@article{2-s2.0-85184518909,

title = {Global nutritional challenges and opportunities: Buckwheat, a potential bridge between nutrient deficiency and food security},

author = { R. Jha and K. Zhang and Y. He and N. Mendler-Drienyovszki and K. Magyar-Tábori and M. Quinet and M. Germ and I. Kreft and V. Meglič and K. Ikeda and M.A. Chapman and D. Janovská and G. Podolska and S. Woo and S. Bruno and M.I. Georgiev and N.K. Chrungoo and A. Betekhtin and M. Zhou},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85184518909&doi=10.1016%2fj.tifs.2024.104365&partnerID=40&md5=2ae7d835cc9ab7f94d8e4da24b0bb173},

doi = {10.1016/j.tifs.2024.104365},

issn = {09242244},

year  = {2024},

date = {2024-01-01},

journal = {Trends in Food Science and Technology},

volume = {145},

publisher = {Elsevier Ltd},

abstract = {Background: The ability to ensure nutritional and food security is seriously threatened by the ever-growing global population. Overreliance on a few staple food crops such as wheat, rice and maize will no longer be able to satisfy the rising demand for future food. Even with increasing agricultural production, over 820 million people are still facing food insecurity and at least 2 billion are facing nutrition insecurity. Therefore, it is imperative to focus on finding simple and sustainable solution to the present threat of global food insecurity. Besides staple food crops, harnessing nutrient-dense, climate-resilient, and locally available crops for production, marketing and consumption as “Smart Foods” for the future is needed. Buckwheat is a potential smart food because of its stress resistance and nutritional properties as well as strong antioxidant activity due to presence of flavonoids. Scope and approach: This paper comprises a comprehensive review of the scientific literature on the valorization of buckwheat crops in terms of germplasm resources, breeding and genetic improvements for yield, bioactive compounds, biological activities and its potential application in food and pharmaceutical industries. Key findings and conclusions: Identification of elite cultivars and exploitation of buckwheat derived gluten-free bakery and non-bakery food stuffs and beverages such as tea, beer and wine should be explored for human consumption. Abundance of bioactive compounds results in high anti-oxidant, anti-microbial, anti-glycemic, anti-cancer properties and other health-promoting activities highlighting buckwheat's potential application as nutraceuticals and pharmaceuticals. © 2024 Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85170843148,

title = {Global epigenetic analysis revealed dynamic fluctuations in levels of DNA methylation and histone modifications in the calli of Fagopyrum with different capacity for morphogenesis},

author = { A. Tomasiak and K. Sala-Cholewa and L.S. Berg and A.J. Brąszewska-Zalewska and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85170843148&doi=10.1007%2fs11240-023-02595-3&partnerID=40&md5=8648c9098bbba39042e86d738aaaf7a0},

doi = {10.1007/s11240-023-02595-3},

issn = {01676857},

year  = {2023},

date = {2023-01-01},

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

volume = {155},

number = {3},

pages = {743-757},

publisher = {Springer Science and Business Media B.V.},

abstract = {Buckwheat characterises with high susceptibility to in vitro tissue culture conditions, which have been researched extensively to study a plethora of processes. F. tataricum morphogenic callus (MC) is characterised by its capacity for morphogenesis for up to ten years of culture, displaying an extraordinary level of genome stability, and comprises of proembryogenic cell complexes (PECC),which are the structures resembling somatic embryos arrested on the pre-globular stage. The non-morphogenic callus (NC) that appears on the surface of MC after approximately two years of culture due to endoreduplication cycles, is characterised by aneuploidy, rapid growth rate and high level of oxidative stress. F. esculentum embryogenic callus (EC) has different morphological and histological features, remains stable for up to three years of culture, has a dense, globular structure, and is capable of forming embryoids from the masses of embryogenic cells, but does not produce a non-embryogenic clone. In this work, immunocytochemical analyses revealed dynamic epigenetic changes in Fagopyrum calli. We demonstrated that; decreased level of H3K4me2 seems to be associated with pluripotency acquisition in F. esculentum EC and F. tataricum MC; DNA hypomethylation appears to be connected with the acquisition of the embryogenic potential and PECC reinitiation in F. tataricum MC. Moreover, we observed that H4K16ac and H4K5ac exhibited the highest variability during the course of passage in NC. Elevated levels of these modifications on day zero and day six for H4K16ac and H4K5ac, respectively, seem to be connected with endoreplication peaks, the processes which are characteristic of this callus. © 2023, The Author(s).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85167662362,

title = {Promotive effect of phytosulfokine - peptide growth factor - on protoplast cultures development in Fagopyrum tataricum (L.) Gaertn},

author = { M. Zaranek and R. Pérez-Pérez and A. Milewska-Hendel and A. Betekhtin and E. Grzebelus},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85167662362&doi=10.1186%2fs12870-023-04402-9&partnerID=40&md5=2294ecea0866096bfd9e83b09d510d07},

