Department of Functional Genomics

Research Group Leader Prof. Anna Nadolska-Orczyk

• Dr. Sebastian Gasparis, assistant professor
• Dr. Adnan Iqbal, postdoc
• MSc Mateusz Przyborowski, assistant
• MSc Karolina Szala, assistant
• MSc Bartosz Jabłoński, assistant
• MSc Joanna Bocian, PhD student of AgroBioTech PhD School
• MSc Michał Miłoszewski, PhD student of AgroBioTech PhD School

Research Group Leader Prof. Wacław Orczyk

• Dr. Marta Dmochowska-Boguta assistant professor
• Dr. Yuliya Kloc assistant
• Dr. Amir Hameed postdoc
• MSc Paweł Poznański, PhD student of AgroBioTech PhD School

Technical Staff of Department of Functional Genomics

• Małgorzata Wojciechowska
• Izabela Skuza
• Agnieszka Głowacka

1. Strategies of using double stranded RNA, chitosan and chitozan nanoparticles (ChNPs) for plant protection (W. Orczyk, A. Hameed, P. Poznański).
2. Building of knowledge on genetic regulation of cytokinins aimed at developing the ideotype of a high-yielding wheat plant (A. Nadolska-Orczyk, B. Jabłoński, J. Bocian)
3. Studies of genetic and molecular factors associated with grain weight and size in barley (S. Gasparis)
4. Transcriptomics and biological basis of barley and Fusarium response for chitosan and ChNPs treatment (W. Orczyk, A. Hameed, P. Poznański).
5. Improvement of biotechnology methods, including genetic transformation and in vitro cultures for production of genetically modified cereal crops (A. Nadolska-Orczyk, S. Gasparis).
6. Understanding the role and the mechanisms of co-regulation of the most important plant hormones (cytokinins, auxins, abscisic acid, brassinosteroids) in the processes determining wheat yield (A. Nadolska-Orczyk, J. Bocian)
7. Characterization of promotor structures and transcription factors regulating cytokinin-dependent genes (A. Nadolska-Orczyk, A. Iqbal)
8. Research on processes and analysis of genes determining tolerance to abiotic stresses, mainly drought (M. Przyborowski)
9. Development of tools to accelerate the cultivation of common wheat and common barley – molecular markers and speed-breeding methods (M. Przyborowski)
10. Application of RNAi and gene editing CRISPR/Cas9 for functional analysis of barley GSK encoding genes – negative regulators of brassinosteroid signaling pathway (Y. Kloc, W. Orczyk, M. Dmochowska-Boguta).
11. CRISPR/Cas9 directed mutagenesis of barley sensitivity genes and obtaining plants with elevated resistance to BaYMV and BaMMV (W. Orczyk, M. Dmochowska-Boguta, Y. Kloc).
12. Characterization of wheat and barley genes and processes involved in plant-pathogen interaction and important in plant resistance (M. Dmochowska-Boguta, W. Orczyk).
13. Utilization of RNA interference (RNAi) and genome editing tools for functional analysis of genes encoding useful agronomic traits (A. Nadolska-Orczyk, W. Orczyk, S. Gasparis, Y. Kloc).
14. Improving of selected cereal plant biotechnology technics including gene editing, transcriptional activation and bioinformatics (whole genome analysis, transcriptomics, promoter structures) (W. Orczyk, A. Hameed. S. Gasparis, A. Nadolska-Orczyk, A. Iqbal, Y. Kloc, M. Przyborowski).

