Original research article

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Apr 2012

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Arabidopsis Hydroponics and Shoot Branching Assay    

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This protocol establishes growth of Arabidopsis seedlings in a hydroponic medium that is suitable for the controlled addition or withdrawal of any number of nutrients, hormones or metabolites to the plants via the roots. In this case, the described protocol is used to assay sensitivity of shoot branching to exogenously supplied strigolactone, typically the artificial strigolactone GR24. Plants deficient in strigolactone synthesis or response will typically exhibit an increased number of axillary branches compared to wild type. Strigolactone synthesis mutants should respond to exogenous GR24 with reduced numbers and length of axillary shoots, while the phenotype of response mutants will not be rescued.

We present here a more detailed protocol extended from that described in Waters et al. (2012).

Materials and Reagents

  1. Rock wool/mineral wool (see http://en.wikipedia.org/wiki/Rock_wool; available from hydroponics suppliers)
  2. GR24, 10 mM in 100% acetone, stored in -20 °C freezer (limited availability; can be purchased from Chiralix: http://www.chiralix.com/rightclick.cfm?id=61574)
  3. Acetone
  4. MilliQ water
  5. Ca(NO3)2
  6. KNO3
  7. NH4NO3
  8. MgSO4.7H2O
  9. KH2PO4
  10. KCl
  11. H3BO3
  12. MnCl2.4H2O
  13. ZnSO4.7 H2O
  14. CuSO4.5 H2O
  15. CoCl2.6 H2O
  16. (NH4)6Mo7O24.4 H2O
  17. Fe-EDTA
  18. 2-(N-morpholino) ethanesulfonic acid, a buffering agent (MES)
  19. 0.5x Hoagland’s nutrient solution (pH 5.9) (see Recipes)
  20. Hoagland’s solutions (see Recipes)


  1. Controlled environment growth chamber or room
  2. Sealed plastic box for growing plants, with transparent lid and with rack to hold 1.5 ml microcentrifuge tubes, e.g. I5100-43, Astral Scientific, NSW, Australia. Also available from:
  3. Black 1.5 ml microcentrifuge tubes (opaque tubes minimizes light transmission and hence algal growth)
  4. Fine forceps
  5. Cork borer, 8 mm diameter, to produce cylinders of rock wool (see http://en.wikipedia.org/wiki/Cork_borer)

    Figure 1. Three-week-old Arabidopsis Ler plants grown in hydroponics according to this protocol. The lid of the box has been removed in this photograph. Grid squares are 1 cm.


  1. Plan how many plants you will need for the experiment. If you use the plastic box suggested above, you can comfortably fit 4 adult plants in a single pot (see Figure 1). If each pot counts as a replicate, and you want four biological replicates, then you will need 4 pots (16 plants) per genotype per treatment. You need at least as many microcentrifuge tubes as plants, plus some spares (10-20%) to allow for failures of seedlings to grow.
  2. Using scissors or a hot scalpel blade, cut off the cap and the bottom 5 mm (or so) from each microcentrifuge tube.
  3. Cut a slice of rock wool about 2 cm in height, saturate with tap water, and place in a suitable plastic dish.
  4. Using the cork borer, very gently punch out a cylinder of wet rock wool. This takes some practice. Push down with very little force, while rotating the puncher left and right to help it work its way down. Often the cylinder will be trapped within the borer; use a suitable implement to gently push it out from the top of the borer. It is important that the cylinders are not crushed, so that the seedling’s root can penetrate the matrix easily (see Figure 2A, B).

    Figure 2. Setting up the rock wool plugs. A. Pushing gently and with a rotating motion, cut a series of cylinders from saturated rock wool using an 8 mm cork borer. When you reach the bottom, push firmly to cut the cylinder free. B. Use a plastic tool to gently push out the cylinder from the borer. C. Place each cylinder in a black microcentrifuge tube, such that the rock wool is level with the top of the tube. D. Place the tubes in the rack. You can fill every hole at this stage.