doi = {10.1186/s12870-023-04402-9},

issn = {14712229},

year  = {2023},

date = {2023-01-01},

journal = {BMC Plant Biology},

volume = {23},

number = {1},

pages = {385-},

publisher = {BioMed Central Ltd},

abstract = {Background: Fagopyrum tataricum (Tartary buckwheat) is a valuable crop of great nutritional importance due to its high level of bioactive compounds. Excellent opportunities to obtain plants with the high level or the desired profile of valuable metabolites may be provided by in vitro cultures. Among known in vitro techniques, protoplast technology is an exciting tool for genetic manipulation to improve crop traits. In that context, protoplast fusion may be applied to generate hybrid cells between different species of Fagopyrum. To apply protoplast cultures to the aforementioned approaches in this research, we established the protoplast-to-plant system in Tartary buckwheat. Results: In this work, cellulase and pectinase activity enabled protoplast isolation from non-morphogenic and morphogenic callus (MC), reaching, on average, 2.3 × 106 protoplasts per g of fresh weight. However, to release protoplasts from hypocotyls, the key step was the application of driselase in the enzyme mixture. We showed that colony formation could be induced after protoplast embedding in agarose compared to the alginate matrix. Protoplasts cultured in a medium based on Kao and Michayluk supplemented with phytosulfokine (PSK) rebuilt cell walls, underwent repeated mitotic division, formed aggregates, which consequently led to callus formation. Plating efficiency, expressing the number of cell aggregate formed, in 10-day-old protoplast cultures varied from 14% for morphogenic callus to 30% for hypocotyls used as a protoplast source. However plant regeneration via somatic embryogenesis and organogenesis occurred only during the cultivation of MC-derived protoplasts. Conclusions: This study demonstrated that the applied protoplast isolation approach facilitated the recovery of viable protoplasts. Moreover, the embedding of protoplasts in an agarose matrix and supplementation of a culture medium with PSK effectively stimulated cell division and further development of Tartary buckwheat protoplast cultures along with the plant regeneration. Together, these results provide the first evidence of developing a protoplast-to-plant system from the MC of Fagopyrum tataricum used as source material. These findings suggest that Tartary buckwheat’s protoplast cultures have potential implications for the species’ somatic hybridization and genetic improvement. © 2023, BioMed Central Ltd., part of Springer Nature.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85163116120,

title = {Efficient and rapid system of plant regeneration via protoplast cultures of Fagopyrum esculentum Moench},

author = { M. Zaranek and R. Pérez-Pérez and A. Milewska-Hendel and E. Grzebelus and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85163116120&doi=10.1007%2fs11240-023-02542-2&partnerID=40&md5=095db46aa63cec8daad37b85250fd60e},

doi = {10.1007/s11240-023-02542-2},

issn = {01676857},

year  = {2023},

date = {2023-01-01},

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

volume = {154},

number = {3},

pages = {673-687},

publisher = {Springer Science and Business Media B.V.},

abstract = {In the present study, a high yield of isolated protoplasts from the agronomically important crop Fagopyrum esculentum was obtained by applying a mixture of cellulase, pectolyase, and driselase. We demonstrated that the yield of morphogenic callus-derived protoplasts was 1 × 106 protoplasts per g of fresh tissue. For hypocotyls used as the protoplast source, the number of released cells was twice lower. The protoplasts, embedded in an agarose matrix and cultured in a modified Kao and Michayluk media supplemented with phytosulfokine, re-enter the cell cycle and start to develop, forming microcalli. The plating efficiency was about 20% in the case of hypocotyl- and morphogenic callus-derived protoplasts. For plant regeneration, the medium was supplemented with different combinations of cytokinin. Somatic embryogenesis and organogenesis occur during the cultivation of the protoplast-derived tissues, depending on the applied protoplast source. For the first time, an effective protoplast-to-plant system for F. esculentum has been developed. © 2023, The Author(s).},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85171835921,

title = {Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum},

author = { A. Piński and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85171835921&doi=10.3389%2ffpls.2023.1270150&partnerID=40&md5=ea62185f60b67f1041241e0c54b337bc},

doi = {10.3389/fpls.2023.1270150},

issn = {1664462X},

year  = {2023},

date = {2023-01-01},

journal = {Frontiers in Plant Science},

volume = {14},

publisher = {Frontiers Media SA},

abstract = {Fagopyrum tataricum (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in F. tataricum is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for F. tataricum callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol’s effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via FtPDS gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in F. tataricum. Copyright © 2023 Pinski and Betekhtin.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85139931114,

title = {The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae)},

author = { G. Yücel and A. Betekhtin and E. CabI and M. Tuna and R. Hasterok and B.A. Kolano},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85139931114&doi=10.3390%2fijms231911033&partnerID=40&md5=420940d23056c306f8913a2a35f4204e},

doi = {10.3390/ijms231911033},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {19},

publisher = {MDPI},

abstract = {The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85124912638,

title = {Buckwheat in Tissue Culture Research: Current Status and Future Perspectives},

author = { A. Tomasiak and M. Zhou and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124912638&doi=10.3390%2fijms23042298&partnerID=40&md5=d714bec6201821083ad36c993ab4dd20},

doi = {10.3390/ijms23042298},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {4},

publisher = {MDPI},

abstract = {Buckwheat is a member of a genus of 23 species, where the two most common species are Fagopyrum esculentum (common buckwheat) and Fagopyrum tataricum (Tartary buckwheat). This pseudocereal is a source of micro and macro nutrients, such as gluten-free proteins and amino acids, fatty acids, bioactive compounds, dietary fibre, fagopyrins, vitamins and minerals. It is gaining in-creasing attention due to its health-promoting properties. Buckwheat is widely susceptible to in vitro conditions which are used to study plantlet regeneration, callus induction, organogenesis, somatic embryogenesis, and the synthesis of phenolic compounds. This review summarises the development of buckwheat in in vitro culture and describes protocols for the regeneration of plantlets from various explants and differing concentrations of plant growth regulators. It also describes callus induction protocols as well as the role of calli in plantlet regeneration. Protocols for establishing hairy root cultures with the use of Agrobacterium rhizogens are useful in the synthesis of secondary metabolites, as well as protocols used for transgenic plants. The review also focuses on the future prospects of buckwheat in tissue culture and the challenges researchers are addressing. © by the authors. Licensee MDPI, Basel, Switzerland.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85110027459,

