR5 and LEC2 promoters, were used to analyse the distribution of auxin to mark embryogenic cells in cultured explants and develop somatic embryos. The analysis showed that at the start of the culture auxin was accumulated in all explant tissues, but from the fourth day onwards its location shifted to the protodermis and subprotodermis of the explant cotyledons. In globular somatic embryos auxin was detected in all cells, with a higher concentration in the protodermis, and in the heart stage its activity was mainly displayed in the shoot, root pole and cotyledon primordia. The embryogenic nature of dividing protodermal and subprotodermal cells accumulating auxin was confirmed by high expression of promoter activity of LEC2 in these cells. Analysis of symplasmic tracer (CFDA) distribution indicated symplasmic isolation between tissues engaged in DSE and other parts of an explant. Symplasmic isolation of somatic embryos from the explant was also detected. © 2007 Springer-Verlag.},

note = {93},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-33846894994,

title = {Hormone-response mutants of Arabidopsis thaliana (L.) Heynh. impaired in somatic embryogenesis},

author = { M.D. Gaj and A. Trojanowska and A. Ujczak and M. Mędrek and A. Kozioł and B. Garbaciak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846894994&doi=10.1007%2fs10725-006-9104-8&partnerID=40&md5=65ce9524b1cf09a51909006c18f4b1ba},

doi = {10.1007/s10725-006-9104-8},

issn = {01676903},

year  = {2006},

date = {2006-01-01},

journal = {Plant Growth Regulation},

volume = {49},

number = {2-3},

pages = {183-197},

publisher = {Springer Netherlands},

abstract = {Plant hormones are considered to be the key factors involved in triggering in vitro induced plant morphogenesis, including somatic embryogenesis (SE). Mutants affected in SE and altered in hormonal response therefore provide valuable material for genetic research on in vitro induced plant embryogenesis. The capacity for SE was studied in 27 mutants with defects in response to different plant hormones: auxin, ABA, gibberellin and cytokinin, and evaluated in 2-week-old mutant and wild-type cultures in terms of their efficiency and productivity. SE was induced in vitro via a direct morphogenic pathway, through the culture of immature zygotic embryos on standard solid medium with 5 μM 2,4-D. The majority of the analyzed mutants displayed a significantly impaired capacity for SE; and those affected belonged to several different hormone-defective groups, including forms affected in auxin (axr4), gibberellin (ga) and ABA (abi; hyl1; cpb20; abh1) response. These mutants showed a significant decrease in embryogenic response as manifested by a low efficiency and/or productivity of SE. Additionally, SE efficiency was analyzed for axr4-1 mutant on media supplemented with different auxins while GA 3 and inhibitors of gibberellins (uniconazol P and paclobutrazol), were applied for pkl1-1-mutant. The selected mutants provide a valuable research tool for studying the molecular mechanisms determining the induction of embryogenesis in cultures of somatic tissues. Their usefulness in further studies is discussed. © 2006 Springer Science+Business Media B.V.},

note = {28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-28244493498,

title = {Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis},

author = { M.D. Gaj and S. Zhang and J.J. Harada and P.G. Lemaux},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-28244493498&doi=10.1007%2fs00425-005-0041-y&partnerID=40&md5=3a0533222aff240b347749ba57385556},

doi = {10.1007/s00425-005-0041-y},

issn = {00320935},

year  = {2005},

date = {2005-01-01},

journal = {Planta},

volume = {222},

number = {6},

pages = {977-988},

abstract = {The capacity for somatic embryogenesis was studied in lec1, lec2 and fus3 mutants of Arabidopsis thaliana (L.) Heynh. It was found that contrary to the response of wild-type cultures, which produced somatic embryos via an efficient, direct process (65-94% of responding explants), lec mutants were strongly impaired in their embryogenic response. Cultures of the mutants formed somatic embryos at a low frequency, ranging from 0.0 to 3.9%. Moreover, somatic embryos were formed from callus tissue through an indirect route in the lec mutants. Total repression of embryogenic potential was observed in double (lec1 lec2; lec1 fus3; lec2 fus3) and triple (fus3 lec1 lec2) mutants. Additionally, mutants were found to exhibit efficient shoot regenerability via organogenesis from root explants. These results provide evidence that, besides their key role in controlling many different aspects of Arabidopsis zygotic embryogenesis, LEC/FUS genes are also essential for in vitro somatic embryogenesis induction. Furthermore, temporal and spatial patterns of auxin distribution during somatic embryogenesis induction were analyzed using transgenic Arabidopsis plants expressing GUS driven by the DR5 promoter. Analysis of data indicated auxin accumulation was rapid in all tissues of the explants of both wild type and the lec2-1 mutant, cultured on somatic embryogenesis induction medium containing 2,4-D. This observation suggests that loss of embryogenic potential in the lec2 mutant in vitro is not related to the distribution of exogenously applied auxin and LEC genes likely function downstream in auxin-induced somatic embryogenesis. © Springer-Verlag 2005.},

