Advances in Chemical PhysicsAdvances in Chemical PhysicsФизиология растений0015-33033034-624XThe Russian Academy of Sciences26945410.31857/S0015330324050017MNFGJUОБЗОРЫReview ArticleМодификация генома растений методами генетической инженерии: направления и пути развитияМодификация генома растений методами генетической инженерии: направления и пути развитияДейнекоЕ. В.
Russian Federation
deineko@bionet.nsc.ruФедеральное государственное бюджетное научное учреждение “Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук”15092024715Генетическая инженерия растений – достижения и перспективы4875011111202411112024Copyright ©; 2024, Russian Academy of SciencesCopyright ©; 2024, Российская академия наук2024Russian Academy of SciencesРоссийская академия наукhttps://journals.rcsi.science/0015-3303/article/view/269454

Развитие и совершенствование методов молекулярной и клеточной биологии существенно расширило возможности исследователей по модификации геномов растительных клеток и послужило основой для развития новых технологий получения рекомбинантных белков, используемых в фармацевтике и других отраслях народного хозяйства, а также стимулировало создание новых высокоурожайных сортов важных сельскохозяйственных культур, устойчивых к неблагоприятным абиотическим и биотическим факторам среды. Перенос генов в растительный геном из других гетерологичных систем поставил перед исследователями ряд вопросов, связанных с функционированием трансгенов в новом окружении генома-реципиента, а также с их влиянием на функционирование собственных генов растения. За последние сорок лет с момента получения первого трансгенного растения возможности этих технологий были существенно углублены и расширены за счет разработки методов геномного редактирования, основанных на системе CRISPR/Cas. Это позволило не только изменять функционирование целевых генов путем нокаутов или исправлять нежелательные мутации, но и вносить гены интереса в заданные исследователем районы-мишени растительного генома. В предлагаемом обзоре рассматриваются основные этапы исследований по модификации геномов растений за последние сорок лет, с акцентом не только на практическую значимость созданных агробиотехнологий, но и на важность для фундаментальных исследований функционирования генов и выявления структурных особенностей организации генома растений.

Развитие и совершенствование методов молекулярной и клеточной биологии существенно расширило возможности исследователей по модификации геномов растительных клеток и послужило основой для развития новых технологий получения рекомбинантных белков, используемых в фармацевтике и других отраслях народного хозяйства, а также стимулировало создание новых высокоурожайных сортов важных сельскохозяйственных культур, устойчивых к неблагоприятным абиотическим и биотическим факторам среды. Перенос генов в растительный геном из других гетерологичных систем поставил перед исследователями ряд вопросов, связанных с функционированием трансгенов в новом окружении генома-реципиента, а также с их влиянием на функционирование собственных генов растения. За последние сорок лет с момента получения первого трансгенного растения возможности этих технологий были существенно углублены и расширены за счет разработки методов геномного редактирования, основанных на системе CRISPR/Cas. Это позволило не только изменять функционирование целевых генов путем нокаутов или исправлять нежелательные мутации, но и вносить гены интереса в заданные исследователем районы-мишени растительного генома. В предлагаемом обзоре рассматриваются основные этапы исследований по модификации геномов растений за последние сорок лет, с акцентом не только на практическую значимость созданных агробиотехнологий, но и на важность для фундаментальных исследований функционирования генов и выявления структурных особенностей организации генома растений.