  5. Make as many rock wool cylinders as are required for the number of microcentrifuge tubes prepared in step 2.
  6. Using forceps, place the cylinders in each tube, and gently press into place so that the cylinder is flush with the top of the tube. Again, do not compress the rock wool (see Figure 2C. It doesn’t matter if the rock wool sticks above the top edge of the tube by a few millimetres, but the closer to the bottom of the tube it is, the less solution you will need to keep it wet).
  7. Dilute some 0.5x Hoagland’s nutrient solution 1 in 2 (i.e. 0.25x), place sufficient in the base of the growth box to come up to the bottom of the rack, and fill the rack’s holes with the tubes containing rock wool. During early growth establishment, all of the positions in the rack can be filled with tubes. Later on, when the plants mature, the tubes will need to be split between multiple racks (see step 13). At this point the tubes and rockwool may be autoclaved, but this is optional.
  8. Wet the tip of some fine forceps, and then pick up about 5-10 Arabidopsis seed. Deposit the seed on the surface of the rock wool, and repeat for all tubes.
  9. Close the lid on the box and stratify the seed at 4 °C for three days.
  10. Transfer the box to a growth room with approx. 100-200 μmol photons m-2 sec-1 light intensity, 21 °C, long days (16 h light) for fast growth. Keep the lid closed.
  11. After about three days, lift the lid gradually over the next three days or so. We use a 1 ml pipette tip to prop the lid open by about 1 cm on the first day, moving it backwards gradually to open the lid further. This helps to protect the seedlings from shock to the drier atmosphere. Check that the nutrient solution is still in contact with the bottom of the tubes; if they dry out, the seedlings will die very quickly! Top up with 0.25x Hoagland’s solution if necessary.
  12. When the seedlings are seven days old, open the lid fully, and thin out the seedlings to 1 per tube, using fine forceps. At this point, replace the nutrient solution with 0.5x Hoagland’s, and commence the GR24 treatment by supplementing with the required volume of GR24 (5 μM final concentration) or acetone for untreated controls. It is suggested that you add the hormone/acetone to the solution in a bottle, mix well and then dispense the required volume into the boxes.
  13. After about 10-12 days, the roots should be coming out of the bottom of the tubes and floating in the medium. At this point, before the roots get too long, split the seedlings across as many boxes as required for your experiment, bearing in mind how much space each plant needs. Dispose of any excess plants (but keep the tubes for any future experiments).
  14. Allow the plants to grow, keeping an eye on the nutrient level. There is a trade-off between time spent looking after the plants, GR24 hormone consumed, and frequency of nutrient exchange. I suggest in the first two weeks of growth, changing the solution every 5 days or so. After three weeks, the plants consume more nutrients, so the solution will need exchanging every 3 to 4 days, depending on humidity. Stability of GR24 is another issue; it is prone to hydrolysis and a very approximate (and generous) guess would be that it has a half-life of 1 week under these conditions. Do not “top up” the solution; replace it fully with fresh solution plus GR24 as required.
  15. When the plants begin to flower, there is no longer any need to continue the GR24 treatment, as all rosette leaves will have been formed. At this point, count the number of rosette leaves, should you want to express numbers of branches per rosette leaf.
  16. When the primary inflorescence stops producing flowers, it is time to count the number of axillary branches and, if desired, the height of the main inflorescence stem. We normally count an axillary branch if it has grown more than 5 mm.

Expected Outcome

  1. For mutants that are deficient in the synthesis or levels of endogenous strigolactones, the number of axillary branches should be reduced relative to untreated controls. For strigolactone insensitive mutants, the number of branches should not be significantly affected. Wild type plants normally do not show a significant reduction in branch number, as it is normally low anyway (1-2 branches, depending on ecotype and growth conditions). In our hands, this method does not lead to complete rescue of the strigolactone-deficient mutant phenotype to wild type levels, but does noticeably reduce branching.


