CoChat
Sign Up
Cited by 15Plant tissue culture and regenerationPlant Molecular Biology ResearchEpigenetics and DNA Methylation

A novel micropropagation of Lycium ruthenicum and epigenetic fidelity assessment of three types of micropropagated plants in vitro and ex vitro

Open access
Gao, Yue, Wang, Qin-Mei, An, Qinxia, Cui, Jianguo, Zhou, Yongbin, Qi, Xinyu, Zhang, Lijie, Li, Lujia·2021·PLOS ONE
DOI 10.1371/journal.pone.0247666PMC PMC7901770
Open this paper in CoChat — free accountOpen PDF

Abstract

Lycium ruthenicum is an excellent eco-economic shrub. Numerous researches have been conducted for the function of its fruits but scarcely focused on the somaclonal variation and DNA methylation. An efficient micropropagation protocol from leaves and stems of L.ruthenicum was developed in this study, in which not only the leaf explants but also the stem explants of L.ruthenicum were dedifferentiated and produced adventitious buds/multiple shoots on one type of medium. Notably, the efficient indirect organogenesis of stem explants was independent of exogenous auxin, which is contrary to the common conclusion that induction and proliferation of calli is dependent on exogenous auxin. We proposed that sucrose supply might be the crucial regulator of stem callus induction and proliferation of L.ruthenicum. Furthermore, results of methylation-sensitive amplified polymorphism (MSAP) showed that DNA methylation somaclonal variation (MSV) of CNG decreased but that of CG increased after acclimatization. Three types of micropropagated plants (from leaf calli, stem calli and axillary buds) were epigenetically diverged more from each other after acclimatization and the ex vitro micropropagated plants should be selected to determine the fidelity. In summary, plants micropropagated from axillary buds and leaves of L.ruthenicum was more fidelity and might be suitable for preservation and propagation of elite germplasm. Also, leaf explants should be used in transformation. Meanwhile, plants from stem calli showed the highest MSV and might be used in somaclonal variation breeding. Moreover, one MSV hotspot was found based on biological replicates. The study not only provided foundations for molecular breeding, somaclonal variation breeding, preservation and propagation of elite germplasm, but also offered clues for further revealing novel mechanisms of both stem-explant dedifferentiation and MSV of L.ruthenicum.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0247666

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Histone proteins can undergo chemical modifications that alter chromatin structure and transcriptional activity, thereby contributing to phenotypic variability in micropropagated plants.

    “Histone proteins, which help package and organize DNA within chromosomes, can undergo chemical modifications that alter chromatin structure and transcriptional activity, thereby contributing to phenotypic variability in micropropagated plants [52,53].”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [53]

    The Introduction says that DNA methylation changes arising from micropropagation can affect phenotype, and the Results examine cytosine methylation in regenerated plants. Searches for histone modifications, chromatin structure, and transcriptional activity found no passage addressing the histone-based mechanism attributed to this source. (LLM, conf=0.75)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 58 · Cited by 15