Research Collaborations:

1. Centre for Advanced Materials and Technologies, Warsaw University of Technology, CEZAMAT, Warsaw
2. Prof. A. Bajguz, Faculty of Biology, University of Bialystok
3. Prof. B. Hasiów-Jaroszewska, Institute of Plant Protection – National Research Institute
4. The Department of Plant Genetics and Biotechnology, Warsaw University of Life Sciences
5. Laboratory of Genomics & Bioinformatics, Institute of Immunology and Experimental Therapy Polish Academy of Sciences

Projects

1. Project NCN OPUS 18, PI Professor Wacław Orczyk “Chitosan nanoparticles functionalized with double stranded RNA as a novel strategy for plant protection”, funding 2 327 640 PLN / 4 years (2020 – 2024).
2. Project NCN OPUS 19, PI Professor Anna Nadolska-Orczyk “Ideotype of high yielding wheat plant based on genetic background of cytokinin-mediated regulation” Funding 2 196 480 PLN / 4 years (2021 – 2025)
3. Project NCN OPUS 20, PI Dr. Sebastian Gasparis “Identification and characterization of genes and other molecular factors determinig grain size and weight in barley (Hordeum vulgare L)” Funding 2 130 920 PLN / 4 years (2021 – 2026)
4. Project NCN Preludium, PI Msc Mateusz Przyborowski “The effect of long-term medium drought on the development of wheat (Triticum aestivum L.) kernels” Funding 210 000 PLN / 3 years (2020 – 2022)
5. Project NCN Preludium 17, PI Dr. Yuliya Kloc “Do the two barley genes HvGSK1.1 and HvGSK1.2 regulate salt tolerance and yield-related traits?” Funding 210 000 PLN / 3 years (2020 – 2023).
6. Project financed by the Ministry of Agriculture and Rural Development, PI Professor Wacław Orczyk “Directed mutagenesis of barley sensitivity genes and obtaining plants with elevated resistance to BaYMV and BaMMV” Funding 230 000 PLN (2023)
7. Project MRiRW, PI Msc Mateusz Przyborowski “Speed breeding as a support for accelerated breeding of summer wheat (Triticum aestivum L.) and spring barley cultivars (Hordeum vulgare L.)” Project financed by the Ministry of Agriculture and Rural Development. Funding 234 750 PLN / 5 years (2021 - 2025)

Selected publications (from 2010)