  1. 0.5 x Hoagland’s nutrient solution (pH 5.9)
    Modified from Heeg et al. (2008)

  2. Hoagland’s solutions
    Use MilliQ water to prepare, store Solutions I and II at room temperature and all others at 4 °C.
    Autoclave all solutions (EXCEPT Solution I) using a cycle with 15 min at 121 °C.
    Stock solution I (500x): 1 M Ca(NO3)2.4H2O 236.2 g/L, filter-sterilise
    Stock solution II (500x): 1 M KNO3 101.1 g/L, autoclave
    Stock solution III (1,000x): 0.5 M NH4NO3 40.0 g/L, autoclave
    Stock solution IV (500x): 0.25 M MgSO4.7H2O 61.6 g/L, autoclave
    Stock solution V (1,000x): 0.25 M KH2PO4 34.0 g/L, autoclave
    Stock solution VI (5,000x): 0.25 M KCl 18.6 g/L, autoclave
    Micro element stock solution (2,000x):
    0.05 M H3BO3 1.546 g
    0.004 M MnCl2.4 H2O 0.396 g
    0.004 M ZnSO4.7 H2O 0.575 g
    0.001 M CuSO4.5 H2O 0.125 g
    0.0003 M CoCl2.6 H2O 0.036 g
    0.00015 M (NH4)6Mo7O24.4 H2O 0.093 g
    Add 500 ml ddH2O, autoclave.
    10 mM Fe-EDTA stock soln. (250x): 367.1 mg/100ml, autoclave.
    Check pH if it is not dissolving and adjust pH to 8.0 using 5 N KOH or 1 N NaOH (if you want to get some Na+ ions into your solution).
    For 10 L of Hoagland’s solution:
    Dissolve 5 g MES in 8 L milliQ water and add, while mixing:
    Stock solution I 20 ml
    Stock solution II 20 ml
    Stock solution III 10 ml
    Stock solution IV 20 ml
    Stock solution V 10 ml
    Stock solution VI 2 ml
    Micro elements 5 ml
    Fe-EDTA 40 ml
    Adjust the pH of the solution with 5 N KOH to pH 5.8-6.0. THIS IS CRITICAL: GR24 is increasingly unstable at low or high pH. Make up volume up to 10 L.


We are grateful to Dr Brent Kaiser (University of Adelaide, Australia) for providing us with the hydroponics method outlined in this protocol. This protocol was further developed from Hoagland and Arnon (1941). The water culture method for growing plants without soil was adapted from miscellaneous publications including Gibeaut et al. (1997) and Tocquin et al. (2003). The work was funded by grants from the Australian Research Council (LP0776252 (RJ) and DP1096717 (MW)).


  1. Gibeaut, D. M., Hulett, J., Cramer, G. R. and Seemann, J. R. (1997). Maximal biomass of Arabidopsis thaliana using a simple, low-maintenance hydroponic method and favorable environmental conditions. Plant Physiol 115(2): 317-319.
  2. Heeg, C., Kruse, C., Jost, R., Gutensohn, M., Ruppert, T., Wirtz, M. and Hell, R. (2008). Analysis of the Arabidopsis O-acetylserine(thiol)lyase gene family demonstrates compartment-specific differences in the regulation of cysteine synthesis. Plant Cell 20(1): 168-185.
  3. Hoagland, D. R. and Arnon, D. I. (1941): The water culture method for growing plants without soil. Miscellaneous Publications 354: 347-461.
  4. Waters, M. T., Nelson, D. C., Scaffidi, A., Flematti, G. R., Sun, Y. K., Dixon, K. W. and Smith, S. M. (2012). Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis. Development 139(7): 1285-1295.
  5. Tocquin, P., Corbesier, L., Havelange, A., Pieltain, A., Kurtem, E., Bernier, G. and Perilleux, C. (2003). A novel high efficiency, low maintenance, hydroponic system for synchronous growth and flowering of Arabidopsis thaliana. BMC Plant Biol 3: 2.
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Copyright: © 2012 The Authors; exclusive licensee Bio-protocol LLC.
How to cite: Waters, M. T., Bussell, J. D. and Jost, R. (2012). Arabidopsis Hydroponics and Shoot Branching Assay. Bio-protocol 2(19): e264. DOI: 10.21769/BioProtoc.264.