Research works printed but not linked: 56

  1. [1]Han L, Ye Y, Suo Y. The resource and economic value of Lycium ruthenicum Murray. Chinese Wild Plant Resour. 2014; 33: 55– 57.
  2. [2]Chen H, Feng Y, Wang L, Yonezawa T, Crabbe MJC, Zhang X, et al Transcriptome profiling of the UV-B stress response in the desert shrub Lycium ruthenicum. Mol Biol Rep. 2015; 42(3): 639– 649. 25366177
  3. [3]Guo YY, Yu HY, Kong DS, Yan F, Zhang YJ. Effects of drought stress on growth and chlorophyll fluorescence of Lycium ruthenicum Murr. seedlings. Photosynthetica. 2016; 54: 524– 531.
  4. [4]Liu Z, Shu Q, Wang L, Yu M, Hu Y, Zhang H, et al Genetic diversity of the endangered and medically important Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers. Biochem Systemat Ecol. 2012; 45: 86– 97.
  5. [5]Lv X, Wang C, Cheng Y, Huang L, Wang Z, Lv X, et al Isolation and structural characterization of a polysaccharide LRP4-A from Lycium ruthenicum Murr. Carbohyd Res. 2013; 365: 20– 25. 23178202
  6. [6]Zhang YM, Chen YN, Pan BR. Distribution and floristics of desert plant communities in the lower reaches of Tarim River, southern Xinjiang, People’s Republic of China. J Arid Environ. 2005; 63: 772– 784.
  7. [7]Peng Q, Lv X, Xu Q, Li Y, Huang L, Du Y. Isolation and structural characterization of the polysaccharide LRGP1 from Lycium ruthenicum. Carbohyd Polym. 2012; 90: 95– 101. 10.1016/j.carbpol.2012.04.067 24751015 · DOI
  8. [8]Duan Y, Chen F, Yao X, Zhu J, Wang C, Zhang J, et al Protective effect of Lycium ruthenicum Murr. against radiation injury in mice. Inter J Env Res Pub Heal. 2015; 12: 8332– 8347. 10.3390/ijerph120708332 26193298 PMC4515725 · DOI
  9. [9]Yan Y, Peng Y, Tang J, Mi J, Lu L, Li X, et al Effects of anthocyanins from the fruit of Lycium ruthenicum Murray on intestinal microbiota. J Funct Foods. 2018; 48: 533– 541.
  10. [10]Wang Y, Luan G, Zhou W, Meng J, Wang H, Hu N. Subcritical water extraction, UPLC-Triple-TOF/MS analysis and antioxidant activity of anthocyanins from Lycium ruthenicum Murr. Food Chem. 2018; 249: 119– 126. 10.1016/j.foodchem.2017.12.078 29407914 · DOI
  11. [11]Huang Z, Huang Q, Ji L, Wang Y, Qi X. Epigenetic regulation of active Chinese herbal components for cancer prevention and treatment: A follow-up review. Pharmacol Res. 2016; 114: 1– 12. 10.1016/j.phrs.2016.09.023 27697644 · DOI
  12. [12]Ni W, Gao T, Wang H, Du Y, Li J, Li C, et al Anti-fatigue activity of polysaccharides from the fruits of four Tibetan Plateau indigenous medicinal plants. J Ethnopharmacol. 2013; 150: 529– 535. 10.1016/j.jep.2013.08.055 24036063 · DOI
  13. [13]Gong Y, Wu J, Li ST. Immuno-enhancement effects of Lycium ruthenicum Murr. polysaccharide on cyclophosphamide-induced immunosuppression in mice. Int J Clin Exp Med. 2015; 8: 20631– 20637. 26884983 PMC4723828
  14. [14]Qiang P, Xu Q, Yin H, Du Y, Li J, Li C, et al Characterization of an immunologically active pectin from the fruits of Lycium ruthenicum. Int J Biol Macromol. 2014; 64: 69– 75. 10.1016/j.ijbiomac.2013.11.030 24315943 · DOI
  15. [15]Tian L, Jiang B, Fan X. Study on anti-aging effect of Lycium ruthenicum Murr. Shiyong Yaowu Yu Linchuang. 2015; 18: 1147– 1150.
  16. [16]Gao H, Yuan X, Wang ZS, Gao Q, Yang J. Profiles and neuroprotective effects of Lycium ruthenicum polyphenols against oxidative stress-induced cytotoxicity in PC12 cells. J Food Biochem. 2020; 44(1): 13112 10.1111/jfbc.13112 31800113 · DOI
  17. [17]Deng KW, Li YL, Xiao M, Wang FH, Zhou P, Zhnag W, et al Lycium ruthenicum Murr. polysaccharide protects cortical neurons against oxygen-glucose deprivation/reperfusion in neonatal hypoxic-ischemic encephalopathy-ScienceDirect. Int J Biol Macromol. 2020; 158: 562– 568. 10.1016/j.ijbiomac.2020.04.122 32380112 · DOI
  18. [18]Wang H, Li J, Tao W, Zhang X, Gao X, Yong J, et al Lycium ruthenicum studies: molecular biology, phytochemistry and pharmacology. Food Chem. 2018; 240: 759– 766. 10.1016/j.foodchem.2017.08.026 28946340 · DOI
  19. [19]Dai G, Qin K, Cao YL, Jiao E, Zhang B. Characteristics of floral dynamic and breeding system of Lycium ruthenicum. Guihaia. 2013; 33(1): 126– 132.