1. Jablonski B, Bajguz A, Bocian J, Orczyk W, Nadolska‐Orczyk A. 2021. Genotype‐dependent effect of silencing of TaCKX1 and TaCKX2 on phytohormone crosstalk and yield‐related traits in wheat. Int. J. Mol. Sci.  22, 11494, https://doi.org/10.3390/ijms222111494
2. Gasparis S, Przyborowski M, Nadolska-Orczyk A. 2021. Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development. Int. J. Mol. Sci.  22, 5087. https://doi.org/10.3390/ijms22105087
3. Jablonski B, Szala K, Przyborowski M, Bajguz A, Chmur M, Gasparis S, Orczyk W, Nadolska-Orczyk A. 2021. TaCKX2.2 Genes Coordinate expression of other TaCKX family members, regulate phytohormone content and yield-related traits of wheat. Int. J. Mol. Sci. 1, 22, 4142. https://doi.org/10.3390/ijms22084142
4. Dmochowska-Boguta M, Kloc Y, Orczyk W. 2021. Polyamine Oxidation Is Indispensable for Wheat (Triticum aestivum L.) Oxidative Response and Necrotic Reactions during Leaf Rust (Puccinia triticina Eriks.) Infection. Plants 10, 2787. https://www.mdpi.com/2223-7747/10/12/2787
5. Szala K, Ogonowska H, Lugowska B, Zmijewska B, Wyszynska R, Dmochowska-Boguta M, Orczyk W, Nadolska-Orczyk A. 2020. Different sets of TaCKX genes affect yield-related traits in wheat plants grown in a controlled environment and in field conditions. BMC Plant Biol 20:496, 1-13, https://doi.org/10.1186/s12870-020-02713-9  
6. Kloc Y, Dmochowska-Boguta M, Zielezinski A, Nadolska-Orczyk A, Karlowski WM, Orczyk W. 2020. Silencing of HvGSK1.1—A GSK3/SHAGGY-Like Kinase–Enhances Barley (Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions. Int. J. Mol. Sci., 21, 6616; https://doi.org/10.3390/ijms21186616
7. Gasparis, S., Przyborowski, M., 2020. An Optimized RNA-Guided Cas9 System for Efficient Simplex and Multiplex Genome Editing in Barley (Hordeum vulgare L.). In: Islam, M. T., et al., Eds.), CRISPR-Cas Methods. Springer US, New York, NY, pp. 117-142 https://doi.org/10.1007/978-1-0716-0616-2_8
8. Przyborowski M, Gasparis S, Kala M, Orczyk W, Nadolska-Orczyk A. 2020. The variability of puroindoline-encoding alleles and their influence on grain hardness in modern wheat cultivars cultivated in Poland, breeding lines, and Polish old landraces (Triticum aestivum L). Agronomy 10 (8), 1075; https://doi.org/10.3390/agronomy10081075
9. Dmochowska-Boguta M, Kloc Y, Zielezinski A, Werecki P, Nadolska-Orczyk A, Karlowski WM, Orczyk W. 2020. TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance. PLoS One 15, e0227713. https://doi.org/10.1371/journal.pone.0227713
10. Jablonski B, Ogonowska H, Szala K, Bajguz A, Orczyk W, Nadolska-Orczyk A. 2020. Silencing of TaCKX1 mediates expression of other TaCKX genes to increase yield parameters in wheat. Int. J. Mol. Sci., 21, 4809; https://doi:10.3390/ijms21134809
11. Swiecicka M, Dmochowska-Boguta M, Orczyk W, Gradzielewska A, Stochmal A, Kowalczyk M, Bolibok L, Rakoczy-Trojanowska M. 2020. Changes in benzoxazinoid contents and the expression of the associated genes in rye (Secale cereale L.) due to brown rust and the inoculation procedure. PLoS One 15: e0233807. https://doi.org/10.1371/journal.pone.0233807
12. Ogonowska H, Barchacka K, Gasparis S, Jabłoński B, Orczyk W, Dmochowska-Boguta M, Nadolska-Orczyk A. 2019. Specificity of Expression of TaCKX Family Genes in Developing Plants of Wheat and Their Co-Operation Within and Among Organs. PLoS ONE 14 (4):e0214239. https://doi.org/10.1371/journal.pone.0214239
13. Gasparis S., Przyborowski M., Kała M., Nadolska-Orczyk A (2019). Knockout of the HvCKX1 or HvCKX3 Gene in Barley (Hordeum vulgare L.) by RNA‐Guided Cas9 Nuclease Affects the Regulation of Cytokinin Metabolism and Root Morphology. Cells, 8, 782: 1-25, doi:10.3390/cells8080782 https://doi.org/10.3390/cells8080782
14. Bajguz A, Orczyk W, Golebiewska A, Chmur M, Piotrowska-Niczyporuk A. 2019. Occurrence of brassinosteroids and influence of 24-epibrassinolide with brassinazole on their content in the leaves and roots of Hordeum vulgare L. cv. Golden Promise. Planta 249, 123-137. https://link.springer.com/article/10.1007/s00425-018-03081-3
15. Gasparis S., Kała M., Przyborowski M., Łyżnik L., Orczyk W., Anna Nadolska-Orczyk. 2018. A simple and efficient CRISPR/Cas9 platform for induction of single and multiple, heritable mutations in barley (Hordeum vulgare L.). Plant Methods, 4:111. https://doi.org/10.1186/s13007-018-0382-8
