Molecular Markers for the Detection and Analysis of Somaclonal Variation

RNA-Seq: a revolutionary tool for transcriptomics

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Somaclonal variation — a novel source of variability from cell cultures for plant improvement

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Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants

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Somaclonal variations and their applications in horticultural crops improvement

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Profiling genome-wide DNA methylation

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Basic concepts and methodologies of DNA marker systems in plant molecular breeding

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DNA methylation, a key regulator of plant development and other processes

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Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

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Trends in plant research using molecular markers

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Plant tissue culture environment as a switch-key of (epi)genetic changes

Bednarek, P. T., & Orłowska, R. (2019) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-019-01724-1 · Cited by 140 · see citing works

Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.).

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Epialleles — a source of random variation in times of stress

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Molecular and genetic analyses of transgenic plants:

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Methylation-sensitive RFLPs: characterisation of two oil palm markers showing somaclonal variation-associated polymorphism

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Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Landey, R. B., Cenci, A., Guyot, R., Bertrand, B., Georget, F., Déchamp, E., Herrera, J. C., Aribi, J., Lashermes, P., & Etienne, H. (2015) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-015-0772-9 · Cited by 81 · see citing works

Assessment of genetic stability amongst micropropagated Ansellia africana, a vulnerable medicinal orchid species of Africa using SCoT markers

Bhattacharyya, P., Kumar, V., & Staden, J. V. (2016) · South African Journal of Botany · doi:10.1016/j.sajb.2016.11.007 · Cited by 76 · see citing works

Molecular changes in protoplast-derived rice plants

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Indirect Organogenesis and Assessment of Somaclonal Variation in Plantlets of Vanilla planifolia Jacks

Ramírez-Mosqueda, M. A., & Iglesias-Andreu, L. G. (2015) · Plant Cell, Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-015-0868-2 · Cited by 60 · see citing works

Tissue Culture-Induced Genetic and Epigenetic Variation in Triticale (× Triticosecale Spp. Wittmack Ex A. Camus 1927) Regenerants

Machczyńska, J., Zimny, J., & Bednarek, P. T. (2015) · Plant Molecular Biology · doi:10.1007/s11103-015-0368-0 · Cited by 59 · see citing works

Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy

Baránek, M., Čechová, J., Raddová, J., Holleinová, V., Ondrušíková, E., & Pidra, M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0126638 · Cited by 57 · see citing works

Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation

Kitimu, S. R., Taylor, J., March, T. J., Tairo, F., Wilkinson, M. J., & Rodríguez López, C. M. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00590 · Cited by 50 · see citing works

Assessment of Genetic and Epigenetic Changes in Virus-Free Garlic (Allium sativum L.) Plants Obtained by Meristem Culture Followed by In Vitro Propagation

Gimenez, M. D., Yañez-Santos, A. M., Paz, R. C., Quiroga, M. P., Marfil, C. F., Conci, V. C., & García-Lampasona, S. C. (2016) · Plant Cell Reports · doi:10.1007/s00299-015-1874-x · Cited by 47 · see citing works

Effect of subculture times on genetic fidelity, endogenous hormone level and pharmaceutical potential of Tetrastigma hemsleyanum callus

Peng, X. X., Zhang, T.-T., & Zhang, J. (2015) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-015-0750-2 · Cited by 46 · see citing works

Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers

Ramones, C. J. C., González, A. I., Ruiz, M. L., & Polanco, C. (2017) · Plant Cell Reports · doi:10.1007/s00299-017-2217-x · Cited by 42 · see citing works

TDZ-induced axillary shoot proliferation of Rhododendron mucronulatum Turcz and assessment of clonal fidelity using DNA-based markers and flow cytometry

Новикова, Т. И., Asbaganov, S. V., Ambros, E. V., & Zaytseva, Y. G. (2020) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-019-10049-9 · Cited by 42 · see citing works

Large-scale propagation of Myrobolan (Prunus cerasifera) in RITA® bioreactors and ISSR-based assessment of genetic conformity

Nasri, A., Baklouti, E., Romdhane, A. B., et al. (2018) · Scientia Horticulturae · doi:10.1016/j.scienta.2018.10.016 · Cited by 41 · see citing works