gene silencingбиобезопасностьгенетическая инженериягеномное редактированиенаследование трансгеновприродно-трансгенные растенияТ-ДНК индуцированные мутацииМинистерство науки и высшего образования Российской ФедерацииMinistry of Science and Higher Education of the Russian FederationFWNR-2022–0022Herrera-Estrella L., Depicker A., Van Montagu M., Schell J. Expression of chimaeric genes transferred into plant cells using a Ti-plasmid-derived vector // Nature. 1983. V. 303. N. 5914. P. 209. https://doi.org/10.1038/303209a0Kamthan A., Chaudhuri1 A., Kamthan M., Datta A. Genetically modified (GM) crops: milestones and new advances in crop improvement // Theor. Appl. Genet. 2016. V. 129. P. 1639. https://doi.org/10.1007/s00122–016–2747–6Marone D., Mastrangelo A. M., Borrelli G. M. From transgenesis to genome editing in crop improvement: applications, marketing, and legal issues // Int. J. Mol. Sci. 2023. V. 24: 7122. https://doi.org/10.3390/ijms24087122Zahmanova G, Aljabali A., Takova K, Minkov G, Tambuwala M., Minkov I., Lomonossoff G. Green biologics: harnessing the power of plants to produce pharmaceuticals // Int. J. Mol. Sci. 2023. V. 24. P. 17575. https://doi.org/10.3390/ijms242417575Eidenberger L., Kogelmann B., Steinkellner H. Plant-based biopharmaceutical engineering // Nat. Rev. Bioeng. 2023. V. 1. P. 426. https://doi.org/10.1038/s44222–023–00044–6Агробиотехнологии в мире / Под ред. К. Г. Скрябина. Москва: Рост Медиа. 2009. C. 126.James C.M., Krattiger A. F. The first decade of crop biotechnology in global review of the field testing and commercialization of transgenic plants: 1986 to 1995 / ISAAA: Ithaca, NY, USA. 1996. V. 1.Kramer M.G., Redenbaugh K. Commercialization of a tomato with an antisense polygalacturonase gene: the FLAVR SAVR™ tomato story // Euphytica. 1994. V. 79. P. 293.James C. Global review of commercialized transgenic crops: 1998. ISAAA Briefs № 8. ISAAA: Ithaca, NY. 1998.James C. Global status of commercialized Biotech/GM Crops: 2010. ISAAA Briefs № 42. ISAAA: Ithaca, NY. 2010.AgbioInvestor.Global GM Crop Area Review May 2023. AgbioInvestor: Pathhead, UK, 2023. https://gm.agbioinvestor.com/downloadsZagorskaya A.A., Deineko E. V. Plant-expression systems: a new stage in production of biopharmaceutical preparations // Russ. J. Plant Physiol. 2021. V. 68. P. 17. https://doi.org/10.1134/S1021443721010210Hood E.E., Kusnadi A., Nikolov Z., Howard J. Molecular farming of industrial proteins from transgenic maize // Chemicals via Higher Plant Bioengineering / Eds. F. Shahidi et al. New York: Plenum. 1999. P. 127.Kusnadi A.R., Evangelista R., Hood E., Howard J., Nikolov Z. Processing of transgenic corn seed and its effect on the recovery of recombinant glucuronidase // Biotechnol. Eng. 1998. V. 60. P. 44.Hood E.E., Witcher D. R., Maddock S., Meyer T., Baszczynski C., Bailey M., Flynn P., Register J., Marshall L., Bond D., Kulisek E., Kusnadi A., Evangelista R., Nikolov Z., Wooge C. et al. Commercial production of avidin from transgenic maize: characterization of transformant, production, processing, extraction and purification // Mol. Breed. 1997. V. 3. P. 291.Witcher D., Hood E., Peterson D., Bailey M., Bond D., Kusnadi A., Evangelista R., Nikolov Z., Wooge C., Mehigh R., Kappel W., Register J., Howard J. A. Commercial production β-glucuronidase (GUS): a model system for the production of proteins in plants // Mol. Breed. 