  20. [20]Pischke MS, Huttlin EL, Hegeman AD, Sussman MR. A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol. 2006; 140: 1255– 1278. 10.1104/pp.105.076059 16489130 PMC1435795 · DOI
  21. [21]Wang QM, Wang L. An evolutionary view of plant tissue culture: somaclonal variation and selection. Plant Cell Rep. 2012; 31: 1535– 1547. 10.1007/s00299-012-1281-5 22610486 · DOI
  22. [22]Wang QM, Wang Y, Sun L, Gao F, Sun W, He J, et al Direct and indirect organogenesis of Clivia miniata and assessment of DNA methylation changes in various regenerated plantlets. Plant Cell Rep. 2012; 31: 1283– 1296. 10.1007/s00299-012-1248-6 22532007 · DOI
  23. [23]Ong-Abdullah M, Ordway JM, Nan J, Ooi SE, Kok SY, Sarpan N, et al Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature. 2015; 525: 533– 537. 10.1038/nature15365 26352475 PMC4857894 · DOI
  24. [24]Golyasnaya N, Tsvetkova N. Mismatch repair. Mol Biol. 2006; 40: 183– 193. 16637261
  25. [25]Bhojwani SS, Dantu PK. Somaclonal variation In: Plant Tissue Culture: An Introductory Text. Springer, India, 2013; pp. 141– 154.
  26. [26]Evans DA. Somaclonal variation—genetic basis and breeding applications. Trends Genet. 1989; 5: 46– 50. 10.1016/0168-9525(89)90021-8 2646795 · DOI
  27. [27]Cichorz S, Gośka M, Mańkowski DR. Miscanthus×giganteus: Regeneration system with assessment of genetic and epigenetic stability in long-term in vitro culture. Ind Crops Prod. 2018; 116: 150– 161.
  28. [29]Wang QM, Wang L, Zhou Y, Cui J, Wang Y, Zhao C. Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation. Plant Cell Rep. 2016; 35: 167– 184. 10.1007/s00299-015-1877-7 26466593 · DOI
  29. [30]Murashige T, Skoog F. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant. 1962; 15: 473– 497.
  30. [31]Wang QM, Gao FZ, Gao X, Zou F, Wang L. Regeneration of Clivia miniata and assessment of clonal fidelity of plantlets. Plant Cell, Tissue Organ Cult. 2012; 109: 191– 200.
  31. [32]López CMR, Wetten AC, Wilkinson MJ. Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. New Phytol. 2010; 186: 856– 868. 10.1111/j.1469-8137.2010.03242.x 20406408 · DOI
  32. [33]Bonin A, Bellemain EP, Pompanon F, Brochmann C, Taberlet P. How to track and assess genotyping errors in population genetics studies. Mol Ecol. 2004; 13: 3261– 3273. 10.1111/j.1365-294X.2004.02346.x 15487987 · DOI
  33. [34]Baurens FC, Nicolleau J, Legavre T, Verdeil J, Monteuuis O. Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker. Tree Physiol. 2004; 24: 401– 407. 10.1093/treephys/24.4.401 14757579 · DOI
  34. [35]Xu K, Liu J, Fan M, Xin W, Hu Y, Xu C. A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs. Genomics. 2012; 100: 116– 124. 10.1016/j.ygeno.2012.05.013 22664253 · DOI
  35. [36]Xu L, Huang H. Genetic and epigenetic controls of plant regeneration. Curr Top Dev Biol. 2014; 108: 1– 33. 10.1016/B978-0-12-391498-9.00009-7 24512704 · DOI
  36. [37]Guo DP, Zhu ZJ, Hu XX, Zheng SJ. Effect of cytokinins on shoot regeneration from cotyledon and leaf segment of stem mustard (Brassica juncea var. tsatsai). Plant Cell, Tissue Organ Cult. 2005; 83: 123– 127.
  37. [38]Duan H, Ding W, Song J, Xu J, Zhou Y. Roles of plant growth substance in callus induction of Achyranthes bidentata. Res Plant Biol. 2016; 6: 6– 13.
  38. [39]Lee EK, Jin YW, Park JH, Yoo YM, Hong SM, Amir R, et al Cultured cambial meristematic cells as a source of plant natural products. Nat Biotechnol. 2010; 28: 1213– 1217. 10.1038/nbt.1693 20972422 · DOI
  39. [40]Sugimoto K, Gordon SP, Meyerowitz EM. Regeneration in plants and animals: Dedifferentiation, transdifferentiation, or just differentiation? Trends Cell Biol. 2011; 21: 212– 218. 10.1016/j.tcb.2010.12.004 21236679 · DOI
  40. [41]Ramzy A, Lieve L, Elodie B, Anne G, Eugénie C, Véronique G, et al Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J. 2009; 57: 626– 644. 10.1111/j.1365-313X.2008.03715.x 18980654 · DOI
  41. [42]Che P, Lall S, Howell SH. Developmental steps in acquiring competence for shoot development in Arabidopsis tissue culture. Planta. 2007; 226: 1183– 1194. 10.1007/s00425-007-0565-4 17581762 · DOI
  42. [43]He C, Chen X, Huang H, Xu L. Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet. 2012; 8: e1002911 10.1371/journal.pgen.1002911 22927830 PMC3426549 · DOI