16. Groszyk J, Yanushevska Y, Zieleziński A, Nadolska-Orczyk A, Karłowski WM, Orczyk W. 2018. Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicate shift in organ-preferential expression. PLoS ONE 13(6):e0199364. https://doi.org/10.1371/journal.pone.0199364
17. Gasparis S., Yanushevska Y., Nadolska-Orczyk A. 2017. Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.). Acta Physiol. Plant., 39:236;1-13. DOI 10.1007/s11738-017-2530-6. https://doi.org/10.1007/s11738-017-2530-6
18. Nadolska-Orczyk A, Rajchel IK, Orczyk W, Gasparis S. 2017. Major genes determining yield-related traits in wheat and barley. Theor. Appl. Genet., 130:1081–1098, DOI : 10.1007/s00122-017-2880-x. https://doi.org/10.1007/s00122-017-2880-x
19. Gasparis S., Kała M., Przyborowski M., Orczyk W., Nadolska-Orczyk A. 2017. Artificial MicroRNA-Based Specific Gene Silencing of Grain Hardness Genes in Polyploid Cereals Appeared to be not Stable over Transgenic Plant Generations. Frontiers in Plant Science, 7:1-13, doi: 10.3389/fpls.2016.02017. https://doi.org/10.3389/fpls.2016.02017
20. Dmochowska-Boguta M.,  Alaba S., Yanushevska Y., Piechota U., Lasota E., Nadolska-Orczyk A., Karlowski WM., Orczyk W. 2015. Pathogen regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina. BMC Genomics, 16:742;1-17. DOI 10.1186/s12864-015-1932-3. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1932-3
21. Zalewski W., Gasparis S., Boczkowska M., Rajchel I.K., Kała M., Orczyk W., Nadolska-Orczyk A. 2014. Expression patterns of HvCKX genes indicate their role in growth and reproductive development of barley. PloS ONE 9(12)1-20: e115729. doi:10.1371/journal.pone.0115729. https://doi.org/10.1371/journal.pone.0115729
22. Dmochowska-Boguta M., Nadolska-Orczyk A., Orczyk W. 2013. Roles of peroxidases and NADPH oxidases in the oxidative response of wheat (Triticum aestivum) to brown rust (Puccinia triticina) infection. Plant Pathol. 62:993-1002. Doi: 10.1111/ppa.12009. https://bsppjournals.onlinelibrary.wiley.com/doi/full/10.1111/ppa.12009
23. Gasparis S., Orczyk W., Nadolska-Orczyk A. 2013. Sina and Sinb genes in triticale do not determine grain hardness contrary to their orthologs Pina and Pinb in wheat. BMC Plant Biology, 13:190:1-12. http://www.biomedcentral.com/1471-2229/13/190
24. Zalewski W., Orczyk W., Gasparis S., Nadolska-Orczyk A. 2012. HvCKX2 gene silencing by biolistic or Agrobacterium-mediated transformation in barley leads to different phenotypes. BMC Plant Biology, 12:206:1-12.  http://www.biomedcentral.com/1471-2229/12/206
25. Binka A., Orczyk W., Nadolska-Orczyk A. 2012. The Agrobacterium-mediated transformation of common wheat (Triticum aestivum L.) and triticale (x Triticosecale Wittmack): role of the binary vector systems and selection cassettes. J. Appl. Genet. 53:1-8. DOI: 10.1007/s13353-011-0064-y. https://doi.org/10.1007/s13353-011-0064-y
26. Kawałek A., Dmochowska-Boguta M., Nadolska-Orczyk A., Orczyk W. 2012. A new BSMV-based vector with modified β molecule allows simultaneous and stable silencing of two genes. Cell. Mol. Biol. Lett. 17: 107-123. DOI: 10.2478/s11658-011-0041-9. https://www.degruyter.com/document/doi/10.2478/s11658-011-0041-9/html
27. Gasparis S., Orczyk W., Zalewski W., Nadolska-Orczyk A. 2011. The RNA-mediated silencing of one of the Pin genes in allohexaploid wheat simultaneously decreases the expression of the other and increases grain hardness. J. Exp. Bot. 62 (11): 4025-4036. DOI:10.1093/jxb/err103. https://doi.org/10.1093/jxb/err103
28. Zalewski W., Galuszka P., Gasparis S., Orczyk W., Nadolska-Orczyk A. 2010. Silencing of the HvCKX1 gene decreases the cytokinin oxidase/dehydrogenase level in barley and leads to higher plant productivity. J. Exp. Bot. 61 (6): 1839-1851. DOI:10.1093/jxb/erq052. https://doi.org/10.1093/jxb/erq052
29. Orczyk W., Dmochowska-Boguta M., Czembor H.J., Nadolska-Orczyk A. 2010. Spatiotemporal patterns of oxidative burst and micronecrosis in resistance of wheat to brown rust infection. Plant Pathol. 59: 567-575. DOI: 10.1111/j.1365-3059.2010.02257.x. https://bsppjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-3059.2010.02257.x