1998. V. 4. P. 301.D’Aoust M.A., Couture M. M., Charland N, Trépanier S., Landry N., Ors F., Vézina L. P. The production of hemagglutininbased virus-like particles in plants: a rapid, efficient and safe response to pandemic influenza // Plant Biotechnol. J. 2010. V. 8. P. 607. https://doi.org/10.1111/j.1467–7652.2009.00496.xWard B.J., Séguin A., Couillard J., Trépanier S., Landry N. Phase III: randomized observer-blind trial to evaluate lot-to-lot consistency of a new plant-derived quadrivalent virus like particle influenza vaccine in adults 18–49 years of age // Lancet. 2021. V. 396. P. 1491. https://doi.org/10.1016/j.vaccine.2021.01.004Stander J., Mbewana S., Meyers A. E. Plant-derived human vaccines: recent developments // BioDrugs. 2022. V. 36. P. 573. https://doi.org/10.1007/s40259–022–00544–8Su H., van Eerde A., Rimstad E., Bock R., Branza-Nichita N., Yakovlev I. A., Clarke J. L. Plant-made vaccines against viral diseases in humans and farm animals // Front. Plant Sci. 2023. V. 14: 1170815. https://doi.org/10.3389/fpls.2023.1170815Rybicki E. P. Plant molecular farming of virus-like nanoparticles as vaccines and reagents // Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 2020. V. 12: e1587. https://doi.org/10.1002/wnan.1587Huebbers J.W., Buyel J. F. On the verge of the market – plant factories for the automated and standardized production of biopharmaceuticals // Biotechnol. Adv. 2021. V.46: 107681. https://doi.org/10.1016/j.biotechadv.2020.107681Schillberg S., Raven N., Fischer R., Twyman R. M., Schiermeyer A. Molecular farming of pharmaceutical proteins using plant suspension cell and tissue cultures // Curr. Pharm. Des. 2013. V. 19. P. 5531.Corbin J. M., McNulty M.J., Macharoen K., McDonald K.A, Nandi S. Тechnoeconomic analysis of semicontinuous bioreactor production of biopharmaceuticals in transgenic rice cell suspension cultures // Biotechnol. Bioeng. 2020. V. 117. P. 3053. https://doi.org/10.1002/bit.27475Kopertekh L., Wilhelm R. Biosafety, risk analysis, and regulatory framework for molecular farming in Europe // Techniques of Plant Molecular Farming. Concepts and Strategies in Plant Sciences / Eds. C. Kole et al. Tools & Springer. 2023. P. 359. https://doi.org/10.1007/978–981–99–4859–8_14Gao F., Wen W., Liu J., Rasheed A., Yin G., Xia X., Wu X., He Zh. Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the chinese wheat cross zhou 8425B/Chinese spring // Front. Plant Sci. 2015. V. 6. P. 1099. https://doi.org/10.3389/fpls.2015.01099Soriano J.M., Alvaro F. Discovering consensus genomic regions in wheat for root-related traits by QTL metaanalysis // Sci. Rep. 2019. V. 9. P. 10537. https://doi.org/10.1038/s41598–019–47038–2Rozanova I.V., Khlestkina E. K. NGS sequencing in barley breeding and genetic studies // Vavilov Journal of Genetics and Breeding. 2020. V. 24. P. 348. https://doi.org/ 10.18699/VJ20.627Stepochkin P.I., Gordeeva E. I., Khlestkina Е. K. Marker-assisted breeding of hybrid lines of Triticum dicoccon (Schrank) Schuebl. × Triticum aethiopicum Jakubz. with purple grain // Proceedings on applied botany, genetics and breeding. 2023. V. 184. P. 139. https://doi.org/10.30901/2227–8834–2023–2–139–148Xu Y., Liu X., Fu J., Wang H., Wang J., Huang C., Prasanna B. M., Olsen M. S., Wang G., Zhang A. Enhancing genetic gain through genomic selection: from livestock to plants // Plant Communications. 