Clonal fidelity of Iris sibirica plants regenerated by somatic embryogenesis and organogenesis in leaf-base culture — RAPD and flow cytometer analyses

Stanišić, M., Raspor, M., Ninković, S., Milošević, S. M., Ćalić, D., Bohanec, B., Trifunović-Momčilov, M. M., Petrić, M., Subotić, A. R., & Jevremović, S. B. (2014) · South African Journal of Botany · doi:10.1016/j.sajb.2014.10.014 · Cited by 40 · see citing works

Evaluation of in vitro shoot multiplication and ISSR marker based assessment of somaclonal variants at different subcultures of vanilla (Vanilla planifolia Jacks)

Pastelín-Solano, M. C., Salinas‐Ruíz, J., González-Arnao, M. T., Castañeda-Castro, O., Tovar, M. E. G., & Bello, J. (2019) · Physiology and Molecular Biology of Plants · doi:10.1007/s12298-019-00645-9 · Cited by 40 · see citing works

Genetic fidelity assessment of long term in vitro shoot cultures and regenerated plants in Japanese plum cvs Santa Rosa and Frontier through RAPD, ISSR and SCoT markers

Thakur, M., Rakshandha, Sharma, V., & Chauhan, A. (2020) · South African Journal of Botany · doi:10.1016/j.sajb.2020.11.005 · Cited by 40 · see citing works

Assessment of somaclonal variation during sugarcane micropropagation in temporary immersion bioreactors by intersimple sequence repeat (ISSR) markers

Martínez‐Estrada, E., Caamal-Velázquez, J. H., Salinas‐Ruíz, J., & Bello, J. (2017) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-017-9852-3 · Cited by 39 · see citing works

Detection of Somaclonal Variations in Tissue Cultured Date Palm (Phoenix dactylifera L.) Using Transposable Element-Based Markers

Mirani, A. A., Teo, C. H., Markhand, G. S., Abul-Soad, A. A., & Harikrishna, J. A. (2020) · Plant Cell, Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-020-01772-y · Cited by 39 · see citing works

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

Orłowska, R., & Bednarek, P. T. (2020) · Plant Molecular Biology · doi:10.1007/s11103-020-00973-5 · Cited by 36 · see citing works

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Боронникова, С. В., & Kalendar, R. N. (2010) · Russian Journal of Genetics · doi:10.1134/s1022795410010060 · Cited by 35 · see citing works

Genetic homogeneity revealed in micropropagated Bauhinia racemosa Lam. using gene targeted markers CBDP and SCoT

Sharma, U., Manoj, K., Shekhawat, N. S., & Kataria, V. (2019) · Physiology and Molecular Biology of Plants · doi:10.1007/s12298-018-00639-z · Cited by 33 · see citing works

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

González-Benito, M. E., Ibáñez, M. Á. T., Pirredda, M., Mira, S., & Martı́n, C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21207459 · Cited by 33 · see citing works

Genetic Evaluation of In Vitro Micropropagated and Regenerated Plants of Cannabis sativa L. Using SSR Molecular Markers

Ioannidis, K., Tomprou, I., Mitsis, V., & Koropouli, P. (2022) · Plants · doi:10.3390/plants11192569 · Cited by 31 · see citing works

Somaclonal Variation and Methods Used for Its Detection

Ranghoo‐Sanmukhiya, V. M. (2020) · Springer eBooks · doi:10.1007/978-981-15-7736-9_1 · Cited by 29 · see citing works

Efficient in vitro plant regeneration from leaf-derived callus and genetic fidelity assessment of an endemic medicinal plant Ranunculus wallichianus Wight & Arnn by using RAPD and ISSR markers

Srinivasan, P., Raja, H. D., & Tamilvanan, R. (2021) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-021-02134-y · Cited by 28 · see citing works

Effects of plant growth regulators and activated charcoal on somaclonal variations of protocorm-like bodies (PLBs) of Dendrobium Sabin Blue orchid

Chin, C. K., Lee, Z. H., Mubbarakh, S. A., Antony, J. J. J., Chew, B. L., & Subramanıam, S. (2019) · Biocatalysis and Agricultural Biotechnology · doi:10.1016/j.bcab.2019.101426 · Cited by 27 · see citing works