note = {211},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-4444247067,

title = {Factors influencing somatic embryogenesis induction and plant regeneration with particular reference to Arabidopsis thaliana (L.) Heynh},

author = { M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-4444247067&doi=10.1023%2fB%3aGROW.0000038275.29262.fb&partnerID=40&md5=d9b3afa20d6273686e147cfd3570414e},

doi = {10.1023/B:GROW.0000038275.29262.fb},

issn = {01676903},

year  = {2004},

date = {2004-01-01},

journal = {Plant Growth Regulation},

volume = {43},

number = {1},

pages = {27-47},

abstract = {The broad applications of somatic embryogenesis, both in basic and applied research, have stimulated studies on the determination of in vitro conditions for the induction of somatic embryos and their conversion into plants. As a result, efficient protocols on SE induction and plant regeneration have recently become available for many plant species, including Arabidopsis thaliana (L.) Heynh., a model plant in genetics and embryogenesis. Studies on factors controlling in vitro plant morphogenesis are highly desirable not only for the development of improved regeneration systems, but also for the analysis of molecular mechanisms underlying plant embryogenesis. This review focuses on the conditions influencing the induction of embryogenic potential in in vitro cultured plant cells. The roles of explant type, endo- and exogenous plant growth regulators and stress factors in the induction of somatic embryogenesis are especially emphasized. Possible mechanisms by which different factors induce or modify embryogenic competence in cultured plant cells are also discussed. Since the production of genetically solid and true-to-type plants is desired, especially for transformation and micropropagation practice, the problem of the genetic characteristics of regenerants, in terms of their chimerism and somaclonal variation, is discussed in some detail. Special consideration is given to A. thaliana - a major model plant species for classical genetics and genomics. Recent availability of efficient embryogenic cultures in this organism makes it possible to benefit from advanced genomic research of Arabidopsis to study plant embryogenesis on the molecular level.},

note = {256},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0036587527,

title = {Stimulation of somatic embryo formation by mutagens and darkness in culture of immature zygotic embryos of Arabidopsis thaliana (L.) Heynh.},

author = { M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036587527&doi=10.1023%2fA%3a1020392014493&partnerID=40&md5=0d9d82f8bc2f5f028421816e0d57ad4e},

doi = {10.1023/A:1020392014493},

issn = {01676903},

year  = {2002},

date = {2002-01-01},

journal = {Plant Growth Regulation},

volume = {37},

number = {1},

pages = {93-98},

abstract = {The aim of the study was to evaluate the influence of light conditions, physical state of the induction medium and the mutagenic treatment on the embryogenic ability of Arabidopsis thaliana (L.) immature zygotic embryos differing in developmental stage. The efficiency of direct somatic embryogenesis (DSE) was analysed in a culture of immature zygotic embryos at an early (ES) and a late (LS) developmental stage. The efficiency of DSE was scored as a percentage of the explants producing somatic embryos. The experiments indicated that the physical state of the induction medium (solid or liquid) did not influence the embryogenic ability of the cultured explants. In the cultures on both solid and liquid induction medium, the ES explants produced somatic embryos with a frequency of 25.8-37.3% i.e. 2.5-3-times lower than LS explants. However, an increase in the embryogenic ability of ES explants (up to 69.8%) was observed when DSE was induced in darkness. Moreover, the stimulation of DSE efficiency in culture of ES explants was also observed after mutagenic treatment. The chemical mutagens, MNH and EMS, applied for explant treatment, both stimulated efficiency of somatic embryo formation in culture of ES explants. The most effective DSE induction was observed when MNH and EMS were applied in doses of 0.125-1.0 mM × 3h and 0.05-0.2% × 18h, respectively. In these treatment combinations the frequency of ES explants forming somatic embryos was found to be about 2 times higher than in the control culture.},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0035045828,

title = {Direct somatic embryogenesis as a rapid and efficient system for in vitro regeneration of Arabidopsis thaliana},

author = { M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035045828&doi=10.1023%2fA%3a1010679614721&partnerID=40&md5=a4e53bfbeae9d2ad5e54829f1b8b186b},

doi = {10.1023/A:1010679614721},

issn = {01676857},

year  = {2001},

date = {2001-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {64},

number = {1},

pages = {39-46},

abstract = {A simple, rapid and effective system to regenerate Arabidopsis plants via direct somatic embryogenesis has been established. Somatic embryogenesis was induced directly during culture of immature zygotic embryos. The frequency of somatic embryogenesis was strongly influenced by the stage of development of the explants. Explants in different developmental stages were cultured on B5 agar medium containing 5 μM 2,4-dichlorophenoxyacetic acid and the highest frequency (up to 90%) of somatic embryogenesis was observed in zygotic embryos with fully-developed cotyledons. The first somatic embryos developing directly from explant tissue were noticed after 8 days of culture. Somatic embryogenesis of a high frequency (87-96%) was observed in cultures of the all six genotypes tested (Columbia, C-24, RLD, Wassilewskaja, Landsberg erecta and Wilna). Subculture of somatic embryos onto auxin-free medium resulted in their conversion into plants with an average frequency of 79.5%. The regenerates showed normal morphological characteristics and were fertile. All 56 analysed plants displayed a diploid number of chromosomes and two out of 96 (2.1%) tested plants carried a chlorophyll or embryo-lethal mutation.},