2020. V. 1. P. 100005. https://doi.org/10.1016/j.xplc.2019.100005Sandhu K.S., Merrick L. F., Sankaran S., Zhang Z., Carter A. H. Prospectus of genomic selection and phenomics in cereal, legume and oilseed breeding programs // Front. Genet. 2022. V. 12. P. 829131. https://doi.org/10.3389/fgene.2021.829131Lebedev V.G., Lebedeva T. N., Chernodubov A. I., Shestibratov K. A. Genomic selection for forest tree improvement: methods, achievements and perspectives // Forests. 2020. V. 11. P. 1190. https://doi.org/10.3390/f11111190Shimatani Z., Nishizawa-Yokoi A., Endo M., Toki S., Terada R. Positive-negative-selection-mediated gene targeting in rice // Front. Plant Sci. 2015. V. 5. P. 748. https://doi.org/10.3389/fpls.2014.00748Nester E. W. Agrobacterium: nature’s genetic engineer // Front. Plant Sci. 2015. V. 5. P. 730. https://doi.org/10.3389/fpls.2014.00730Chu P., Agapito-Tenfen S. Z. Unintended genomic outcomes in current and next generation gm techniques: a systematic review // Plants. 2022. V. 11. https://doi.org/10.3390/plants11212997Jupe F., Rivkin A. C., Michael T. P., Zander M., Motley S. T., Sandoval J. P., Keith Slotkin R., Chen H., Castanon R., Nery J. R., Ecker J. R. The complex architecture and epigenomic impact of plant T-DNA insertions // PLoS Genet. 2019. V. 15. P. 1. https://doi.org/10.1371/journal.pgen.1007819.Дейнеко Е.В.. Новоселя Т. В., Загорская А. А., Филипенко Е. А., Шумный В. К. Стабильность экcпрессии и наследования гена nptII в популяции транcгенных растений табака // Доклады академии наук. 1999. Т. 369. С. 420.Dehio Ch., Schell J. Stable expression of a single-copy rolA genein transgenic Arabidopsis thaliana plants allow an exhaustive mutagenic analysis of the transgene-associated phenotype // Mol. Gen. Genet. 1993. V. 241. P. 359. https://doi.org/10.1007/BF00284689Iglesis V.A., Moscone E. A., Papp I., Neuhuber F., Michalowski S., Phelan T., Spiker S., Matzke M., Matzke A. J. Molecular and cytogenetic analyses of stably and unstably expressed transgene loci in tobacco // Plant Cell. 1997. V. 9. P. 1251. https://doi.org/10.1105/tpc.9.8.1251Matzke M.A., Neuhuber F., Matzke A. J.M. A variety of epistatic interraction can occur between partially homologous transgene loci brought together by sexual crossing // Mol. Gen. Genet. 1993. V. 236. P. 379. https://doi.org/10.1007/BF00277137Matzke A.J.M., Neuhuber F., Park Y. D., Ambros P. F., Matzke M. A. Homology-dependent gene silencing in transgenic plants: epistatic silencing loci contain multiple copies of metilated transgenes // Mol. Gen. Genet. 1994. V. 244. P. 218. https://doi.org/10.1007/BF00285449Rajeevkumar S, Anunanthini P., Sathishkumar R. Epigenetic silencing in transgenic plants // Front. Plant Sci. 2015. V. 6. P. 693. https://doi.org/10.3389/fpls.2015.00693Gelvin S. B. Integration of Agrobacterium T-DNA into the plant genome // Annu. Rev. Genet. 2017. V. 51. P. 195. https://doi.org/10.1146/annurev-genet-120215–035320Feldmann K.A. T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum // Plant J. 1991. V. 1. P. 71. https://doi.org/10.1111/j.1365–313X.1991.00071.xGang H., Li G., Zhang M., Zhao Y., Jiang J., Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant // BMC Genom. 2019. V. 20. P. 1. https://doi.org/10.1186/s12864–019–5636-yPucker B., Kleinbölting N., Weisshaar B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis // BMC Genom. 2021. V. 22. P. 1. https://doi.org/10.1186/s12864–021–07877–8Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity // Science. 