title = {3,4‐dehydro‐l‐proline induces programmed cell death in the roots of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and J. Kwaśniewska and Ł. Chajec and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110027459&doi=10.3390%2fijms22147548&partnerID=40&md5=045642b6770419a71c99a63d6dd94f4c},

doi = {10.3390/ijms22147548},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {14},

publisher = {MDPI},

abstract = {As cell wall proteins, the hydroxyproline‐rich glycoproteins (HRGPs) take part in plant growth and various developmental processes. To fulfil their functions, HRGPs, extensins (EXTs) in particular, undergo the hydroxylation of proline by the prolyl‐4‐hydroxylases. The activity of these enzymes can be inhibited with 3,4‐dehydro‐L‐proline (3;4‐DHP), which enables its application to reveal the functions of the HRGPs. Thus, to study the involvement of HRGPs in the development of root hairs and roots, we treated seedlings of Brachypodium distachyon with 250 μM, 500 μM, and 750 μM of 3,4‐DHP. The histological observations showed that the root epidermis cells and the cortex cells beneath them ruptured. The immunostaining experiments using the JIM20 antibody, which recognizes the EXT epitopes, demonstrated the higher abundance of this epitope in the control compared to the treated samples. The transmission electron microscopy analyses revealed morphological and ultrastructural features that are typical for the vacuolar‐type of cell death. Using the TUNEL test (terminal deoxynucleotidyl transferase dUTP nick end labelling), we showed an increase in the number of nuclei with damaged DNA in the roots that had been treated with 3,4‐DHP compared to the control. Finally, an analysis of two metacaspases’ gene activity revealed an increase in their expression in the treated roots. Altogether, our results show that inhibiting the prolyl‐4‐hydroxyl-ases with 3,4‐DHP results in a vacuolar‐type of cell death in roots, thereby highlighting the important role of HRGPs in root hair development and root growth. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85108260977,

title = {Changes in the cell wall proteome of leaves in response to high temperature stress in brachypodium distachyon},

author = { A. Piński and A. Betekhtin and B. Skupien‐rabian and U. Jankowska and E. Jamet and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108260977&doi=10.3390%2fijms22136750&partnerID=40&md5=bd0c6a761d804c4e3473abb1174f406e},

doi = {10.3390/ijms22136750},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {13},

publisher = {MDPI},

abstract = {High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non‐redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over‐accumulated and 42 were under‐accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over‐ and 12 under‐accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85086465275,

title = {From single cell to plants: Mesophyll protoplasts as a versatile system for investigating plant cell reprogramming},

author = { T. Pasternak and K. Lystvan and A. Betekhtin and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086465275&doi=10.3390%2fijms21124195&partnerID=40&md5=0b8504d08f47ad16842619f402944d4f},

doi = {10.3390/ijms21124195},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {12},

pages = {1-15},

publisher = {MDPI AG},

abstract = {Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are effectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, differentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85085871596,

title = {A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum},

author = { K. Hus and A. Betekhtin and A. Piński and M. Rojek-Jelonek and E. Grzebelus and C. Nibau and M. Gao and K.E. Jaeger and G. Jenkins and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085871596&doi=10.3389%2ffpls.2020.00614&partnerID=40&md5=b86deda01a9059410a6d9ffe28faed8e},

doi = {10.3389/fpls.2020.00614},

issn = {1664462X},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Plant Science},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {The CRISPR/Cas9 system enables precise genome editing and is a useful tool for functional genomic studies. Here we report a detailed protocol for targeted genome editing in the model grass Brachypodium distachyon and its allotetraploid relative B. hybridum, describing gRNA design, a transient protoplast assay to test gRNA efficiency, Agrobacterium-mediated transformation and the selection and analysis of regenerated plants. In B. distachyon, we targeted the gene encoding phytoene desaturase (PDS), which is a crucial enzyme in the chlorophyll biosynthesis pathway. The albino phenotype of mutants obtained confirmed the effectiveness of the protocol for functional gene analysis. Additionally, we targeted two genes related to cell wall maintenance, encoding a fasciclin-like arabinogalactan protein (FLA) and a pectin methylesterase (PME), also in B. distachyon. Two genes encoding cyclin-dependent kinases (CDKG1 and CDKG2), which may be involved in DNA recombination were targeted in both B. distachyon and B. hybridum. Cas9 activity induces mainly insertions or deletions, resulting in frameshift mutations that, may lead to premature stop codons. Because of the close phylogenetic relationship between Brachypodium species and key temperate cereals and forage grasses, this protocol should be easily adapted to target genes underpinning agronomically important traits. © Copyright © 2020 Hus, Betekhtin, Pinski, Rojek-Jelonek, Grzebelus, Nibau, Gao, Jaeger, Jenkins, Doonan and Hasterok.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079083785,

title = {In vitro tissue culture in brachypodium: Applications and challenges},

author = { A. Betekhtin and K. Hus and M. Rojek-Jelonek and E.U. Kurczyńska and C. Nibau and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079083785&doi=10.3390%2fijms21031037&partnerID=40&md5=f5b279c30079e29e77cf4ca674cd3454},

doi = {10.3390/ijms21031037},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {3},

