Cultivation of Arabidopsis thaliana in a Laboratory Environment

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Arabidopsis thaliana (L.) Heynh. is one of the major model organisms used in different areas of science: plant physiology and biochemistry, developmental biology, genetic engineering, genome editing, etc. These model plants possess the following advantages: short life cycle, simple cultivation, sequenced and rather well annotated genome, and numerous available reports concerning transcriptome, proteome, metabolic pathways, and mutations. The technique of A. thaliana cultivation under laboratory conditions is an important aspect of investigations dealing with this plant as a model. Choice of the growing mode depends on the goal of investigation as well as on quantity and type of required biomaterial. The aim of this work is to review the techniques of A. thaliana cultivation and their applicability to different tasks.

About the authors

V. A. Fridman

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

Email: VikaFridman@gmail.com
Moscow, Russia

V. S. Fadeev

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

Email: VikaFridman@gmail.com
Moscow, Russia

A. A. Tyurin

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

Email: VikaFridman@gmail.com
Moscow, Russia

I. S. Demyanchuk

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

Email: VikaFridman@gmail.com
Moscow, Russia

I. V. Goldenkova-Pavlova

Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

Author for correspondence.
Email: VikaFridman@gmail.com
Moscow, Russia

References

  1. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana // Nature. 2000. V. 408. P. 796. https://doi.org/10.1038/35048692
  2. Borrelli V.M.G., Brambilla V., Rogowsky P., Marocco A., Lanubile A. The enhancement of plant disease resistance using CRISPR/Cas9 technology // Front. Plant Sci. 2018. V. 9. https://doi.org/10.3389/FPLS.2018.01245
  3. Zhao Y., Zhang C., Liu W., Gao W., Liu C., Song G., Li W.X., Mao L., Chen B., Xu Y., Li X., Xie C. An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design // Sci. Rep. 2016. V. 6. https://doi.org/10.1038/SREP23890
  4. Pyott D.E., Sheehan E., Molnar A. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants // Mol. Plant Pathol. 2016. V. 17. P. 1276. https://doi.org/10.1111/MPP.12417
  5. Murashige T., Skoog F. A revised medium for rapid growth and bio assays with tobacco tissue cultures // Physiol. Plant. 1962. V. 15. P. 473. https://doi.org/10.1111/j.1399-3054.1962.tb08052.x
  6. Lindsey B.E., Rivero L., Calhoun C.S., Grotewold E., Brkljacic J. Standardized method for high-throughput sterilization of Arabidopsis seeds // J. Visualized Exp. 2017. V. 2017. P. e56587. https://doi.org/10.3791/56587
  7. Ried M.K., Banhara A., Hwu F.Y., Binder A., Gust A.A., Höfle C., Hückelhoven R., Nürnberger T., Parniske M. A set of Arabidopsis genes involved in the accommodation of the downy mildew pathogen Hyaloperonospora arabidopsidis // PLoS Pathog. 2019. V. 15. P. 1. https://doi.org/10.1371/JOURNAL.PPAT.1007747
  8. Niñoles R., Ruiz-Pastor C.M., Arjona-Mudarra P., Casañ J., Renard J., Bueso E., Mateos R., Serrano R., Gadea J. Transcription factor DOF4.1 regulates seed longevity in Arabidopsis via seed permeability and modulation of seed storage protein accumulation // Front. Plant Sci. 2022. V. 13. P. 1. https://doi.org/10.3389/FPLS.2022.915184
  9. Ugena L., Hýlová A., Podlešáková K., Humplík J.F., Doležal K., Diego N. de, Spíchal L. Characterization of biostimulant mode of action using novel multi-trait high-throughput screening of Arabidopsis germination and rosette growth // Front. Plant Sci. 2018. V. 9. P. 1. https://doi.org/10.3389/FPLS.2018.01327