2012. V. 337. P. 816. https://doi.org/10.1126/science.1225829Zhang Y., Iaffaldano B., Qi Y. CRISPR ribonucleoprotein-mediated genetic engineering in plants // Plant Communications. V. 2. P. 100168. https://doi.org/10.1016/j.xplc.2021.100168Pramanik D., Shelake R. M., Kim M. J., Kim J. Y. CRISPR-mediated engineering across the central dogma in plant biology for basic research and crop improvement // Mol. Plant. 2021. V. 14. P. 127. https://doi.org/10.1016/j.molp.2020.11.002Liu H., Chen W., Li Y., Sun L., Chai Y., Chen H., Nie H., Huang C. CRISPR/Cas9 technology and its utility for crop improvement // Int. J. Mol. Sci. 2022. V. 23. P. 1. https://doi.org/10.3390/ijms231810442Permyakova N.V., Deineko E. V. Crop improvement: comparison of transgenesis and gene editing // Horticulturae. 2024. V. 10. P. 57. https://doi.org/10.3390/horticulturae10010057Das T., Anand U., Pal T., Mandal S., Kumar M., Radha, Gopalakrishnan A. V., Lastra J. M.P., Dey A. Exploring the potential of CRISPR/Cas genome editing for vegetable crop improvement: an overview of challenges and approaches // Biotechnol. Bioeng. 2023. V. 120. P. 1215. https://doi.org/10.1002/bit.28344Guo Y., Zhao G., Gao X., Zhang L., Zhang Y., Cai X., Yuan X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement // Planta. 2023. V. 258. P. 1. https://doi.org/10.1007/s00425–023–04187-zDas S., Kwon M., Kim J. Y. Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants // Front. Plant Sci. 2024. V. 15. P. 1279738. https://doi.org/10.3389/fpls.2024.1279738Cao H.X., Vu G. T.H., Gailing O. CRISPR/Cas genome editing and applications in forest tree breeding // Genome Modified Plants and Microbes in Food and Agriculture / Academic Press, 2024. P. 343. https://doi.org/10.1016/B978–0–443–18444–4.00001–6Rukavtsova E.B., Zakharchenko N. S., Lebedev V. G., Shestibratov K. A. CRISPR-Cas genome editing for horticultural crops improvement: advantages and prospects // Horticulturae. 2023. V. 9. P. 38. https://doi.org/10.3390/ horticulturae9010038Dong O.X., Yu S., Jain R., Zhang N., Duong P. Q., Butler C., Li Y., Lipzen A., Martin J. A., Barry K. W., Schmutz J., Tian L., Ronald P. C. Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9 // Nat. Commun. 2020. V. 11. P. 1. https://doi.org/10.1038/s41467–020–14981-yYang W., Feng H., Zhang X., Zhang J., Doonan J. H., Batchelor W. D., Xiong L., Yan J. Crop phenomics and high-throughput phenotyping: past decades, current challenges, and future perspectives // Mol. Plant. 2020. V. 13. P. 187. https://doi.org/10.1016/j.molp.2020.01.00Shin S., Hyun Kim S., Wook Shin S., Marie Grav L., Ebdrup Pedersen L., Seong Lee J., Min Lee G. Comprehensive analysis of genomic safe harbors as target sitesfor stable expression of the heterologous gene in HEK293 cells // ACS Synth. Biol. 2020. V. 9. P. 1263.Hilliard W., Lee K. H. A compendium of stable hotspots in the CHO genome // Biotechnol. Bioeng. 2023. V. 120. P. 2133. https://doi.org/10.1002/bit.28390Miyata Y., Tokumoto S., Arai T., Shaikhutdinov N., Deviatiiarov R., Fuse H., Gogoleva N., Garushyants S., Cherkasov A., Ryabova A., Gazizova G., Cornette R., Shagimardanova E., Gusev O., Kikawada T. Identification of genomic safe harbors in the anhydrobiotic cell line, Pv11 // Genes. 