publisher = {MDPI AG},

abstract = {Brachypodium distachyon has become an excellent model for plant breeding and bioenergy grasses that permits many fundamental questions in grass biology to be addressed. One of the constraints to performing research in many grasses has been the difficulty with which they can be genetically transformed and the generally low frequency of such transformations. In this review, we discuss the contribution that transformation techniques have made in Brachypodium biology as well as how Brachypodium could be used to determine the factors that might contribute to transformation efficiency. In particular, we highlight the latest research on the mechanisms that govern the gradual loss of embryogenic potential in a tissue culture and propose using B. distachyon as a model for other recalcitrant monocots. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85083080937,

title = {CDKG1 is required for meiotic and somatic recombination intermediate processing in Arabidopsis[CC-BY]},

author = { C. Nibau and A. Lloyd and D. Dadarou and A. Betekhtin and F. Tsilimigka and D.W. Phillips and J.H. Doonan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85083080937&doi=10.1105%2fTPC.19.00942&partnerID=40&md5=5cb6b706debef08279ea057cace774cd},

doi = {10.1105/TPC.19.00942},

issn = {10404651},

year  = {2020},

date = {2020-01-01},

journal = {Plant Cell},

volume = {32},

number = {4},

pages = {1308-1322},

publisher = {American Society of Plant Biologists},

abstract = {The Arabidopsis (Arabidopsis thaliana) cyclin-dependent kinase G1 (CDKG1) is necessary for recombination and synapsis during male meiosis at high ambient temperature. In the cdkg1-1 mutant, synapsis is impaired and there is a dramatic reduction in the number of class I crossovers, resulting in univalents at metaphase I and pollen sterility. Here, we demonstrate that CDKG1 is necessary for the processing of recombination intermediates in the canonical ZMM recombination pathway and that loss of CDKG1 results in increased class II crossovers. While synapsis and events associated with class I crossovers are severely compromised in a cdkg1-1 mutant, they can be restored by increasing the number of recombination intermediates in the double cdkg1-1 fancm-1 mutant. Despite this, recombination intermediates are not correctly resolved, leading to the formation of chromosome aggregates at metaphase I. Our results show that CDKG1 acts early in the recombination process and is necessary to stabilize recombination intermediates. Finally, we show that the effect on recombination is not restricted to meiosis and that CDKG1 is also required for normal levels of DNA damage-induced homologous recombination in somatic tissues. © 2020 The Authors.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85074666863,

title = {Comparatively barcoded chromosomes of brachypodium perennials tell the story of their karyotype structure and evolution},

author = { J. Lusinska and A. Betekhtin and D. López-Alvarez and P. Catalán and G. Jenkins and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074666863&doi=10.3390%2fijms20225557&partnerID=40&md5=1e87ac6eba426f4ef1f180cb67cf71f1},

doi = {10.3390/ijms20225557},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {22},

publisher = {MDPI AG},

abstract = {The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85061604241,

title = {Stability and instability processes in the calli of Fagopyrum tataricum that have different morphogenic potentials},

author = { A. Betekhtin and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061604241&doi=10.1007%2fs11240-019-01575-w&partnerID=40&md5=645591d8a95ce3e965e098b879213554},

doi = {10.1007/s11240-019-01575-w},

issn = {01676857},

year  = {2019},

date = {2019-01-01},

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

volume = {137},

number = {2},

pages = {343-357},

publisher = {Springer Netherlands},

abstract = {The morphogenic callus (MC) of Fagopyrum tataricum contains a large amount of flavonoids, especially rutin, and exhibits a high level of antioxidant activity. A non-morphogenic callus (NC) may appear on the surface of the MC after two to three years of cultivation and is then subjected to a consistently high level of oxidative stress. The elucidation of the molecular background of this instability is essential for gaining a better understanding of the somaclonal variation mechanisms in tissue cultures that have different morphogenic potentials. Thus, in this study we show that continuous oxidative stress in a NC might be connected with a rapid senescence process and as a result, in the upregulation of the genes that are connected with the telomere complexity, ethylene biosynthesis and the expression of DNA methyltransferases. Moreover, we analysed the presence of the hydroxyproline-rich glycoproteins in the calli and demonstrated the differences between the MC and NC. The LM2 antibody can be useful as a marker of the cells in the MC that are embryogenically determined, while the MAC207 antibody seems to be a positive marker of a MC as its signal was absent in the NC. This study also provides the first report on the effect of trichostatin A on the DNA methyltransferases and demethylases in a MC. © 2019, The Author(s).},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85066960172,

title = {Hydroxyproline-rich glycoproteins as markers of temperature stress in the leaves of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and K. Sala and K. Godel-Jędrychowska and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066960172&doi=10.3390%2fijms20102571&partnerID=40&md5=83367841b3aa36bbcbe19816364135ad},

doi = {10.3390/ijms20102571},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {10},