  10. Adhikari N.D., Bates P.D., Browse J. WRINKLED1 rescues feedback inhibition of fatty acid synthesis in hydroxylase-expressing seeds // Plant Physiol. 2016. V. 171. P. 179. https://doi.org/10.1104/PP.15.01906
  11. Lothier J., Gaufichon L., Sormani R., Lemaître T., Azzopardi M., Morin H., Chardon F., Reisdorf-Cren M., Avice J.C., Masclaux-Daubresse C. The cytosolic glutamine synthetase GLN1;2 plays a role in the control of plant growth and ammonium homeostasis in Arabidopsis rosettes when nitrate supply is not limiting // J. Exp. Bot. 2011. V. 62. P. 1375. https://doi.org/10.1093/JXB/ERQ299
  12. Cui D., Yin Y., Wang J., Wang Z., Ding H., Ma R., Jiao Z. Research on the physio-biochemical mechanism of non-thermal plasma-regulated seed germination and early seedling development in Arabidopsis // Front. Plant Sci. 2019. V. 10. P. 1. https://doi.org/10.3389/FPLS.2019.01322
  13. Han X., Tang S., An Y., Zheng D.C., Xia X.L., Yin W.L. Overexpression of the poplar NF-YB7 transcription factor confers drought tolerance and improves water-use efficiency in Arabidopsis // J. Exp. Bot. 2013. V. 64. P. 4589. https://doi.org/10.1093/JXB/ERT262
  14. Vandepol N., Liber J., Yocca A., Matlock J., Edger P., Bonito G. Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species // PLoS One. 2022. V. 17. P. 1. https://doi.org/10.1371/JOURNAL.PONE.0261908
  15. Ciou H.S., Tsai Y.L., Chiu C.C. Arabidopsis chloroplast J protein DJC75/CRRJ mediates nitrate-promoted seed germination in the dark // Ann. Bot. 2020. V. 125. P. 1091. https://doi.org/10.1093/AOB/MCAA040
  16. Seok H.Y., Bae H., Kim T., Mehdi S.M.M., Nguyen L.V., Lee S.Y., Moon Y.H. Non-TZF protein ATC3H59/ZFWD3 is involved in seed germination, seedling development, and seed development, interacting with PPPDE family protein Desi1 in Arabidopsis // Int. J. Mol. Sci. 2021. V. 22. P. 1. https://doi.org/10.3390/IJMS22094738
  17. Lim S.D., Yim W.C., Liu D., Hu R., Yang X., Cushman J.C. A Vitis vinifera basic helix–loop–helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield // Plant Biotechnol. J. 2018. V. 16. P. 1595. https://doi.org/10.1111/PBI.12898
  18. Bayon S., Chen G., Weselake R.J., Browse J. A small phospholipase A2-α from castor catalyzes the removal of hydroxy fatty acids from phosphatidylcholine in transgenic Arabidopsis seeds // Plant Physiol. 2015. V. 167. P. 1259. https://doi.org/10.1104/PP.114.253641
  19. Takatani N., Ito T., Kiba T., Mori M., Miyamoto T., Maeda S.I., Omata T. Effects of high CO2 on growth and metabolism of Arabidopsis seedlings during growth with a constantly limited supply of nitrogen // Plant Cell Physiol. 2014. V. 55. P. 281. https://doi.org/10.1093/PCP/PCT186
  20. Ariyarathne M.A., Wone B.W.M. Overexpression of the Selaginella lepidophylla bHLH transcription factor enhances water-use efficiency, growth, and development in Arabidopsis // Plant Sci. 2022. V. 315. P. 111129. https://doi.org/10.1016/J.PLANTSCI.2021.111129
  21. Lucek K., Hohmann N., Willi Y. Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopsis lyrata // Mol. Ecol. 2019. V. 28. P. 1043. https://doi.org/10.1111/MEC.15035
  22. Koiwa H., Bressan R.A., Hasegawa P.M. Identification of plant stress-responsive determinants in Arabidopsis by large-scale forward genetic screens // J. Exp. Bot. 2006. V. 57. P. 1119. https://doi.org/10.1093/JXB/ERJ093
  23. Tholen D., Voesenek L.A.C.J., Poorter H. Ethylene insensitivity does not increase leaf area or relative growth rate in Arabidopsis, Nicotiana tabacum, and Petunia x hybrida // Plant Physiol. 2004. V. 134. P. 1803. https://doi.org/10.1104/PP.103.034389