2022. V. 13. P. 406. https://doi.org/10.3390/genes13030406Permyakova N.V., Marenkova T. V., Belavin P. A., Zagorskaya A. A., Sidorchuk Y. V., Uvarova E. A., Kuznetsov V. V., Rozov S. M., Deineko E. V. Assessment of the level of accumulation of the difn protein integrated by the knock‐in method into the region of the histone H3.3 gene of Arabidopsis thaliana // Cells. 2021. V. 10. P. 2137. https://doi.org/10.3390/cells10082137Torres C.S., Osalla M. T.B., Gopela J. L.N., Torres D. M.S. Public perception of agricultural biotechnology: 16 years after the public debates on GM crops // Department of Agriculture Biotech Program Office, International Service for the Acquisition of Agri-biotech Applications, Inc., College of Development Communication, UP Los Baños, and Southeast Asian Regional Center for Graduate Study and Research in Agriculture: Los Baños, Laguna, Philippines. 2023.Zhang J. Overview of global GMO development // AgNews. 25 February. 2021. https://news.agropages.com/News/NewsDetail---38175.htmSendhil R.R., Nyika J., Yadav S., Mackolil J., Prashat R. G., Workie E., Ragupathy R., Ramasundaram P. Genetically modified foods: bibliometric analysis on consumer perception and preference // GM Crops & Food. 2022. V. 13. P. 65. https://doi.org/10.1080/21645698.2022.2038525Graham Brookes P. G. Genetically modified (GM) crop use 1996–2020: environmental impacts associated with pesticide use change // GM Crops & Food. 2022. V. 13. P. 262. https://doi.org/10.1080/21645698.2022.2118497Lebedev V., Lebedeva T., Tikhonova E., Shestibratov K. Assessing impacts of transgenic plants on soil using functional indicators: twenty years of research and perspectives // Plants. 2022. V. 11. P. 2439. https://doi.org/10.3390/plants11182439White F.F., Garfinkel D. J., Huffman G. A., Gordon M. P., Nesterer E. W. Sequence homologous to Agrobacterium rhizogenes Т-DNA in the genomes of uninfected plants // Nature. 1983. V. 301. P. 348. https://doi.org/10.1038/30348a0Matveeva T.V., Bogomaz D. I., Pavlova O. A., Nester E. W., Lutova L. A. Horizontal gene transfer from Agrobacterium to the plant Linaria in nature // Mol. Plant Microbe Interact. 2012. V. 25. P. 1542. https://doi.org/10.1094/MPMI-07–12–0169-RZhidkin R., Zhurbenko P., Bogomaz O., Gorodilova E., Katsapov I., Antropov D., Matveeva T. Biodiversity of rolB/C-like natural transgene in the genus Vaccinium L. and its application for phylogenetic studies // Int. J. Mol. Sci. 2023. V. 24. P. 6932. https://doi.org/10.3390/ijms24086932Chen K., Zhurbenko P., Danilov L., Matveeva T., Otten L. Conservation of an Agrobacterium cT-DNA insert in Camellia section Thea reveals the ancient origin of tea plants from a genetically modified ancestor // Front. Plant Sci. 2022 V. 13. P. 997762. https://doi.org/10.3389/fpls.2022.997762Kyndt T., Quispe D., Zhai H., Jarret R., Ghislain M., Liu Q., Gheysen G., Kreuze J. F. The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: an example of a naturally transgenic food crop // Proc. Natl. Acad. Sci. USA. 2015. V. 112. P. 5844. https://doi.org/10.1073/pnas.1419685112Svoboda P. Key mechanistic principles and considerations concerning RNA interference // Front. Plant Sci. 2020. V. 11. P. 1237. https://doi.org/10.3389/fpls.2020.01237Smith N.A., Singh S. P., Wang M. B., Stoutjesdijk P. A., Green A. G., Waterhouse P. M. Total silencing by intron-spliced hairpin RNAs // Nature. 