Genetic Basis of Somaclonal Variation

Bibliographic References

• Adhikari S, Saha S, Biswas A et al (2017) Application of molecular markers in plant genome analysis: a review. Nucleus 60:283–297. https://doi.org/10.1007/s13237-017-0214-7
• Alves E, Ballesteros I, Linacero R, Vázquez AM (2005) RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome. Theor Appl Genet 111:431–436. https://doi.org/10.1007/S00122-005-2013-9
• Baránek M, Čechová J, Kovacs T et al (2016) Use of combined MSAP and NGS techniques to identify differentially methylated regions in somaclones: a case study of two stable somatic wheat mutants. PLoS One 11. https://doi.org/10.1371/JOURNAL.PONE.0165749
• Bradaï F, Sánchez-Romero C, Martín C (2019) Somaclonal variation in olive (Olea europaea L.) plants regenerated via somatic embryogenesis: influence of genotype and culture age on genetic stability. Sci Hortic (Amsterdam) 251:260–266. https://doi.org/10.1016/j.scienta.2019.03.010
• Campbell BC, LeMare S, Piperidis G, Godwin ID (2011) IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol Breed 27:193–206. https://doi.org/10.1007/s11032-010-9422-4
• Catalano C, Abbate L, Motisi A et al (2021) Autotetraploid emergence via somatic embryogenesis in vitis vinifera induces marked morphological changes in shoots, mature leaves, and stomata. Cells 10. https://doi.org/10.3390/cells10061336
• Chen J, Iannone MA, Li MS et al (2000) A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 10:549–557. https://doi.org/10.1101/GR.10.4.549
• Currais L, Loureiro J, Santos C, Canhoto JM (2013) Ploidy stability in embryogenic cultures and regenerated plantlets of tamarillo. Plant Cell Tissue Organ Cult 114:149–159. https://doi.org/10.1007/s11240-013-0311-5
• Duta-Cornescu G, Constantin N, Pojoga DM et al (2023) Somaclonal variation—advantage or disadvantage in micropropagation of the medicinal plants. Int J Mol Sci 24:838. https://doi.org/10.3390/ijms24010838
• Filkowski J, Besplug J, Burke P et al (2003) Genotoxicity of 2,4-D and dicamba revealed by transgenic Arabidopsis thaliana plants harboring recombination and point mutation markers. Mutat Res Toxicol Environ Mutagen 542:23–32. https://doi.org/10.1016/J.MRGENTOX.2003.07.008
• Gautam N, Bhattacharya A (2021) Molecular marker based assessment of genetic homogeneity within the in vitro regenerated plants of Crocus sativus L.—a globally important high value spice crop. S Afr J Bot 140:461–467. https://doi.org/10.1016/j.sajb.2021.03.038
• Gemayel R, Cho J, Boeynaems S, Verstrepen KJ (2012) Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences. Genes (Basel) 3:461–480. https://doi.org/10.3390/genes3030461
• Ghorbanpour M, Khadivi-Khub A (2015) Somaclonal variation in callus samples of Plantago major using inter-simple sequence repeat marker. Caryologia 68:19–24. https://doi.org/10.1080/00087114.2014.998128
• Grafi G, Avivi Y (2004) Stem cells: a lesson from dedifferentiation. Trends Biotechnol 22:388–389. https://doi.org/10.1016/J.TIBTECH.2004.06.001
• Grafi G, Florentin A, Ransbotyn V, Morgenstern Y (2011) The stem cell state in plant development and in response to stress. Front Plant Sci 2. https://doi.org/10.3389/fpls.2011.00053
• Hirochika H (1997) Retrotransposons of rice: their regulation and use for genome analysis. Plant Mol Biol 35:231–240. https://doi.org/10.1007/978-94-011-5794-0_22
• Hirochika H, Sugimoto K, Otsuki Y et al (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A 93:7783. https://doi.org/10.1073/PNAS.93.15.7783
• Ioannidis K, Tomprou I, Mitsis V, Koropouli P (2022) Genetic evaluation of in vitro micropropagated and regenerated plants of Cannabis sativa L. using SSR molecular markers. Plants 11:1–17. https://doi.org/10.3390/plants11192569
• Jeong IS, Yoon UH, Lee GS et al (2013) SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing. Rice 6:1–12. https://doi.org/10.1186/1939-8433-6-1
• Jiang C, Mithani A, Gan X et al (2011) Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr Biol 21:1385–1390. https://doi.org/10.1016/j.cub.2011.07.002
• Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43:179–188. https://doi.org/10.1023/A:1006423110134