Selected publications (2009 - 2000)

1. Nadolska-Orczyk A., Gasparis S., Orczyk W. 2009. The determinants of grain texture in cereals. J. Appl. Genet. 50: 185-197. https://link.springer.com/article/10.1007/BF03195672
2. Gasparis S., Bregier C., Orczyk W., Nadolska-Orczyk A. 2008. Agrobacterium-mediated transformation of oat (Avena sativa L) cultivars via immature embryo and leaf explants. Plant Cell Rep. 27: 1721-1729. DOI: 10.1007/s00299-008-0593-y https://link.springer.com/article/10.1007/s00299-008-0593-y
3. Przetakiewicz J., Nadolska-Orczyk A., Kuc D., Orczyk W. 2007. Tetraploid somatic hybrids of potato (Solanum tuberosum L.) obtained from diploid breeding lines. Cell Mol. Biol. Lett. 12: 253-267. https://link.springer.com/article/10.2478/s11658-006-0068-5
4. Nadolska-Orczyk A., Pietrusinska A., Binka-Wyrwa A., Kuc D, Orczyk W. 2007. Diploid potato (Solanum tuberosum L.) as a model crop to study transgene expression. Cell Mol. Biol. Lett. 12: 206-219. https://link.springer.com/article/10.2478/s11658-006-0064-9
5. Nadolska-Orczyk A., Przetakiewicz A., Kopera K., Binka A., Orczyk W. 2005. Efficient method of Agrobacterium-mediated transformation for triticale (x Triticosecale Wittmack). J. Plant Growth Reg. 24: 2-10. IF = 2.8. https://link.springer.com/article/10.1007/s00344-004-0046-y
6. Przetakiewicz A., Karaś A., Orczyk W., Nadolska-Orczyk A. 2004. Agrobacterium-mediated transformation of polyploid cereals. The efficiency of selection and transgene expression in wheat. Cell Mol. Biol. Lett. 9: 903-917.
7. Przetakiewicz A., Orczyk W., Nadolska-Orczyk A. 2003. The effect of auxin on plant regeneration of wheat, barley and triticale. Plant Cell, Tissue Org. Cult. 73: 245-256. https://link.springer.com/article/10.1023/A:1023030511800
8. Przetakiewicz J., Nadolska-Orczyk A., Orczyk W. 2002. The Use of RAPD and Semi-random Markers to Screen Somatic Hybrids Between Diploid Lines of Solanum tuberosum L. Cell Mol. Biol. Lett. 7:  6711-676.
9. Nadolska-Orczyk A., Orczyk W. 2000. Study of the factors influencing Agrobacterium-mediated transformation of pea (Pisum sativum L.). Mol. Breed. 6: 185-194 https://link.springer.com/article/10.1023/A:1009679908948