If you have any questions/comments about this protocol, you are highly recommended to post here. We will invite the authors of this protocol as well as some of its users to address your questions/comments. To make it easier for them to help you, you are encouraged to post your data including images for the troubleshooting.

If you have any questions/comments about this protocol, you are highly recommended to post here. We will invite the authors of this protocol as well as some of its users to address your questions/comments. To make it easier for them to help you, you are encouraged to post your data including images for the troubleshooting.

Agricultural Genetic Engineering, Nigde Omer Halisdemir University
Mark, did you use any aeration during the growth? How does it affect the growth?
8/7/2013 2:19:16 PM Reply
Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Australia

No: for simplicity and ease of scaling, we did not use or try aeration. The boxes we use measure about 13 cm x 9 cm (LxW) and we add 160 ml of solution to each. That gives a decent surface area:volume ratio, or so it would seem. The solution, when changed every three days or so, either contains sufficient oxygen, or there is enough gas exchange through the other holes in the boxes. I have not formally compared growth rates with those of plants grown on soil or in other hydroponics systems, but they *seem* to grow pretty normally, flower, set seed etc. Probably aeration would help but it does complicate the set up. A maximum of six plants per pot is tolerable, though I prefer to use four to give them a bit more space. Depends in part on how valuable your media/compounds are.

8/7/2013 6:37:09 PM Reply

Mayvel Lapuz
University of the Philippines
Sir, I like to know if you monitored the concentration during the duration of the study. If yes, What methods did you use?
7/20/2013 3:56:08 AM Reply
Mayvel Lapuz
University of the Philippines

I mean the concentration of the substrate.

7/20/2013 3:56:53 AM Reply

Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Australia

The simple answer is no, we did not measure the concentration of GR24 during the study. It is possible to do so by HPLC to monitor degradation. From our tests, the half-life of GR24 at pH5.7 is about 3 days, but we have not explicitly measured its half-life in Hoaglands media.

7/21/2013 9:56:18 PM Reply

Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, AustraliaAuthor
I would make up a 1x Hoagland's solution, by doubling all the volumes of the various component solutions. I would then make up a NaCl solution of twice the required strength, and mix 1:1 with the 1x Hoagland's. So to make various NaCl concentrations, just make several NaCl solutions of 2x the final concentration desired.

e.g. to treat plants with 150 mM NaCl in 0.5x Hoagland's, mix equal volumes of 1x Hoagland's with 300 mM NaCl.
12/17/2012 4:24:40 PM Reply
iam aske about how can i mixed Hoagland solution with NaCl at different concetration
12/16/2012 6:28:50 PM Reply
I am using your protocol to do phosphate assays, and I am curious: do you make your Hoagland's in lab or do you purchase it? If you purchase it, from where? Thank you.
10/15/2012 8:40:09 AM Reply
Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Australia

We make each of the stock solutions ourselves in the lab. This is potentially expensive if you have to buy all the reagents, especially considering how little you need of some of the micronutrients. Some of the micronutrients can be substituted, e.g. ZnCl2 rather than ZnSO4, as it is the Zn2+ rather than the Cl- or SO4- that matters.

10/15/2012 10:52:36 PM Reply

Charles Parrish
North Carolina State University

Thank you, Dr. Waters. I would also like to know where you purchased the rockwool used in your experiment, and what type of rockwool it is? Thank you.

2/5/2013 7:45:09 AM Reply

Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Australia

Hi Charles

We get our rock wool from these guys in Australia:


The manufacturer is Grodan, and you may be able to find alocal distributor here:


2/12/2013 6:27:24 PM Reply

Mark T Waters
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Australia

And more information on what rock wool actually is:


2/12/2013 6:28:23 PM Reply

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