• Kalendar R, Muterko A, Boronnikova S (2021) Retrotransposable elements: DNA fingerprinting and the assessment of genetic diversity. Methods Mol Biol 2222:263–286. https://doi.org/10.1007/978-1-0716-0997-2_15
• Khapilina O, Turzhanova A, Danilova A et al (2021) Primer binding site (PBS) profiling of genetic diversity of natural populations of endemic species Allium ledebourianum Schult. Biotech 10:23. https://doi.org/10.3390/biotech10040023
• Kikuchi K, Terauchit K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421(6919):167–170. https://doi.org/10.1038/nature01218
• Kılınç FM, Süzerer V, Çiftçi YÖ et al (2015) Clonal micropropagation of Pistacia lentiscus L. and assessment of genetic stability using IRAP markers. Plant Growth Regul 75:75–88. https://doi.org/10.1007/s10725-014-9933-9
• Komatsu M, Shimamoto K, Kyozuka J (2003) Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. Plant Cell 15:1934–1944. https://doi.org/10.1105/TPC.011809
• Kour B, Kour G, Kaul S, Dhar MK (2014) In vitro mass multiplication and assessment of genetic stability of in vitro raised Artemisia absinthium L. plants using ISSR and SSAP molecular markers. Adv Bot 2014:1–7. https://doi.org/10.1155/2014/727020
• Krishna H, lizadeh M, Singh D et al (2016) Somaclonal variations and their applications in horticultural crops improvement. 3 Biotech 6:1–18. https://doi.org/10.1007/s13205-016-0389-7
• Larkin PJ, Scowcroft WR (1981) Somaclonal variation—a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–214. https://doi.org/10.1007/BF02342540
• Liberatore CM, Rodolfi M, Beghè D et al (2020) In vitro leaf-derived organogenesis and somaclonal variant detection in Humulus lupulus L. In Vitro Cell Dev Biol Plant 56:865–874. https://doi.org/10.1007/s11627-020-10088-7
• Linacero R, Vázquez AM (1992) Cytogenetic variation in rye regenerated plants and their progeny. Genome 35:428–430. https://doi.org/10.1139/g92-063
• Linacero R, Vázquez AM (1993) Somaclonal variation in rye. Mutat Res Lett 302:201–205. https://doi.org/10.1016/0165-7992(93)90105-5
• Liu Q, Yang Y, Liu J et al (2022) Establishment of regeneration system of Pyrus and the genetic stability analysis of regenerated population. Plant Cell Tissue Organ Cult 152(1):215–228. https://doi.org/10.1007/S11240-022-02378-2
• Long Y, Yang Y, Pan G, Shen Y (2022) New insights into tissue culture plant-regeneration mechanisms. Front Plant Sci 13:2112. https://doi.org/10.3389/FPLS.2022.926752
• Mirani AA, Teo CH, Markhand GS et al (2020) Detection of somaclonal variations in tissue cultured date palm (Phoenix dactylifera L.) using transposable element-based markers. Plant Cell Tissue Organ Cult 141:119–130. https://doi.org/10.1007/s11240-020-01772-y
• Mirzaei L, Yadollahi A, Kermani MJ et al (2021) Evaluation of genetic stability in olive callus-induced and meristem-induced shoots using flow cytometry and amplified fragment length polymorphism techniques. Plant Methods 17:1–15. https://doi.org/10.1186/s13007-021-00724-7
• Miyao A, Tanaka K, Murata K et al (2003) Target site specificity of the Tos17 Retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771. https://doi.org/10.1105/TPC.012559
• Miyao A, Iwasaki Y, Kitano H et al (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63:625. https://doi.org/10.1007/S11103-006-9118-7
• Miyao A, Nakagome M, Ohnuma T et al (2012) Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol 53:256–264. https://doi.org/10.1093/pcp/pcr172
• Noormohammadi Z, Habibollahi H, Farahani F, Sheidai M (2020) Molecular analysis of somaclonal variation in Linum usitatissimum and L. album. Plant Gene 24:100261. https://doi.org/10.1016/j.plgene.2020.100261
• Nwauzoma A, Jaja E (2013) A review of somaclonal variation in plantain (Musa spp): mechanisms and applications. J Appl Biosci 67:5252–5260. https://doi.org/10.4314/jab.v67i0.95046
• Ochatt SJ, Patat-Ochatt EM, Moessner A (2011) Ploidy level determination within the context of in vitro breeding. Plant Cell Tissue Organ Cult 104:329–341. https://doi.org/10.1007/s11240-011-9918-6