  24. Matuszkiewicz M., Koter M.D., Filipecki M. Limited ventilation causes stress and changes in Arabidopsis morphological, physiological and molecular phenotype during in vitro growth // Plant Physiol. Biochem. 2019. V. 135. P. 554. https://doi.org/10.1016/J.PLAPHY.2018.11.003
  25. Basu P., Kruse C.P.S., Luesse D.R., Wyatt S.E. Growth in spaceflight hardware results in alterations to the transcriptome and proteome // Life Sci. Space Res. 2017. V. 15. P. 88. https://doi.org/10.1016/J.LSSR.2017.09.001
  26. Ryu C.M., Faragt M.A., Hu C.H., Reddy M.S., Wei H.X., Paré P.W., Kloepper J.W. Bacterial volatiles promote growth in Arabidopsis // Proc. Natl. Acad. Sci. U. S. A. 2003. V. 100. P. 4927. https://doi.org/10.1073/PNAS.0730845100
  27. Xie X., Zhang H., Paré P.W. Sustained growth promotion in Arabidopsis with long-term exposure to the beneficial soil bacterium Bacillus subtilis (GB03) // Plant Signal. Behav. 2009. V. 4. P. 948. https://doi.org/10.4161/PSB.4.10.9709
  28. Bac-Molenaar J.A., Granier C., Keurentjes J.J.B., Vreugdenhil D. Genome-wide association mapping of time-dependent growth responses to moderate drought stress in Arabidopsis // Plant, Cell Environ. 2016. V. 39. P. 88. https://doi.org/10.1111/PCE.12595
  29. Yang Z., Liu J., Tischer S.V., Christmann A., Windisch W., Schnyder H., Grill E. Leveraging abscisic acid receptors for efficient water use in Arabidopsis // Proc. Natl. Acad. Sci. U. S. A. 2016. V. 113. P. 6791. https://doi.org/10.1073/PNAS.1601954113
  30. Cross J.M., von Korff M., Altmann T., Bartzetko L., Sulpice R., Gibon Y., Palacios N., Stitt M. Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions // Plant Physiol. 2006. V. 142. P. 1574. https://doi.org/10.1104/PP.106.086629
  31. Drake T., Keating M., Summers R., Yochikawa A., Pitman T., Dodd A.N. The cultivation of Arabidopsis for experimental research using commercially available peat-based and peat-free growing media // PLoS One. 2016. V. 11. P. 1. https://doi.org/10.1371/JOURNAL.PONE.0153625
  32. Rutter M.T., Murren C.J., Callahan H.S., Bisner A.M., Leebens-Mack J., Wolyniak M.J., Strand A.E. Distributed phenomics with the unPAK project reveals the effects of mutations // Plant J. 2019. V. 100. P. 199. https://doi.org/10.1111/TPJ.14427
  33. Groot M.P., Kubisch A., Ouborg N.J., Pagel J., Schmid K.J., Vergeer P., Lampei C. Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin // New Phytol. 2017. V. 215. P. 1221. https://doi.org/10.1111/NPH.14642
  34. Granier C., Aguirrezabal L., Chenu K., Cookson S.J., Dauzat M., Hamard P., Thioux J.J., Rolland G., Bouchier-Combaud S., Lebaudy A., Muller B., Simonneau T., Tardieu F. PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit // New Phytol. 2006. V. 169. P. 623. https://doi.org/10.1111/J.1469-8137.2005.01609.X
  35. Diaz C., Lemaître T., Christ A., Azzopardi M., Kato Y., Sato F., Morot-Gaudry J.F., le Dily F., Masclaux-Daubresse C. Nitrogen recycling and remobilization are differentially controlled by leaf senescence and development stage in Arabidopsis under low nitrogen nutrition // Plant Physiol. 2008. V. 147. P. 1437. https://doi.org/10.1104/PP.108.119040
  36. Zhang X., Henriques R., Lin S.S., Niu Q.W., Chua N.H. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method // Nat. Protoc. 2006. V. 1. P. 641. https://doi.org/10.1038/nprot.2006.97
  37. Guo D., Song X., Yuan M., Wang Z., Ge W., Wang L., Wang J., Wang X. RNA-Seq profiling shows divergent gene expression patterns in Arabidopsis grown under different densities // Front. Plant Sci. 2017. V. 8. P. 1. https://doi.org/10.3389/FPLS.2017.02001