  43. [44]Sugimoto K, Jiao Y. Meyerowitz E.M. Arabidopsis regeneration from multiple tissues occurs via a root development pathway. Dev Cell. 2010; 18: 463– 471. 10.1016/j.devcel.2010.02.004 20230752 · DOI
  44. [45]Barbier F, Lunn JE, Beveridge CA. Ready, steady, go! A sugar hit starts the race to shoot branching. Curr Opin Plant Bio. 2015; 25: 39– 45. 25938609
  45. [46]Correa LDR, Troleis J, Mastroberti AA, Mariath JEA, Fett-Neto AG. Distinct modes of adventitious rooting in Arabidopsis thaliana. Plant Biol (Stuttgart, Germany). 2012; 14: 100– 109. 10.1111/j.1438-8677.2011.00468.x 21974782 · DOI
  46. [47]Greenwood MS, Cui X, Xu F. Response to auxin changes during maturation related loss of adventitious rooting competence in loblolly pine (Pinus taeda) stem cuttings. Physiol Plant. 2011; 111: 373– 380. 11240922
  47. [48]Barbier F, Péron T, Lecerf M, Perez-Garcia M, Barrière Q, Rolčík J. Sucrose is an early modulator of the key hormonal mechanisms controlling bud outgrowth in Rosa hybrida. J Exp Bot. 2015; erv047. 10.1093/jxb/erv047 25873679 PMC4986866 · DOI
  48. [49]Mason MG, Ross JJ, Babst BA, Wienclaw BN, Beveridge CA. Sugar demand, not auxin, is the initial regulator of apical dominance. P Natl Acad Sci. 2014; 111: 6092– 6097. PMC4000805 24711430
  49. [50]Wingler A. Transitioning to the next phase: the role of sugar signaling throughout the plant life cycle. Plant Physiol. 2018; 176: 1075– 1084. 10.1104/pp.17.01229 28974627 PMC5813577 · DOI
  50. [51]Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008; 452: 215– 219. 10.1038/nature06745 18278030 PMC2377394 · DOI
  51. [52]Fu C, Li L, Wu W, Li M, Yu X, Yu L. Assessment of genetic and epigenetic variation during long-term Taxus cell culture. Plant Cell Rep. 2012; 31: 132– 1331. 10.1007/s00299-012-1251-y 22562779 · DOI
  52. [53]Gao X, Yang D, Cao D, Man Ao, Sui X, Wang Q, et al In vitro micropropagation of Freesia hybrida and the assessment of genetic and epigenetic stability in regenerated plantlets. J Plant Growth Regul. 2010; 29: 257– 267.
  53. [54]Li A, Hu BQ, Xue Z-Y, Chen L, Wang W, Song W, et al DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP. Plant Mol Biol Rep. 2011; 29: 784– 793. 10.1007/s11105-010-0280-3 24415835 PMC3881574 · DOI
  54. [55]Rathore MS, Jha B. DNA methylation and methylation polymorphism in genetically stable In vitro regenerates of Jatropha curcas L. using methylation-sensitive AFLP markers. Appl Biochem Biotechnol. 2016; 178: 1002– 1014. 10.1007/s12010-015-1924-4 26588922 · DOI
  55. [56]Keyte AL, Percifield R, Liu B, Wendel JF. Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). J Hered. 2006; 97: 444– 450. 10.1093/jhered/esl023 16987937 · DOI
  56. [58]Stroud HB, Ding SA, Simon S, Feng S, Bellizzi M, Pellegrini M, et al Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife. 2013; 2: e00354 10.7554/eLife.00354 23539454 PMC3601819 · DOI

Authors
Gao, Y., Wang, Q.-M., An, Q., Cui, J., Zhou, Y., Qi, X., Zhang, L., & Li, L.
Affiliations
Shenyang Agricultural University (CN)
Corresponding author
  • Gao, Yue
  • Wang, Qin-Mei
  • An, Qinxia
  • Cui, Jianguo
  • Zhou, Yongbin
  • Qi, Xinyu
  • Zhang, Lijie
  • Li, Lujia
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2021-02-23
Volume
16
Issue
2
Pages
e0247666
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0247666
PMC
PMC7901770
OpenAlex
W3129923581
Cited by
15
References
58
Citations by year
2025: 6 · 2024: 3 · 2023: 2 · 2022: 1 · 2021: 3
FWCI
0.71
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (31600546)
  • Scientific Research Fund of Liaoning Provincial Education Department (LSNJC202023)
  • Opening Project of State Key Laboratory of Tree Genetics and Breeding (K2019202)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
Lycium ruthenicum, micropropagation, somaclonal variation, DNA methylation, leaf explants, axillary buds, acclimatization, MSA-P, germplasm conservation
MeSH terms
Plant Breeding, Plant Leaves, Plant Roots, Plant Shoots, DNA Methylation, Lycium, Epigenesis, Genetic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review