publisher = {MDPI AG},

abstract = {Plants frequently encounter diverse abiotic stresses, one of which is environmental thermal stress. To cope with these stresses, plants have developed a range of mechanisms, including altering the cell wall architecture, which is facilitated by the arabinogalactan proteins (AGP) and extensins (EXT). In order to characterise the localisation of the epitopes of the AGP and EXT, which are induced by the stress connected with a low (4◦ C) or a high (40◦ C) temperature, in the leaves of Brachypodium distachyon, we performed immunohistochemical analyses using the antibodies that bind to selected AGP (JIM8; JIM13; JIM16; LM2 and MAC207), pectin/AGP (LM6) as well as EXT (JIM11; JIM12 and JIM20). The analyses of the epitopes of the AGP indicated their presence in the phloem and in the inner bundle sheath (JIM8; JIM13; JIM16 and LM2). The JIM16 epitope was less abundant in the leaves from the low or high temperature compared to the control leaves. The LM2 epitope was more abundant in the leaves that had been subjected to the high temperatures. In the case of JIM13 and MAC207, no changes were observed at the different temperatures. The epitopes of the EXT were primarily observed in the mesophyll and xylem cells of the major vascular bundle (JIM11; JIM12 and JIM20) and no correlation was observed between the presence of the epitopes and the temperature stress. We also analysed changes in the level of transcript accumulation of some of the genes encoding EXT, EXT-like receptor kinases and AGP in the response to the temperature stress. In both cases, although we observed the upregulation of the genes encoding AGP in stressed plants, the changes were more pronounced at the high temperature. Similar changes were observed in the expression profiles of the EXT and EXT-like receptor kinase genes. Our findings may be relevant for genetic engineering of plants with increased resistance to the temperature stress. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85065116283,

title = {Defining the genetic basis of plant–endophytic bacteria interactions},

author = { A. Piński and A. Betekhtin and K.T. Hupert-Kocurek and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065116283&doi=10.3390%2fijms20081947&partnerID=40&md5=96b5990897aec8304bac8977b991dff7},

doi = {10.3390/ijms20081947},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

publisher = {MDPI AG},

abstract = {Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85061128284,

title = {Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and E.A. Wolny and A. Betekhtin and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061128284&doi=10.1093%2fjxb%2fery425&partnerID=40&md5=a123ef59aae852b182e62c863f89ff7c},

doi = {10.1093/jxb/ery425},

issn = {00220957},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Experimental Botany},

volume = {70},

number = {3},

pages = {871-883},

publisher = {Oxford University Press},

abstract = {Nucleolar dominance is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus while the rDNA loci derived from the other progenitor are transcriptionally silenced. There is substantial evidence that nucleolar dominance is regulated developmentally. This study focuses upon the establishment and/or maintenance of nucleolar dominance during different stages of development in the model grass allotetraploid Brachypodium hybridum. Fluorescence in situ hybridization with a 25S rDNA probe to cells in three-dimensional cytogenetic preparations showed that nucleolar dominance is present not only in root meristematic and differentiated cells of this species, but also in male meiocytes at prophase I, tetrads of microspores, and different embryonic tissues. The inactive state of Brachypodium stacei-originated rDNA loci was confirmed by silver staining. Only B. distachyon-derived 35S rDNA loci formed nucleoli in the aforementioned tissues, whereas B. stacei-like loci remained highly condensed and thus transcriptionally suppressed. The establishment of nucleolar dominance during earlier stages of B. hybridum embryo development cannot be ruled out. However, we propose that gradual pseudogenization of B. stacei-like loci in the evolution of the allotetraploid seems to be more likely. © 2018 The Author(s).},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85057991726,

title = {Cell wall epitopes and endoploidy as reporters of embryogenic potential in brachypodium distachyon callus culture},

author = { A. Betekhtin and M. Rojek-Jelonek and K. Nowak and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057991726&doi=10.3390%2fijms19123811&partnerID=40&md5=a019f7df04ed76fd5a1440b62abca7ae},

doi = {10.3390/ijms19123811},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {12},

publisher = {MDPI AG},

abstract = {Effective regeneration of callus tissue into embryos and then into whole plants is essential for plant biotechnology. The embryonic potential is often low and can further decrease with time in culture, which limits the utilisation of calli for transformation procedures and in vitro propagation. In this study, we show that the loss of embryogenic potential in callus cultures of Brachypodium distachyon is progressive over time. Flow cytometry analyses indicated endoploidy levels increased in 60-and 90-day-old calli with effective loss of the 2C DNA content peak in the latter. Analysis of indolic compounds content revealed a decrease in 60-and 90-day-old calli compared to either freshly isolated explants or 30-day-old calli. Immunohistochemical analysis revealed a decrease in arabinogalactan proteins (AGP) signal with the time of culture, but extensin (EXT) epitopes either increased (JIM12 epitopes) or decreased (JIM11 epitopes). The transcript accumulation levels of AGPs and EXTs confirmed these results, with most of AGP and EXT transcripts gradually decreasing. Some chimeric EXT transcripts significantly increased on the 30th day of culture, perhaps because of an increased embryogenic potential. Selected somatic embryogenesis-related genes and cyclins demonstrated a gradual decrease of transcript accumulation for YUCCA (YUC), AINTEGUMENTA-LIKE (AIL), BABY BOOM (BBM), and CLAVATA (CLV3) genes, as well as for most of the cyclins, starting from the 30th day of culture. Notably, WUSCHEL (WUS) transcript was detectable only on the 30th and 60th day and was not detectable in the zygotic embryos and in 90-day-old calli. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054137635,

title = {Germination and the early stages of seedling development in brachypodium distachyon},

author = { E.A. Wolny and A. Betekhtin and M. Rojek-Jelonek and A.J. Brąszewska-Zalewska and J. Lusinska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054137635&doi=10.3390%2fijms19102916&partnerID=40&md5=6bc3a0bce97cc709e1970b6a859568af},

doi = {10.3390/ijms19102916},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {10},