Patents

1. Gasparis S., Orczyk W., Jończyk M., Sowiński P., Nadolska-Orczyk A. 2018. „Sekwencja nukleotydowa syntetycznego genu Cas9, kaseta kierująca sgRNA do edytowania genomu roślinnego i wydajny system do ukierunkowanej mutagenezy wybranego regionu genomu roślinnego” Patent No. 235163 granted by the Patent Office of the Republic of Poland 06.07.2020.
2. Orczyk W., Nadolska-Orczyk A., Dmochowska-Boguta M. 2011. „Sposób wyciszania genu rośliny zbożowej oraz wektor wirusowy do wyciszania rośliny zbożowej”. Patent granted by the Patent Office of the Republic of Poland 07.12.2017
3. Nadolska-Orczyk A., Galuszka P., Zalewski W., Orczyk W. ”A DNA cassette, binary vector, and strain of A. tumefaciens and a method of producing cereal plant of increased productivity and/or root mass” Patent granted by the Patent Office of Canada 11.04.2017 – Number CA 2 762 556 (V88127CA)
4. Nadolska-Orczyk A., Galuszka P., Zalewski W., Orczyk W. „Kaseta DNA, wektor binarny, szczep A. tumefaciens oraz sposób otrzymywania rośliny zbożowej o zwiększonej produktywności i/lub masie korzenia” Patent granted by the Patent Office of the Republic of Poland 31.08.2016– No. 222498
5. Nadolska-Orczyk A., Galuszka P., Zalewski W., Orczyk W. A DNA cassette, binary vector, and strain of A. tumefaciens and a method of producing cereal plant of increased productivity and/or root mass. Patent No. 388118 granted by the Patent Office of the Republic of Austria 12.05.2016
6. Nadolska-Orczyk A., Galuszka P., Zalewski W., Orczyk W. ”New DNA cassette comprising an expression promoter, cereal CKX cytokinin oxidase gene, intron, and transcription terminator, useful for increasing the productivity and/or root mass of cereal plants” Patent Number:  WO2010138011-A1 02 Dec 2010; AU2010253552-A1 08 Dec 2011; CA2762556-A1 02 Dec 2010; EP2435574-A1 04 Apr 2012; US2012102600-A1 26 Apr 2012; EP2435574-B1 15 Jul 2015 Patent granted by the European Patent Office – EP2435574-B1 15.07.2015
7. Nadolska-Orczyk A., Bińka A., Orczyk W. „T-DNA wektora binarnego do zwiększania wydajności ekspresji transgenu u roślin oraz sposób zwiększania ekspresji transgenu u roślin” Patent nr PL 219560 granted by the Patent Office of the Republic of Poland 29.05.2015 WUP 05/15.​

Patent applications

1. Przyborowski M., Nadolska-Orczyk A. „Test molekularny zawierający zestaw starterów do jednoczesnej identyfikacji trzech alleli genu Pinb” Patent application filed with the Patent Office of the Republic of Poland 30.10.2020, nr P.435854.

Awards

1. Anna Nadolska-Orczyk, Sebastian Gasparis, Wacław Orczyk, Yuliya Kloc. Award for a set of publications “Functional studies of agronomically important genes in the development and productivity of cereal crops using modern molecular tools.” II Department of Biological and Agricultural Sciences of the Polish Academy of Sciences, Warsaw, 2021.
2. Anna Nadolska-Orczyk, Wacław Orczyk, Sebastian Gasparis, Marta Dmochowska-Boguta, Wojciech Zalewski. Award for outstanding research achievements „Cereals biotechnology: introduction of RNAi technology and other functional genomics methods for determination of genes function, and for obtaining barley, wheat and triticale lines with improved agronomical traits.” II Department of Biological and Agricultural Sciences of the Polish Academy of Sciences, Warsaw, 2014
3. Wojciech Zalewski PhD thesis, promoter Professor dr hab. Anna Nadolska-OrczykPrime Minister Award of the for outstanding doctoral thesis, Warsaw, 2014
4. Agnieszka Bińka PhD thesis, promoter Professor dr hab. Anna Nadolska-OrczykPrime Minister Award of the for outstanding doctoral thesis, Warsaw, 2012
5. Annual Awards of the Director of the Institute for individual scientists of Departments of Functional Genomics and Genetic Engineering (former) for publication in high impact international journals.