  38. Hershey D.R. Solution culture hydroponics: history and inexpensive equipment // Amer. Biol. Teach. 1994. V. 56. P. 111. https://doi.org/10.2307/4449764
  39. Rodecap K.D., Tingey D.T., Lee E.H. Iron nutrition influence on cadmium accumulation by Arabidopsis thaliana (L.) Heynh. // J. Environ. Qual. 1994. V. 23. P. 239. https://doi.org/10.2134/JEQ1994.00472425002300020004X
  40. Lemaître T., Gaufichon L., Boutet-Mercey S., Christ A., Masclaux-Daubresse C. Enzymatic and metabolic diagnostic of nitrogen deficiency in Arabidopsis thaliana Wassileskija accession // Plant Cell Physiol. 2008. V. 49. P. 1056. https://doi.org/10.1093/PCP/PCN081
  41. Conn S.J., Hocking B., Dayod M., Xu B., Athman A., Henderson S., Aukett L., Conn V., Shearer M.K., Fuentes S., Tyerman S.D., Gilliham M. Protocol: Optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants // Plant Meth. 2013. V. 9. P. 1. https://doi.org/10.1186/1746-4811-9-4
  42. Robison M.M., Smid M.P.L., Wolyn D.J. High-quality and homogeneous Arabidopsis thaliana plants from a simple and inexpensive method of hydroponic cultivation // Can. J. Bot. 2006. V. 84. P. 1009. https://doi.org/10.1139/b06-054
  43. Delhaize E., Randall P.J. Characterization of a phosphate-accumulator mutant of Arabidopsis thaliana // Plant Physiol. 1995. V. 107. P. 207. https://doi.org/10.1104/PP.107.1.207
  44. Hirai M.Y., Fujiwara T., Chino M., Naito S. Effects of sulfate concentrations on the expression of a soybean seed storage protein gene and its reversibility in transgenic Arabidopsis thaliana // Plant Cell Physiol. 1995. V. 36. P. 1331.
  45. Berezin I., Elazar M., Gaash R., Avramov-Mor M., Shaul O. The use of hydroponic growth systems to study the root and shoot ionome of Arabidopsis thaliana // Hydroponics – a standard methodology for plant biological researches. 2012. https://doi.org/10.5772/36558
  46. Hermans C., Verbruggen N. Physiological characterization of Mg deficiency in Arabidopsis thaliana // J. Exp. Bot. 2005. V. 56. P. 2153. https://doi.org/10.1093/JXB/ERI215
  47. Johnston-Monje D., Gutiérrez J.P., Lopez-Lavalle L.A.B. Seed-transmitted bacteria and fungi dominate juvenile plant microbiomes // Front. Microbiol. 2021. V. 12. P. 1. https://doi.org/10.3389/FMICB.2021.737616
  48. Ahn S.J., Shin R., Schachtman D.P. Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake // Plant Physiol. 2004. V. 134. P. 1135. https://doi.org/10.1104/PP.103.034660
  49. Yoo S.D., Cho Y.H., Sheen J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis // Nat. Protoc. 2007. V. 2. P. 1565. https://doi.org/10.1038/nprot.2007.199
  50. Harrison S.J., Mott E.K., Parsley K., Aspinall S., Gray J.C., Cottage A. A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following floral dip transformation // Plant Meth. 2006. V. 2. P. 1. https://doi.org/10.1186/1746-4811-2-19/FIGURES/4
  51. Smeets K., Ruytinx J., van Belleghem F., Semane B., Lin D., Vangronsveld J., Cuypers A. Critical evaluation and statistical validation of a hydroponic culture system for Arabidopsis thaliana // Plant Physiol. Biochem. 2008. V. 46. P. 212. https://doi.org/10.1016/J.PLAPHY.2007.09.014
  52. Arteca R.N., Arteca J.M. A novel method for growing Arabidopsis thaliana plants hydroponically // Physiol. Plant. 2000. V. 108. P. 188. https://doi.org/10.1034/J.1399-3054.2000.108002188.X
  53. Gibeaut D.M., Hulett J., Cramer G.R., Seemann J.R. Maximal biomass of Arabidopsis thaliana using a simple, low-maintenance hydroponic method and favorable environmental conditions // Plant Physiol. 1997. V. 115. P. 317. https://doi.org/10.1104/PP.115.2.317