publisher = {MDPI AG},

abstract = {Successful germination and seedling development are crucial steps in the growth of a new plant. In this study, we investigated the course of the cell cycle during germination in relation to grain hydration in the model grass Brachypodium distachyon (Brachypodium) for the first time. Flow cytometry was performed to monitor the cell cycle progression during germination and to estimate DNA content in embryo tissues. The analyses of whole zygotic embryos revealed that the relative DNA content was 2C, 4C, 8C, and 16C. Endoreplicated nuclei were detected in the scutellum and coleorhiza cells, whereas the rest of the embryo tissues only had nuclei with a 2C and 4C DNA content. This study was accompanied by a spatiotemporal profile analysis of the DNA synthetic activity in the organs of Brachypodium embryos during germination using EdU labelling. Upon imbibition, nuclear DNA replication was initiated in the radicle within 11 h and subsequently spread towards the plumule. The first EdU-labelled prophases were observed after 14 h of imbibition. Analysis of selected genes that are involved in the regulation of the cell cycle, such as those encoding cyclin-dependent kinases and cyclins, demonstrated an increase in their expression profiles. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054793804,

title = {Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum},

author = { J. Lusinska and J. Majka and A. Betekhtin and K. Susek and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054793804&doi=10.1093%2faob%2fmcy086&partnerID=40&md5=502a5a8f625a9f3465e1961f5b82860d},

doi = {10.1093/aob/mcy086},

issn = {03057364},

year  = {2018},

date = {2018-01-01},

journal = {Annals of Botany},

volume = {122},

number = {3},

pages = {445-459},

publisher = {Oxford University Press},

abstract = {Background and Aims The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F; Armero A; Pont C; Klopp C; Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs). Methods Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones. Key Results All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2; Os8; Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement. Conclusions mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid. © 2018 The Author(s).},

note = {22},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048889878,

title = {5-Azacitidine induces cell death in a tissue culture of brachypodium distachyon},

author = { A. Betekhtin and A. Milewska-Hendel and Ł. Chajec and M. Rojek-Jelonek and K. Nowak and J. Kwaśniewska and E.A. Wolny and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048889878&doi=10.3390%2fijms19061806&partnerID=40&md5=72a6b817774ef0346f00f6530b07a6ac},

doi = {10.3390/ijms19061806},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {6},

publisher = {MDPI AG},

abstract = {Morphological and histological observations revealed that, at a concentration of 50 µM, 5-azacitidine (5-azaC) totally inhibited the induction of embryogenic masses (EM), while the cultivation of explants (zygotic embryos; ZEs) in the presence of 5 µM of 5-azaC led to the formation of a callus with EM in 10% of the cases. Transmission electron microscopy (TEM) analyzes revealed the presence of the morphological and ultrastructural features that are typical for the vacuolar type of cell death in the callus cells that were treated. A TUNEL assay confirmed the presence of DNA double-strand breaks for the callus cells that had been treated with both 5 and 50 µM 5-azaC concentrations. Analysis of the gene expression of selected cell death markers demonstrated a reduced expression of metacaspase, protein executer 1 (EX1), and thioredoxin (TRX) in the callus cells that had been treated compared to the control culture. The strongest increase in the gene activity was characteristic for glutathione S-transferase (GST). Our studies also included an analysis of the distribution of some arabinogalactan proteins (AGPs) and extensin epitopes, which can be used as markers of cells that are undergoing death in a Brachypodium distachyon tissue culture. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85042854293,

title = {Organ and tissue-specific localisation of selected cell wall epitopes in the zygotic embryo of Brachypodium distachyon},

author = { A. Betekhtin and A. Milewska-Hendel and J. Lusinska and Ł. Chajec and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042854293&doi=10.3390%2fijms19030725&partnerID=40&md5=f697b77194807b245593766f2c341404},

doi = {10.3390/ijms19030725},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {3},

publisher = {MDPI AG},

abstract = {The plant cell wall shows a great diversity regarding its chemical composition, which may vary significantly even during different developmental stages. In this study, we analysed the distribution of several cell wall epitopes in embryos of Brachypodium distachyon (Brachypodium). We also described the variations in the nucleus shape and the number of nucleoli that occurred in some embryo cells. The use of transmission electron microscopy, and histological and immunolocalisation techniques permitted the distribution of selected arabinogalactan proteins, extensins, pectins, and hemicelluloses on the embryo surface, internal cell compartments, and in the context of the cell wall ultrastructure to be demonstrated. We revealed that the majority of arabinogalactan proteins and extensins were distributed on the cell surface and that pectins were the main component of the seed coat and other parts, such as the mesocotyl cell walls and the radicula. Hemicelluloses were localised in the cell wall and outside of the radicula protodermis, respectively. The specific arrangement of those components may indicate their significance during embryo development and seed germination, thus suggesting the importance of their protective functions. Despite the differences in the cell wall composition, we found that some of the antibodies can be used as markers to identify specific cells and the parts of the developing Brachypodium embryo. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85058241904,

title = {Assessment of the molecular cytogenetic, morphometric and biochemical parameters of Deschampsia Antarctica from its southern range limit in maritime Antarctic},

author = { D. Navrotska and I. Andreev and A. Betekhtin and M. Rojek-Jelonek and I. Parnikoza and G. Myryuta and O. Poronnik and N. Miryuta and J. Szymanowska-Pułka and V. Grakhov and R. Ivannikov and R. Hasterok and V. Kunakh},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058241904&doi=10.24425%2f118759&partnerID=40&md5=4c9a8d4e1bb3c73145abf3503963325d},