2000. V. 407. P. 319. https://doi.org/10.1038/35030305Teng C., Zhang C., Guo F., Song L., Fang Y. Advances in the study of the transcriptional regulation mechanism of plant miRNAs // Life. 2023. V. 13. P. 1917. https://doi.org/10.3390/life13091917Zhang Y., Niu N., Li S., Liu Y., Xue C., Wang H., Liu M., Zhao J. Virus-induced gene silencing (VIGS) in Chinese Jujube // Plants. 2023. V.12. P. 2115. https://doi.org/10.3390/plants12112115Mestiri I., Norre F., Gallego M. E., White C. I. Multiple host-cell recombination pathways act in Agrobacterium-mediated transformation of plant cells // Plant J. 2014. V. 7. P. 511. https://doi.org/10.1111/tpj.12398Park S.Y., Vaghchhipawala Z., Vasudevan B., Lee L-Y., Shen Y., Singer K., Waterworth W. M., Zhang Z. J., West C. E., Mysore K. S., Gelvin S. B. Agrobacterium T-DNA integration into the plant genomecan occur without the activity of key non-homologousend-joining proteins // Plant J. 2015. V. 81. P. 934. https://doi.org/10.1111/tpj.12779Kleinboelting N., Huep G., Appelhagen I., Viehoever P., Li Y., Weisshaar B. The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair-based insertion mechanism // Mol. Plant. 2015. V. 8. P. 1651. https://doi.org/10.1016/j.molp.2015.08.011Azpiroz-Leehan R., Feldmann K. A. T-DNA insertion mutagenesis in Arabidopsis: going back and forth // Trends Genet. 1997. V. 13. P. 152. https://doi.org/10.1016/S0168–9525(97)01094–9Gang H., Liu G., Zhang M., Zhao Y., Jiang J., Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant // BMC Genom. 2019. V. 20. P. 311. https://doi.org/10.1186/s12864–019–5636-yPucker B., Kleinbölting N., Weisshaar B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis // BMC Genom. 2021. V. 22. P. 599. https://doi.org/10.1186/s12864–021–07877–8Chen X., Dong Y., Huang Y., Fan J., Yang M., Zhang J. Whole-genome resequencing using nextgeneration and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741 // BMC Genom. 2021. V. 22. P. 329. https://doi.org/10.1186/s12864–021–07625-yThomson G., Dickinson L., JacobY. Genomic consequences associated with Agrobacterium-mediated transformation of plants // Plant J. 2024. V. 117. P. 342. https://doi.org/10.1111/tpj.16496Permyakova N.V., Marenkova T. V., Belavin P. A., Zagorskaya A. A., Sidorchuk Y. V., Deineko E. V. CRISPR/Cas9-mediated targeted DNA integration: rearrangements at the junction of plant and plasmid DNA // Int. J. Mol. Sci. 2022. V. 23. P. 8636. https://doi.org/10.3390/ijms2318636Matveeva T. V. Agrobacterium-mediated transformation in the evolution of plants // Curr. Top. Microbiol. Immunol. 2018. V. 418. P. 421. https://doi.org/10.1007/82_2018_80Matveeva T.V., Otten L. Widespread occurrence of natural genetic transformation of plants by Agrobacterium // Plant Mol. Biol. 2019. V. 101. P. 415. https://doi.org/10.1007/s11103–019–00913-yMatveeva T.V., Sokornova S. V. Biological traits of naturally transgenic plants and their evolutional roles // Russ. J. Plant Physiol. 2017. V. 64. P. 635. https://doi.org/10.1134/S1021443717050089Khafizova G.V., Sierro N., Ivanov N. V., Sokornova S. V., Polev D. E., Matveeva T. V. Nicotiana noctiflora Hook. genome contains two cellular T-DNAs with functional genes // Plants. 2023. V. 12. P. 3787. https://doi.org/10.3390/plants12223787Vasyutkina E.A., Yugay Y. A., Grigorchuk V. P., Grishchenko O. V., Sorokina M. R., Yaroshenko Y. L., Kudinova O. D., Stepochkina V. D., Bulgakov V. P., Shkryl Y. N. Effect of stress signals and Ib-rolB/C overexpression on secondary metabolite biosynthesis in cell cultures of Ipomoea batatas // Int. J. Mol. Sci. 2022. V. 23. P. 15100. https://doi.org/10.3390/ijms232315100Матвеева Т. В. Зачем растениям агробактериальные гены? // Экологическая генетика. 