• Oono K (1985) Putative homozygous mutations in regenerated plants of rice. Mol Gen Genet MGG 198:377–384. https://doi.org/10.1007/BF00332926
• Park D, Park SH, Kim YS et al (2019) NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population. Genes Genomics 41:213–222. https://doi.org/10.1007/s13258-018-0754-5
• Park JS, Park JH, Kim SJ, Park YD (2020) Genome analysis of tissue culture-derived variations in regenerated Brassica rapa ssp. pekinensis plants using next-generation sequencing. Hortic Environ Biotechnol 61:549–558. https://doi.org/10.1007/s13580-020-00237-7
• Qin Y, Shin KS, Woo HJ, Lim MH (2018) Genomic variations of rice regenerants from tissue culture revealed by whole genome re-sequencing. Plant Breed Biotechnol 6:426–433. https://doi.org/10.9787/PBB.2018.6.4.426
• Rahmani MS, Pijut PM, Shabanian N, Nasri M (2015) Genetic fidelity assessment of in vitro-regenerated plants of Albizia julibrissin using SCoT and IRAP fingerprinting. In Vitro Cell Dev Biol Plant 51:407–419. https://doi.org/10.1007/s11627-015-9692-y
• Ramírez-Mosqueda MA, Iglesias-Andreu LG (2015) Indirect organogenesis and assessment of somaclonal variation in plantlets of Vanilla planifolia Jacks. Plant Cell Tissue Organ Cult 123:657–664. https://doi.org/10.1007/s11240-015-0868-2
• Sato M, Hosokawa M, Doi M (2011) Somaclonal variation is induced de novo via the tissue culture process: a study quantifying mutated cells in Saintpaulia. PLoS ONE 6:e23541. https://doi.org/10.1371/JOURNAL.PONE.0023541
• Shen X, Chen J, Kane ME, Henny RJ (2007) Assessment of somaclonal variation in Dieffenbachia plants regenerated through indirect shoot organogenesis. Plant Cell Tissue Organ Cult 91:21–27. https://doi.org/10.1007/s11240-007-9273-9
• Silva TCR, Carvalho CR (2014) Vertical heterogeneity of DNA ploidy level assessed by flow cytometry in calli of Passiflora Cincinnata. In Vitro Cell Dev Biol Plant 50:158–165. https://doi.org/10.1007/s11627-013-9582-0
• Skarzyńska A, Pawełkowicz M, Pląder W (2020) Genome-wide discovery of DNA variants in cucumber somaclonal lines. Gene 736. https://doi.org/10.1016/j.gene.2020.144412
• Slazak B, Sliwinska E, Saługa M et al (2015) Micropropagation of Viola uliginosa (Violaceae) for endangered species conservation and for somaclonal variation-enhanced cyclotide biosynthesis. Plant Cell Tissue Organ Cult 120:179–190. https://doi.org/10.1007/s11240-014-0592-3
• Smith AM, Hansey CN, Kaeppler SM (2012) TCUP: a novel hAT transposon active in maize tissue culture. Front Plant Sci 3:6. https://doi.org/10.3389/fpls.2012.00006
• Tanurdzic M, Vaughn MW, Jiang H et al (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLOS Biol 6:e302. https://doi.org/10.1371/JOURNAL.PBIO.0060302
• Thakur M, Rakshandha SV, Chauhan A (2021) 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. S Afr J Bot 140:428–433. https://doi.org/10.1016/j.sajb.2020.11.005
• Tican A, Câmpeanu G, Chiru N, Ivanovici D (2008) Using of unconventional methods for obtaining somaclonal variations, having as goal making of new potato varieties with resistance at diseases and pests. Roum Biotechnol Lett 13:3791–3798
• Tikendra L, Koijam AS, Nongdam P (2019) Molecular markers based genetic fidelity assessment of micropropagated Dendrobium chrysotoxum Lindl. Meta Gene 20:100562. https://doi.org/10.1016/j.mgene.2019.100562
• Tikendra L, Potshangbam AM, Dey A et al (2021) RAPD, ISSR, and SCoT markers based genetic stability assessment of micropropagated Dendrobium fimbriatum Lindl. var. oculatum Hk. f.- an important endangered orchid. Physiol Mol Biol Plants 27:341–357. https://doi.org/10.1007/s12298-021-00939-x
• Wang X, Wu R, Lin X et al (2013) Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC Plant Biol 13:1–12. https://doi.org/10.1186/1471-2229-13-77
• Wang C, Tian M, Zhang Y, Ouyang T (2019) Molecular spectrum of somaclonal variation in PLB-regenerated Oncidium revealed by SLAF-seq. Plant Cell Tissue Organ Cult 137:541–552. https://doi.org/10.1007/s11240-019-01589-4
• Zhang D, Wang Z, Wang N et al (2014) Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications. PLoS ONE 9:5–7. https://doi.org/10.1371/journal.pone.0096879