In vitro shoot production, morphological alterations and genetic instability of Melocactus glaucescens (Cactaceae), an endangered species endemic to eastern Brazil

Torres-Silva, G., Resende, S. V., Brito, A. L., Bezerra, H. B., de Santana, J. R. F., & Schnadelbach, A. S. (2018) · South African Journal of Botany · doi:10.1016/j.sajb.2018.01.001 · Cited by 25 · see citing works

High frequency plant regeneration from cotyledonary node explants of Cucumis sativus L. cultivar ‘Green Long’ via adventitious shoot organogenesis and assessment of genetic fidelity by RAPD-PCR technology

Venkatachalam, P., Jinu, U., Sangeetha, P., et al. (2018) · 3 Biotech · doi:10.1007/s13205-018-1083-8 · Cited by 24 · see citing works

Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4

Hou, B., Tsai, Y.-H., Chiang, M.-H., Tsao, S.-M., Huang, S.-H., Chao, C.-P., & Chen, H. (2022) · BMC Genomics · doi:10.1186/s12864-022-08692-5 · Cited by 22 · see citing works

In vitro regeneration of Guizotia abyssinica Cass. and evaluation of genetic fidelity through RAPD markers

Baghel, S., & Bansal, Y. K. (2017) · South African Journal of Botany · doi:10.1016/j.sajb.2017.01.002 · Cited by 20 · see citing works

Somaclonal Variation for Sugarcane Improvement

Manchanda, P., Kaur, A., & Gosal, S. S. (2018) · Springer eBooks · doi:10.1007/978-3-319-78283-6_9 · Cited by 20 · see citing works

Epigenomic insight of lingonberry and health-promoting traits during micropropagation

Sikdar, A., Sharma, U., Barua, R., Igamberdiev, A. U., & Debnath, S. C. (2022) · Scientific Reports · doi:10.1038/s41598-022-16530-7 · Cited by 20 · see citing works

Efficient invitro plant regeneration from cotyledon-derived callus cultures of sesame (Sesamum indicum L.) and genetic analysis of True-to-Type regenerants using RAPD and SSR markers

Anandan, R., Prakash, M., Deenadhayalan, T., Nivetha, R., & Kumar, N. S. (2018) · South African Journal of Botany · doi:10.1016/j.sajb.2018.09.020 · Cited by 18 · see citing works

In vitro leaf-derived organogenesis and somaclonal variant detection in Humulus lupulus L.

Liberatore, C. M., Rodolfi, M., Beghè, D., Fabbri, A., Ganino, T., & Chiancone, B. (2020) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-020-10088-7 · Cited by 18 · see citing works

An Efficient Somatic Embryogenesis Protocol for Citrus jambhiri and Assessment of Clonal Fidelity of Plantlets Using RAPD Markers

Savita, Pati, P. K., Virk, G. S., & Nagpal, A. (2015) · Journal of Plant Growth Regulation · doi:10.1007/s00344-014-9465-6 · Cited by 17 · see citing works

Genome-wide discovery of DNA variants in cucumber somaclonal lines

Skarzyńska, A., Pawełkowicz, M. E., & Pląder, W. (2020) · Gene · doi:10.1016/j.gene.2020.144412 · Cited by 17 · see citing works

Evaluation of genetic stability in olive callus-induced and meristem-induced shoots using flow cytometry and amplified fragment length polymorphism techniques

Mirzaei, L., Yadollahi, A., Kermani, M. J., Naderpour, M., Zeinanloo, A. A., Farsi, M., & Davoodi, D. (2021) · Plant Methods · doi:10.1186/s13007-021-00724-7 · Cited by 16 · see citing works

Variation burst during dedifferentiation and increased CHH-type DNA methylation after 30 years of in vitro culture of sweet orange

Wang, X., Ke, L., Wang, S., Fu, J., Xu, J., Hao, Y., Kang, C., Guo, W., Deng, X., & Xu, Q. (2022) · Horticulture Research · doi:10.1093/hr/uhab036 · Cited by 16 · see citing works

Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers

Akdemir, H., Süzerer, V., Tilkat, E., Onay, A., & Çiftçi, Y. Ö. (2016) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-016-2168-7 · Cited by 15 · see citing works