doi = {10.24425/118759},

issn = {01380338},

year  = {2018},

date = {2018-01-01},

journal = {Polish Polar Research},

volume = {39},

number = {4},

pages = {525-548},

publisher = {Polish Academy of Sciences},

abstract = {Different chromosomal forms of Deschampsia antarctica Desv. (Poaceae), including diploids (2n=26), hypotriploid (2n=36-38) and a genotype with an occasional occurrence of B chromosome (2n=261B) that originated from southern marginal populations (Argentine Islands region; maritime Antarctic) were studied using molecular cytogenetic, morphometric and biochemical methods. FISH analysis revealed variations in the number of rDNA sites between the diploid and hypotriploid plants. The genome size varied among plants with a different chromosome number and was on average 10.88 pg/2C for diploids and 16.46 pg/2C for hypotriploid. The mean values of leaf length of plants grown in vitro varied within a range of 5.23-9.56 cm. The total phenolic content ranged from 51.10 to 105.40 mg/g, and the total flavonoid content ranged from 1.22 to 4.67 mg/g. The amount of phenolic compounds did not differ significantly between the genotypes, while a variation in the flavonoid content was observed for L59 and DAR12. The diploids did not differ significantly among each other in terms of the number of rDNA loci, but differed slightly in their genome size. The individuals of DAR12 carrying B chromosome were similar to other diploids in terms of their genome size, but statistically differed in leaf length. The hypotriploid had both a greater number of rDNA sites and a larger genome size. No statistical correlations were observed between the genome size and leaf length or genome size and accumulation of phenolic and flavonoid compounds. The results of this study suggest that D. antarctica plants from the southern edge of the range are characterised by the heterogeneity of the studied parameters. © 2018 Walter de Gruyter GmbH.All right reserved.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85014957702,

title = {Nuclear genome stability in long-term cultivated callus lines of Fagopyrum tataricum (L.) Gaertn},

author = { A. Betekhtin and M. Rojek-Jelonek and J. Jaskowiak and A. Milewska-Hendel and J. Kwaśniewska and Y. Kostyukova and E.U. Kurczyńska and N. Rumyantseva and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014957702&doi=10.1371%2fjournal.pone.0173537&partnerID=40&md5=8a4e7fc7b0fee91c193c03db23eaecb2},

doi = {10.1371/journal.pone.0173537},

issn = {19326203},

year  = {2017},

date = {2017-01-01},

journal = {PLoS ONE},

volume = {12},

number = {3},

publisher = {Public Library of Science},

abstract = {Long-term cultivated Fagopyrum tataricum (L.) Gaertn. (Tartary buckwheat) morphogenic and non-morphogenic callus lines are interesting systems for gaining a better understanding of the mechanisms that are responsible for the genetic stability and instability of a plant tissue culture. In this work, we used histological sections and transmission electron microscopy to identify and describe the morphology of the nuclei of all of the analysed callus lines. We demonstrated that the embryogenic callus cells had prominent round nuclei that did not contain heterochromatin clumps in contrast to the non-morphogenic callus lines, in which we found nuclei that had multiple lobes. Flow cytometry analysis revealed significant differences in the relative DNA content between the analysed calli. All of the analysed morphogenic callus lines had peaks from 2C to 8C as compared to the nonmorphogenic callus lines, whose peaks did not reflect any regular DNA content and exceeded 8C and 16C for the line 6p1 and 16C and 32C for the callus line 10p2A. The results showed that non-morphogenic calli are of an aneuploid nature. The TUNEL test enabled us to visualise the nuclei that had DNA fragmentation in both the morphogenic and non-morphogenic lines. We revealed significantly higher frequencies of positively labelled nuclei in the non-morphogenic lines than in the morphogenic lines. In the case of the morphogenic lines, the highest observed frequency of TUNEL-positive nuclei was 7.7% for lines 2-3. In the non-morphogenic calli, the highest level of DNA damage (68.5%) was revealed in line 6p1. These results clearly indicate greater genome stability in the morphogenic lines. © 2017 Betekhtin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84997354235,

title = {Spatial distribution of selected chemical cell wall components in the embryogenic callus of brachypodium distachyon},

author = { A. Betekhtin and M. Rojek-Jelonek and A. Milewska-Hendel and R. Gawecki and J. Karcz and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84997354235&doi=10.1371%2fjournal.pone.0167426&partnerID=40&md5=d5dadb0308d02b7c3e39490a13f7fd39},

doi = {10.1371/journal.pone.0167426},

issn = {19326203},

year  = {2016},

date = {2016-01-01},

journal = {PLoS ONE},

volume = {11},

number = {11},

publisher = {Public Library of Science},

abstract = {Brachypodium distachyon L. Beauv. (Brachypodium) is a species that has become an excellent model system for gaining a better understanding of various areas of grass biology and improving plant breeding. Although there are some studies of an in vitro Brachypodium culture including somatic embryogenesis, detailed knowledge of the composition of the main cell wall components in the embryogenic callus in this species is missing. Therefore, using the immunocytochemical approach, we targeted 17 different antigens of which five were against the arabinogalactan proteins (AGP), three were against extensins, six recognised pectic epitopes and two recognised hemicelluloses. These studies were complemented by histological and scanning electron microscopy (SEM) analyses. We revealed that the characteristic cell wall components of Brachypodium embryogenic calli are AGP epitopes that are recognised by the JIM16 and LM2 antibodies, an extensin epitope that is recognised by the JIM11 antibody and a pectic epitopes that is recognised by the LM6 antibody. Furthermore, we demonstrated that AGPs and pectins are the components of the extracellular matrix network in Brachypodium embryogenic culture. Additionally, SEM analysis demonstrated the presence of an extracellular matrix on the surface of the calli cells. In conclusion, the chemical compositions of the cell walls and ECMSN of Brachypodium callus show spatial differences that correlate with the embryogenic character of the cells. Thus, the distribution of pectins, AGPs and hemicelluloses can be used as molecular markers of embryogenic cells. The presented data extends the knowledge about the chemical composition of the embryogenic callus cells of Brachypodium. © 2016 Betekhtin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {21},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84916624831,