2021. Т. 19. С. 365. https://doi.org/10.17816/ecogen89905Matzke M.A., Priming M., Tronovsky J., Matzke A. J.M. Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants // EMBO J. 1989. V. 8. P. 643. https://doi.org/10.1002/i.1460–2075.1989.tb.03421.xScheid M.O., Pazkowsky J., Potrycus I. Reversible inactivation of a transgene in Arabidopsis thaliana // Mol. Gen. Genet. 1991. V. 228. P. 104. https://doi.org/10.1007/BF00282454Finnegan J., McElroy D. Transgene inactivation: plants fight back! // Nat. Biotechnol. 1994. V. 12. P. 883. https://doi.org./10.1038/nbt0994–883Vaucheret H. Epigenetic management of self and non-self: lessons from 40 years of transgenic plants // C. R. Biol. 2023. V. 345. P. 149. https://doi.org/10.5802/crbiol.96Animasaun D.A., Lawrence J. A. Antisense RNA (asRNA) technology: the concept and applications in crop improvement and sustainable agriculture // Mol. Biol. Rep. 2023. V. 50. P. 9545. https://doi.org/10.1007/s11033–023–08814–6Rajput M., Choudhary K., Kumar M., Vivekanand V., Chawade A., Ortiz R., Pareek N. RNA interference and CRISPR/Cas gene editing for crop improvement: paradigm shift towards sustainable agriculture // Plants. 2021. V. 10. P. 1914. https://doi.org/10.3390/plants10091914Zhao G., Cheng Q., Zhao Y., Wu F., Mu B., Gao J., Yang L., Yan J., Zhang H., Cui X, Chen Q. The abscisic acid–responsive element binding factors MAPKKK18 module regulates abscisic acid-induced leaf senescence in Arabidopsis // J. Biol. Chem. 2023. V. 9. P. 103060. https://doi.org/10.1016/j.jbc.2023.103060Klimek-ChodackaM., Oleszkiewicz T., Lowder L. G., Qi Y., Baranski R. Efficient CRISPR/Cas9-based genome editing in carrot cells // Plant Cell Rep. 2018. V. 37. P. 575. https://doi.org/10.1007/s00299–018–2252–2Mercx S., Smargiasso N., Chaumont F., De Pauw E., Boutry M., Navarre C. Inactivation of the β(1,2)-xylosyltransferase and the α(1,3)-fucosyltransferase genes in Nicotiana tabacum BY-2 cells by a multiplex CRISPR/Cas9 strategy results in glycoproteins without plant-specific glycans // Front. Plant Sci. 2017. V. 8. P. 403. https://doi.org/10.3389/fpls.2017.00403Sheva M., Hanania U., Ariel T., Turbovski A., Rathod V. K.R., Oz D., Tekoah Y., Shaaltiel Y. Sequential genome editing and induced excision of the transgene in N. tabacum BY2 cells // Front. Plant Sci. 2020. V. 11. P. 607174. https://doi.org/10.3389/fpls.2020.607174Miroshnichenko D., Timerbaev V., Divashuk M., Pushin A., Alekseeva V., Kroupin P., Bazhenov M., Samarina M., Ermolaev A., Karlov G., Dolgov S. CRISPR/Cas9-mediated мultiplexed multi-allelic mutagenesis of genes located on A, B and R subgenomes of hexaploid triticale // Plant Cell Rep. 2024. V. 43. P. 59. https://doi.org/10.1007/s00299–023–03139-xZhang S., Zhang R., Gao J., Gu T., Song G., Li W., Li D., Li Y., Li G. Highly efficient and heritable targeted mutagenesis in wheat via the Agrobacterium tumefaciens-mediated CRISPR/Cas9 system // Int. J. Mol. Sci. 2019. V. 20. P. 4257. https://doi.org/10.3390/ijms20174257Karki U., Fang H., Guo W., UnnoldCofre C., Xu J. Cellular engineering of plant cells for improved therapeutic protein production// Plant Cell Rep. 2021. V. 40. P. 1087. https://doi.org/10.1007/s00299–021–02693–6