Medium Composition Affects the Tissue Culture-Induced Variation in Triticale Regenerants

Pachota, K. A., Orłowska, R., & Bednarek, P. T. (2022) · Plant Cell, Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-022-02327-z · Cited by 15 · see citing works

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

Rajewski, A. C., Carter-House, D., Stajich, J., & Litt, A. (2021) · BMC Genomics · doi:10.1186/s12864-021-07489-2 · Cited by 14 · see citing works

Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (Brassica rapa ssp. pekinensis) by Next-Generation Sequencing

Kim, S., Park, J.-S., Shin, Y.-H., & Park, Y. (2021) · Genes · doi:10.3390/genes12050621 · Cited by 14 · see citing works

High-frequency direct shoot organogenesis from garlic (Allium sativum L.) inflorescence and clonal fidelity assessment in regenerants

Wen, Y., Liu, X., Liu, H., et al. (2020) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-020-01785-7 · Cited by 14 · see citing works

Clonal fidelity investigation of micropropagated hardened plants of jackfruit tree (Artocarpus heterophyllus L.) with RAPD markers

Kader, A., Sinha, S. N., & Ghosh, P. (2022) · Journal of Genetic Engineering and Biotechnology · doi:10.1186/s43141-022-00426-0 · Cited by 13 · see citing works

High-Frequency Plant Regeneration, Genetic Uniformity, and Flow Cytometric Analysis of Regenerants in Rutachalepensis L.

Qahtan, A. A., Faisal, M., Alatar, A. A., & Abdel-Salam, E. M. (2021) · Plants · doi:10.3390/plants10122820 · Cited by 13 · see citing works

Somaclonal Variation

Leva, A., & Rinaldi, L. M. R. (2016) · Encyclopedia of Applied Plant Sciences · doi:10.1016/b978-0-12-394807-6.00150-7 · Cited by 13 · see citing works

Determining the genetic stability of micropropagated sugarcane using inter-simple sequence repeat markers

de Hsie, B. S., de Brito, J. Z., Nova, M. X. V., et al. (2015) · Genetics and Molecular Research · doi:10.4238/2015.december.21.38 · Cited by 12 · see citing works

Induction of Somatic Embryogenesis and Evaluation of Genetic Stability in Regenerated Plants of Magnolia Dealbata

CHAVEZ-CORTAZAR, A., MATA-ROSAS, M., OYAMA, K., SAMAIN, M. S., & QUESADA, M. (2020) · Biologia plantarum · doi:10.32615/bp.2020.006 · Cited by 12 · see citing works

Ratio of Somaclonal Variation and the Phytohormonal Content of Citrus × latifolia in Three In Vitro Culture Systems

Bulbarela-Marini, J. E., Gómez‐Merino, F. C., Galindo-Tovar, M. E., Pastelín-Solano, M. C., Murguía‐González, J., Núñez-Pastrana, R., & Castañeda-Castro, O. (2022) · Journal of Plant Growth Regulation · doi:10.1007/s00344-022-10796-x · Cited by 11 · see citing works

Genome analysis of tissue culture-derived variations in regenerated Brassica rapa ssp. pekinensis plants using next-generation sequencing

Park, J.-S., Park, J., Kim, S., & Park, Y. (2020) · Horticulture Environment and Biotechnology · doi:10.1007/s13580-020-00237-7 · Cited by 10 · see citing works

Genetic homogeneity assessment of in vitro-regenerated plantlets of Nyctanthes arbor-tristis L. and comparative evaluation of bioactive metabolites and antioxidant activity

Rath, S. C., Seth, S., Mishra, S. K., Yadav, P. K., Gupta, A., & Panigrahi, J. (2019) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-019-10004-8 · Cited by 10 · see citing works

In vitro multiplication and genetic stability of two species of Micranthocereus Backeb. (Cactaceae) endemic to Bahia, Brazil

Civatti, L. M., Marchi, M. N. G., Schnadelbach, A. S., & Bellintani, M. C. (2017) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-017-1304-6 · Cited by 10 · see citing works

Clonal Fidelity and Genetic Diversity of Micropropagated Hancornia speciosa Gomes (Apocynaceae) as Evaluated by Molecular Markers