note = {106},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0033265539,

title = {Selection of valine-resistance in callus culture of Arabidopsis thaliana (L.) Heynh. Derived from leaf explants},

author = { M.D. Gaj and G. Czaja and M. Nawrot},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033265539&partnerID=40&md5=605a01483d2938d9cc057244f279742d},

issn = {00016977},

year  = {1999},

date = {1999-01-01},

journal = {Acta Societatis Botanicorum Poloniae},

volume = {68},

number = {3},

pages = {211-215},

publisher = {Polish Botanical Society},

abstract = {The selection of valine-resistant mutants was carried out in leaf explant cultures of three Arabidopsis thaliana (L.) Heynh. ecotypes: C-24, RLD and Columbia. The valine concentration used for in vitro selection, lethal for seed-growing plants, has not affected callus formation and growth. However, strong inhibition of shoot regeneration ability of calli growing under selection pressure was noticed. In total, 1043 explants were cultured on valine medium and 18 shoots were regenerated with an average frequency of 1.7 shoots per 100 calli. Most R1 shoots were sterile and seeds were collected from 3 plants. The transmission of valine-resistance to the sexual progeny of these plants was scored and the increased level of valine-resistance was found in progeny of one line - 61C. This line originated from the culture of Columbia leaf explant and displayed tetraploid chromosome number.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0032420606,

title = {Somatic embryogenesis and plant regeneration in callus culture of tef, Eragrostis tef (Zucc.) Trotter},

author = { A. Kebebew and M.D. Gaj and M. Maluszynski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032420606&doi=10.1007%2fs002990050549&partnerID=40&md5=adf532666389a6c144381cbb03e3821d},

doi = {10.1007/s002990050549},

issn = {07217714},

year  = {1998},

date = {1998-01-01},

journal = {Plant Cell Reports},

volume = {18},

number = {1-2},

pages = {154-158},

abstract = {The study was carried out to establish in vitro culture conditions for plant regeneration of tef, Eragrostis tef (Zucc.) Trotter. Mature seeds of two Ethiopian varieties, DZ-01-354 and DZ-01-196, were used to initiate callus cultures on Murashige and Skoog (MS) medium with different auxins. Four- and 8-week-old calli induced on a medium with 2.0 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D) were subcultured onto various media to induce somatic embryogenesis. Compact, nodulated, embryogenic callus was observed after transfer onto MS-callus proliferating (CP) medium. Embryogenic tissue appeared on soft and amorphous callus and developed into somatic embryos during a subsequent subculture to MS embryo-promoting (EP) media. Various growth regulator combinations were tested in CP and EP media to obtain a high efficiency of somatic embryo formation. The highest frequency of calli forming somatic embryos (56.1-68.3%) was observed when CP media with 2.0 or 4.0 mg/l 2,3,5-triiodobenzoic acid were employed and then cultures were transferred to EP media with 0.5 mg/l 2,4-D and 0.5 mg/l kinetin followed by 0.5 mg/l indole-3-acetic acid and 0.5 mg/l N6-benzyladenine. Plant development from somatic embryos was obtained on MS medium supplemented with 1.0 mg/l gibberellic acid. On average, 71.2% of calli displaying somatic embryos converted into plants. Regenerated plants were successfully transferred to soil. Neither chlorophyll-deficient plants nor morphological variants were found among regenerants. All regenerated plants were fertile.},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0030353393,

title = {The High Frequency of Variegated Forms After in Vitro Mutagenesis in Saintpaulia Ionantha Wendl},

author = { M. Gaj and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030353393&partnerID=40&md5=788f26b3aed8419946f36dd6621b17a0},

issn = {00016977},

year  = {1996},

date = {1996-01-01},

journal = {Acta Societatis Botanicorum Poloniae},

volume = {65},

number = {3-4},

pages = {339-343},

publisher = {Polish Botanical Society},

abstract = {The leaf-explants of Saintpaulia ionantha Wendl. var.'miniature' were treated by different doses of MNH and cultured on shoot regeneration medium. A strong toxic effect of some MNH doses on expiant survival during the first two subcultures was noticed. The expiants surviving treatment regenerated shoots with the efficiency comparable to the control. The high number of shoots regenerated from mutagenised leaves showed chlorophyll chimerism (so-called variegated forms). The use of 5 mM MNH for 1.5 or 2 h was found very effective, as 100% of survived explants regenerated variegated shoots. Besides hundreds of variegated forms also leaf-shape and flower-colour variants were observed in MNH-treated culture. Somaclonal variation was not observed in the control culture. The results indicate the great efficiency of in vitro applied MNH for induction of morphological variants of Saintpaulia, and especially variegated forms.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}