title = {Reconstructing the evolution of Brachypodium genomes using comparative chromosome painting},

author = { A. Betekhtin and G. Jenkins and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84916624831&doi=10.1371%2fjournal.pone.0115108&partnerID=40&md5=fa11d2743b8558bfd90660d8bae52e55},

doi = {10.1371/journal.pone.0115108},

issn = {19326203},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {12},

publisher = {Public Library of Science},

abstract = {Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n=10; B. sylvaticum 2n=18; B. pinnatum 2n=16; 2n=18; B. arbuscula 2n=18 and B. stacei 2n=20) three allotetraploids (B. pinnatum 2n=28; B. phoenicoides 2n=28 and B. hybridum 2n=30), and two species of unknown ploidy (B. retusum 2n=38 and B. mexicanum 2n=40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n =18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon. ©2014 Betekhtin et al.},

note = {38},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84871108499,

title = {A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)},

author = { D. López-Alvarez and M.L. López-Herranz and A. Betekhtin and P. Catalán},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84871108499&doi=10.1371%2fjournal.pone.0051058&partnerID=40&md5=3a09dd77583738e687f9cc2ae614db82},

doi = {10.1371/journal.pone.0051058},

issn = {19326203},

year  = {2012},

date = {2012-01-01},

journal = {PLoS ONE},

volume = {7},

number = {12},

abstract = {Background: Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). Methodology/Principal Findings: We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS; GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. Conclusion/Significance: Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents. © 2012 López-Alvarez et al.},

note = {50},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84856757620,

title = {Evolution and taxonomic split of the model grass Brachypodium distachyon},

author = { P. Catalán and J. Müller and R. Hasterok and G. Jenkins and L.A.J. Mur and T. Langdon and A. Betekhtin and D. Siwińska and M. Pimentel and D. López-Alvarez},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856757620&doi=10.1093%2faob%2fmcr294&partnerID=40&md5=9bd59148b57fadf44df0564a599ed16b},

doi = {10.1093/aob/mcr294},

issn = {03057364},

year  = {2012},

date = {2012-01-01},

journal = {Annals of Botany},

volume = {109},

number = {2},

pages = {385-405},

abstract = {Background and Aims Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n= 10; 20; 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species. Methods Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF; trnLF) and five nuclear (ITS; ETS; CAL; DGAT; GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated. Key Results The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n= 10 and 2n= 20 cytotypes represent two different diploid taxa, whereas the 2n= 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n= 20 and 2n= 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n= 30 cytotype. The 2n= 20 lineage was older and mutated significantly faster than the 2n= 10 lineage and all the core perennial Brachypodium species. Conclusions The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n= 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n= 20 and 2n= 30 cytotypes. © 2011 The Author.},

note = {118},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-80054097796,

title = {Painting the chromosomes of Brachypodium-current status and future prospects},

author = { D. Idziak-Helmcke and A. Betekhtin and E.A. Wolny and K. Susek and J. Wright and M. Febrer and M.W. Bevan and G. Jenkins and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80054097796&doi=10.1007%2fs00412-011-0326-9&partnerID=40&md5=e58f0c0baf758f71c389d6c6eb612290},

doi = {10.1007/s00412-011-0326-9},

issn = {00095915},

year  = {2011},

date = {2011-01-01},

journal = {Chromosoma},

volume = {120},

number = {5},

pages = {469-479},

abstract = {Chromosome painting is one of the most powerful and spectacular tools of modern molecular cytogenetics, enabling complex analyses of nuclear genome structure and evolution. For many years, this technique was restricted to the study of mammalian chromosomes, as it failed to work in plant genomes due mainly to the presence of large amounts of repetitive DNA common to all the chromosomes of the complement. The availability of ordered, chromosome-specific BAC clones of Arabidopsis thaliana containing relatively little repetitive genomic DNA enabled the first chromosome painting in dicotyledonous plants. Here, we show for the first time chromosome painting in three different cytotypes of a monocotyledonous plant-the model grass, Brachypodium distachyon. Possible directions of further detailed studies are proposed, such as the evolution of grass karyotypes, the behaviour of meiotic chromosomes, and the analysis of chromosome distribution at interphase. © 2011 The Author(s).},

note = {46},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-78149437473,

title = {An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research},

author = { M. Febrer and J.L. Goicoechea and J. Wright and N. McKenzie and X. Song and J. Lin and K. Collura and M. Wissotski and Y. Yu and J.S.S. Ammiraju and E.A. Wolny and D. Idziak-Helmcke and A. Betekhtin and D. Kudrna and R. Hasterok and R.A. Wing and M.W. Bevan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78149437473&doi=10.1371%2fjournal.pone.0013461&partnerID=40&md5=d1ddbfdfca8fbfda0316627d6007d582},

doi = {10.1371/journal.pone.0013461},

issn = {19326203},

year  = {2010},

date = {2010-01-01},

journal = {PLoS ONE},

volume = {5},

number = {10},

abstract = {The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation. © 2010 Febrer et al.},

note = {41},

keywords = {},

pubstate = {published},

tppubtype = {article}

}