Costa, G. F. D., Cabral, P. D. S., Silva, F. G., Rubio Neto, A., & Mendonça, M. A. C. (2022) · Forests · doi:10.3390/f13101645 · Cited by 8 · see citing works

Assessment of somaclonal variation occurrence in micropropagated Mansonia altissimia (A. Chev.) A. Chev. using molecular marker

Oseni, O. M., Nailwal, T. K., & Pande, V. (2022) · South African Journal of Botany · doi:10.1016/j.sajb.2022.06.041 · Cited by 5 · see citing works

Biometric Measurements and Genetic Instability Assessment of In Vitro Micro-Shoots Culture of Populus alba

Hussien, E. T., Ahmed, M. F., & Ahmed, E. Z. (2022) · Plant Physiology Reports · doi:10.1007/s40502-022-00682-9 · Cited by 5 · see citing works

Nucleotide Sequence Variation in Long-Term Tissue Cultures of Chinese Ginseng (Panax ginseng C. A. Mey.)

Liu, S., Wang, X., Ding, N., Liu, Y., Li, N., Ma, Y., Zhao, J., Wang, Z., Li, X., Fu, X., et al. (2021) · Plants · doi:10.3390/plants11010079 · Cited by 4 · see citing works

Abiotic Stress Induces Morphological, Physiological, and Genetic Changes in Orthosiphon stamineus Benth. In Vitro Cultures

Ali, H., Sallahuddin, N., Shamsudin, N. H. A., Zain, N. A. M., Ibrahim, M. H., & Yaacob, J. S. (2022) · Horticulturae · doi:10.3390/horticulturae8020153 · Cited by 4 · see citing works

Comparison of tissue culture-induced variation in triticale regenerants obtained by androgenesis and somatic embryogenesis

Pachota, K. A. (2022) · Cereal Research Communications · doi:10.1007/s42976-022-00300-2 · Cited by 2 · see citing works

Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives

Majumder, S., Igamberdiev, A. U., & Debnath, S. C. (2025) · Agronomy · doi:10.3390/agronomy15061489 · Cited by 46 · see citing works

Transcriptomic Signatures of Somaclonal Variation

López-Hernández, F., & Cortés, A. J. (2026) · Concepts and strategies in plant sciences · doi:10.1007/978-981-95-5183-5_5 · Cited by 3 · see citing works

Genetic and epigenetic fidelity of garlic cryopreserved plant material compared to field collections

Martı́n, C., Nagel, M., Ibáñez, M. Á. T., Senula, A., Pirredda, M., & González-Benito, M. E. (2025) · Scientia Horticulturae · doi:10.1016/j.scienta.2025.114132 · Cited by 3 · see citing works

The curious origins of a high-stress training technique mainlining: its molecular, biochemical, and agronomic perspectives for the cultivation of Cannabis sativa

Ijoma, G. N., Mannie, T., Nurmahomed, W., et al. (2025) · Journal of Cannabis Research · doi:10.1186/s42238-025-00339-y

Molecular Markers Used in the Analysis of Somaclonal Variation During Plant Tissue Culture

Núñez-Pastrana, R., Cruz‐Cruz, C. A., Rodríguez-Deméneghi, M. V., Llarena‐Hernández, R. C., & Ramírez-Mosqueda, M. A. (2023) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9789815165555123010004 · Cited by 1 · see citing works

Plant Tissue Culture and Molecular Markers

Tamayo‐Ordoñez, M. C., Huijara-Vasconselos, J. J., Quiroz-Moreno, A., et al. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-818-4_26 · Cited by 6 · see citing works

Selection of Molecular Markers for the Estimation of Somaclonal Variation

Martínez, O. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8594-4_6 · Cited by 10 · see citing works

GENETIC VARIABILITY OF CULTURED PLANT TISSUES UNDER NORMAL CONDITIONS AND UNDER STRESS

Yu.I., D., Osipova, E. S., Solov’eva, A. I., et al. (2012) · DOAJ (DOAJ: Directory of Open Access Journals)

Molecular Analysis Of Somaclonal Variation In Tissue Culture Derived Bananas Using Msap And Ssr Markers

Sales, E. K., & Butardo, N. G. (2014) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.1093517 · Cited by 17 · see citing works