  54. Martinez-Zapater J.M., Coupland G., Dean C., Koornneef M. The transition to flowering in Arabidopsis // Cold Spring Harbor Laboratory Press. 1994. P. 403
  55. Conn S.J., Conn V., Tyerman S.D., Kaiser B.N., Leigh R.A., Gilliham M. Magnesium transporters, MGT2/MRS2-1 and MGT3/MRS2-5, are important for magnesium partitioning within Arabidopsis thaliana mesophyll vacuoles // New Phytol. 2011. V. 190. P. 583. https://doi.org/10.1111/J.1469-8137.2010.03619.X
  56. Conn S.J., Gilliham M., Athman A., Schreiber A.W., Baumann U., Moller I., Cheng N.H., Stancombe M.A., Hirschi K.D., Webb A.A.R., Burton R., Kaiser B.N., Tyerman S.D., Leigh R.A. Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis // Plant Cell. 2011. V. 23. P. 240. https://doi.org/10.1105/TPC.109.072769
  57. Schlesier B., Bréton F., Mock H.P. A hydroponic culture system for growing Arabidopsis thaliana plantlets under sterile conditions // Plant Mol. Biol. Rep. 2012. V. 21. P. 449. https://doi.org/10.1007/BF02772594
  58. Tocquin P., Corbesier L., Havelange A., Pieltain A., Kurtem E., Bernier G., Périlleux C. A novel high efficiency, low maintenance, hydroponic system for synchronous growth and flowering of Arabidopsis thaliana // BMC Plant Biol. 2003. V. 3. P. 1. https://doi.org/10.1186/1471-2229-3-2/TABLES/3
  59. Rhee S.Y. Bioinformatic resources, challenges, and opportunities using Arabidopsis as a model organism in a post-genomic era // Plant Physiol. 2000. V. 124. P. 1460. https://doi.org/10.1104/PP.124.4.1460
  60. Boller T., Felix G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors // Annu. Rev. Plant Biol. 2009. V. 60. P. 379. https://doi.org/10.1146/ANNUREV.ARPLANT.57. 032905.105346
  61. Huang C., Verrillo F., Renzone G., Arena S., Rocco M., Scaloni A., Marra M. Response to biotic and oxidative stress in Arabidopsis thaliana: Analysis of variably phosphorylated proteins // J. Proteomics. 2011. V. 74. P. 1934. https://doi.org/10.1016/J.JPROT.2011.05.016
  62. Huttner D., Bar-zvi D. An improved, simple, hydroponic method for growing Arabidopsis thaliana // Plant Mol. Biol. Rep. 2012. V. 21. P. 59. https://doi.org/10.1007/BF02773397
  63. Holdsworth M.J., Bentsink L., Soppe W.J.J. Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination // New Phytol. 2008. V. 179. P. 33. https://doi.org/10.1111/J.1469-8137.2008.02437.X
  64. Umezawa T., Okamoto M., Kushiro T., Nambara E., Oono Y., Seki M., Kobayashi M., Koshiba T., Kamiya Y., Shinozaki K. CYP707A3, a major ABA 8′-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana // Plant J. 2006. V. 46. P. 171. https://doi.org/10.1111/J.1365-313X.2006.02683.X
  65. Wang X., Yesbergenova-Cuny Z., Biniek C., Bailly C., El-Maarouf-Bouteau H., Corbineau F. Revisiting the role of ethylene and N-end rule pathway on chilling-induced dormancy release in Arabidopsis seeds // Int. J. Mol. Sci. 2018. V. 19. P. 3577. https://doi.org/10.3390/IJMS19113577
  66. Hoagland D.R. The water-culture method for growing plants without soil. Berkeley, Calif: College of Agriculture, University of California. 1950. P. 41.
  67. Gamborg O.L., Eveleigh D.E. Culture methods and detection of glucanases in suspension cultures of wheat and barley // Can. J. Biochem. 1968. V. 46. P. 417. https://doi.org/10.1139/O68-063

Supplementary files

Supplementary Files
Action
1. JATS XML
Download
2.

Download (556KB)
Indexing metadata
3.

Download (458KB)
Indexing metadata
4.

Download (595KB)
Indexing metadata

Copyright (c) 2023 В.А. Фридман, В.С. Фадеев, А.А. Тюрин, И.С. Демьянчук, И.В. Голденкова-Павлова

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies