• Professor Sprout

How To Clone Cannabis Part 2

Professor Sprout’s Guide to Cloning Cannabis Part Two: Cutting and Prepping Clones and Growing Bonsai Micro-Mothers


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Building a kick ass cloning machine is only half the battle. Once you’ve completed my DIY aeroponic cloner build, you still need to know how to cut clones and dial your environment in to ensure 100% rooting success. The good news is with an aero cloner you have far more room for error, which is why it is my preferred cloning method. Follow these steps and I guarantee that each and every cutting you take will sprout roots and grow into a happy little tree.

Note: Before you cut your clones it’s recommended that you prep your cloning machine by filling it with chlorinated tap water ph adjusted to 5.8-6.0. If your tap water is above 0.5 EC (350ppm on the 7 scale) then it is advisable to use reverse osmosis water. The self-serve water stations you see everywhere are typically reverse osmosis water, and one large 5 gallon blue water jug is the perfect amount of water to fill my DIY cloning machine. There is no need to add any nutrients to the water at this point, as plain water works just as well. Running the cloner for a few hours before you load it with your cuttings oxygenates the water and brings the temperature up to a comfortable level for your fresh cuttings. I often run mine for 24 hours prior to loading to ensure there are no leaks or malfunctions.

Note 2: If you prefer to seal the lid of your cloner with silicone to prevent any chance of leaks (not always necessary, but recommended) make sure you do this 48 hours before cutting your clones to ensure plenty of time for the silicon to cure. Remove all of the cloning collars to allow airflow into the reservoir to dry the silicone. Once the silicone is dry, you can fill the reservoir by pouring water through the holes in the top of the lid.

Step One: Select a healthy donor plant.

This is absolutely essential to cloning success and the importance of this crucial factor cannot be overstated. You must start with a well fed and happy donor plant (called the mother) to take your cuttings from. Anemic, sickly, and malnourished cuttings will not survive the cloning process. Once you have removed the shoot from the mother plant it will be forced to feed off the nutrition stored in the stems and leaves. If you start with a cutting that is already nutrient deficient, it will not have the necessary energy to maintain life support while at the same time grow fresh roots. Many slow to root clones are a direct result of being taken from a donor plant with an unhealthy metabolism. Healthy mothers = healthy clones.

Step Two: Top your plant to create multiple main shoots.

If you are trying to clone a plant started from seed, the temptation will be to cut the main stem off and try to root the top. The problem with this, is that the main stem on a plant grown from seed is thick-walled, hollow, and difficult to clone. There is also such a large concentration of auxins (growth hormones) in the main stem of a seed-grown plant, that the growth is often very soft and supple. This is not a desirable trait for your cutting selections. A very high percentage of main stem cuttings (again, from seed plants specifically - not clones) will fail. It can be done, if necessary, but your margin of error will be very slim. You will have far greater success with secondary shoots so I suggest planning ahead and preparing your donor plant early in it's life cycle to produce many secondary shoots.

This Pink Flamingo male was grown from seed, and although the main stem looks strong and healthy, it will be the most difficult part of this plant to clone

The main stem from a cannabis plant grown from seed is thick, hollow, and difficult to clone.

In order to prepare your plant to become a viable mother/cutting donor, you’ll want to start early in the life life cycle by ‘topping’ or pinching off the main stem. You can do this at any point after the second or third set of leaflets have emerged. I would recommend waiting until the plant has developed at least five or six sets of leaves and has adequately filled out a seedling container with a thick web of roots. This will ensure continued strong growth and a relatively short downtime.


By cutting the main stem off just above the emerging branches of the secondary shoots, you will cause these secondary shoots to increase their growth rate and reach for the light in competition with the other branches to become new main stems. This creates multiple plant tops and is a fantastic way to increase the number of viable clones you can take from a donor plant. This trick also creates much improved yields come bloom time.

Cut the main stem to increase secondary shoot growth

Topping your plant in this fashion will also force your plant to grow into more of a wide bush, as opposed to the typical tall, tapered, christmas tree shape of an unaltered cannabis plant. This creates a wider and more level canopy that can be advantageous when using artificial indoor lighting due to more even light distribution. This also helps maximize the number of potential bud sites.

Step Three: No too soft, not too hard, but just right.

As I already mentioned, your best rooting success will come from the secondary shoots that grow up towards the light after the main stem has been severed. However, if you’re running high amount of nutrients, intense lighting, warm temperatures, and high humidity, you may find that these shoots become soft and weak due to rapid growth. These are not ideal for cloning.


You want to select shoots that have some structural integrity. The stem should be firm, but not woody. The leaves should also be springy and not floppy. Soft stems will quickly turn to mush in your cloner, and woody stems will take forever to root. You need them to be just right.


Keep your mothers in relatively cool temperatures before taking clones. Don’t be concerned if your stems begin to turn a little purple or red. This is caused by the cooler temperatures slowing calcium and magnesium uptake, which will result in the stems becoming more fibrous and stiff. For clones, this is actually helpful as the stems are less likely to turn to mush, giving you a longer window of opportunity where rooting can take place. As long as the foliage is a nice deep green with no deficiencies, your clones will root rapidly.


Notes on Maintaining Mother Plants

As a cannabis breeder, I don’t require large numbers of clones like a flower production facility would need. Therefore, I prefer to keep a small selection of my elite male and females in bonsai form. This allows me to keep very small plants long term with maximum efficiency. This is an excellent method for the home grower who may only need to take a handful of clones each season.


For these bonsai micro-mothers I maintain them in half gallon containers of organic soil under T-8 fluorescent lights on custom built shelves. I feed a weekly low dose of balanced organic nutrients, such as Medi-One (4-3-3 ) from Green Planet. I find the ideal conditions to keep these plants in is a relatively cool temperature (20-22 celsius) in 45-50% humidity with the lighting kept close to the plant tops. This results in slow but healthy growth, strong stems, and compact plants.

Compact bonsai-style micro mothers are easy to keep long term by constantly trimming away new growth, leaving only a few short stems intact

When I require clones from a particular strain to do a breeding run, I will transplant the mother into a large container of fresh soil and move it to a room with warmer temperatures, higher humidity and more intense lighting to encourage it to grow rapidly. I then take clones for my seed production, while also setting aide the healthiest duplicate to take over the role as the new mother.


Step Four: Sanitize Everything!

This is a crucial step. Make sure to thoroughly sanitize your scissors, scalpel, cutting board; absolutely everything that will come into contact with your cuttings. Use a 10% bleach solution or 70% isopropyl alcohol to wipe down all of your tools. Wash your hands thoroughly, and use sterile gloves if possible. You will be creating an open wound in which any opportunistic pathogen can take hold and infect your cuttings quite easily. This can lead to tissue necrosis (black splotches on your stems), and ultimately, death. If one clone ends up contaminated, it can quickly spread through the water in your cloning machine and contaminate all of the others, so please take this step seriously.


Step Five: Snip Clones

Once you have thoroughly sanitized and dried your tools, it’s time to take your cuttings. Fill a glass with cool, chlorinated tap water (the chlorine will help keep things sterile) to place your cuttings in. Using very sharp scissors, cut off your shoots just above a node. I recommend taking cuttings that are approximately six inches long, with healthy deep green foliage, erect leaves, and firm (but not woody) stems.


Before placing your cuttings in the glass of water, clip off all foliage save for the very top set of leaves. Trim the leaves by gripping the shoot in your hand and clipping the ends flush with your fist. By removing all unnecessary foliage, you’ll dramatically reduce water loss from the cutting, which will keep it from wilting prematurely. If you leave too much foliage the amount of water the cutting requires to remain firm and upright will outpace it’s ability to absorb it through osmosis. Since there is no longer a root system for the cutting to drink from, you must dramatically reduce the water demands in order for it to survive the rooting process.

Place your cuttings in the glass of water while you finish removing the remainder of your clones. Since I often take clones from many different strains at once, I will also label the clones with green painters tape wrapped around the stem.


Step Six: Shave and Dip Cuttings

Now it’s time to prep the cuttings for the cloning machine. To do this you’ll want a clean and sanitized cutting board, a scalpel with a new blade that has been cleaned with rubbing alcohol, a large shot glass, and rooting hormone gel (not powder).


The rooting hormone I prefer to use is a gel based product called Rootech by Technaflora. I’ve used others, but this is the brand I always end up going back to as it provides very consistent success. You do not want to use powders in a cloning machine since they can cake on the stems, reducing water uptake as well as clogging the pump and misters.

The Rootech gel is quite thick, so I like to mix it half and half with filtered water to dilute it and allow it to more easily penetrate the clone stems. You’ll need to stir the mixture thoroughly in order to get it to evenly dissolve into the water. It should readily drip from your stirring utensil. If not, it's too thick, and you should dilute it further.


One by one, I take the cuttings from the glass of water create a fresh diagonal cut half an inch up front the bottom. As scissors tend to crush the stems somewhat, this fresh slice will be much cleaner and less likely to result in dead tissue.


I then carefully slice off thin layers from the outer skin of the stem to expose the inner cambium. This is where the new root cells will emerge from, and exposing this layer results in faster rooting. This step isn’t entirely necessary as roots will eventually push through the outer skin, but it does speed the process somewhat. You have to be careful to not cut too deep past the cambium though as this generally leads to dead tissue and rot. This can get a little tricky, but basically what you’re aiming for is to just gently shave off a very thin slice. Too little is better than too much. Keep your scalpel angel very shallow, and only remove material form the bottom one to two inches of the cutting.

Once you have shaved the stem, place the cutting in the shot glass with the rooting hormone, and let it sit to absorb the gel while you process the remaining cuttings. I like to let them sit in the mixture for at least five to ten minutes. When all cuttings are shaved and dipped and have rested for a minimum of five minutes in the gel, you can place them in the cloning collars.

Step Seven: Loading Clone Machine

At this point your cloner should be full of water (to just below the level of the spray manifold - around 5 gallons worth), ph adjusted, and have been running for at least a few hours.


You’ll then place one clone in each collar, with the stem hanging down below the bottom of the basket by at least an inch or two. You do not want the stem to actually be submerged in water. This is why I recommend taking clones that are around 6” in total length, as this will give you a few inches above the collar, and a few inches below, without submerging them.

Only let your cutting protrude from the bottom of the basket by an inch or two

Notes on Nutrients: Cuttings do not require nutrients to sprout roots. In many cases, adding nutrients to the cloner tub will actually hinder root growth so I do not advise adding anything at all for the first week. If you so choose, you can add a small amount of a bloom nutrient after the first week; once root bumps are clearly visible on your stems. At this point you can add 0.5 EC (350ppm on the 7 scale) of a basic bloom nutrient that contains phosphorous and potassium. There is no need to spend a fortune on fancy and expensive cloning nutrients.


I generally don’t bother adding anything but ph adjusted tap water, and still achieve roots ready to transplant in 10 days on average. If your clones are having trouble developing roots and can’t seem to get past the root-bump stage (which is usually due to improper water temperature or clones that were harvested from a malnourished mother plant with a weak metabolism) adding a little bit of food can sometimes give them the energy they need to push through. Olivia’s Cloning Solution is a product I’ve used with great success in the past, and it’s quite inexpensive. Another great option is General Hydroponics Flora Series Bloom (0-5-4). Again, just 0.5 EC of either of these nutrients is all you need.


A well used bottle of Olivia's. A little goes a long way.

Step Eight: Set Pump Timer

I use a cycling timer for my cloner pump that allows me to set on and off intervals down to a single minute on an infinite loop. You may be tempted to use a standard timer but I recommend against it for a couple of reasons. First, many timers only have a specific number of programmable cycles, such as ten per day, which will not be sufficient. You need a timer that you can set to run on and off every few minutes. Second, if you run the pump too long, it may heat up the water too much which can lead to rotten stems. I learned this by having two clone machines identical in design except for the pump. The machine with the larger pump always had a terrible success rate, while the other one would root nearly 100% of the cuttings. It took a long time to realize that a) the spray from the clone misters with the powerful pump was so strong it was retarding root growth and b) the pump warmed up the water so much the clones would often rot before they would root.


A minute timer with infinite loop capability is critical to cloning success

Depending on the time of year and ambient temperature levels, I run my pump all the way from 24 hours a day in the winter (when temperatures are very cold in my cloning room at 15 degrees Celcius/59 degrees Fahrenheit) down to intervals of 1 minute on, 5 minutes off during the summer. All things being equal, I get the best results with a 1 minute on two minute off interval when daytime temperatures hover around 20 degrees Celsius.


Step Nine: Temperature Check

Temperature of your cloning environment is absolutely crucial. This is the one detail that you absolutely cannot overlook if you want to have success. A few degrees can make or break you here. I often will not even attempt to clone in the heat of the summer when our temperatures routinely surpass 40c/104f. Unless I can keep the cloning room right around 20c/68f, which requires round the clock air conditioning during the summer months, it’s just not worth the trouble. Heat = clone death. Period. Stems turn to mush, bacteria proliferates in the water, slime builds up in your reservoir, clones wilt and die.


I know many people swear by heat mats, humidity domes, and jiffy pucks for cloning, but this method has only resulted in a compost bin full of dead cuttings and soggy peat pucks for me. The only way I get roots 100% of the time is when I keep the temperature of the room (and thus the water in my cloning machine) between 18c/64.4f, and 22c/71.5f. Anything higher or lower than that and I begin to have problems.


The whole rooting process is really about starting with very healthy cuttings, and then keeping them in the goldilocks zone of precise temperature long enough for them to take root. If your environment is perfect, you can stick healthy cuttings in a beer bottle full of tap water on a window sill and eventually get roots. Using the cloning machine just speeds the process up substantially.


Step Ten: Humidity Check

Humidity is far less of a concern when using a hydroponic aero cloner since you are providing a constant supply of cool, oxygenated water directly to the stem in a sealed environment. Humidity domes are unnecessary, and will often only result in breeding mold and mildew.


I do, however, keep a spray bottle of filtered water next to my cloning machine and mist the cuttings twice a day for the first three days. This helps prevent any premature wilting during the first few days while the cuttings are adapting to life without roots.


After three days the cuttings should be fully saturated to optimal hydration levels and will be perky and healthy. After this point there is usually no need to continue spraying unless you live in an arid environment (less than 40% humidity).

Step Eleven: Lighting

You do not want to blast your clones with too much light. More light increases the rate of photosynthesis. Since your cuttings do not have a root system to provide them with nutrients, they must depend on their internal reservoirs of food. As photosynthesis increases, the nutrient demands increase, and the clones will begin to turn yellow, discolour, and become sickly.


I find the ideal light source for my DIY cloning machine to be a pair of two foot 6500k “daylight” T5 fluorescent bulbs. This provides the cuttings all the light they need to develop roots with minimal heat production. Although LED’s produce very little heat, they are often too bright, so stick with the T5s. I hang them around 12” above the plant tops for the first few days, and then incrementally lower them an inch per day until they are 6” above the tops.

I like to leave my lights on 24/7 when cloning. This keeps the environment very consistent and stable which is less stressful to the vulnerable cuttings. This also allows the use of the relatively dim 2ft T5 bulbs while still accumulating enough photons to drive adequate photosynthesis for maintaining foliage and pushing root growth. I have experimented with many different light cycles and by far my best results have been with lights on 24 hours a day.

Step Twelve: Planting

If you follow all these steps to the letter, in a week to ten days you’re going to be seeing brand new roots form on the stems of your cuttings. At first they will just be tiny little bumps or calluses, which will then begin to sprout into bright white tendrils. Left in the cloning machine long enough, they will grow long and stringy and will drop down into your reservoir.

The tiny white speck is the very first sign of root-bump emergence
Many root bumps forming

I prefer to transplant at what I call the ‘porcupine’ stage, where the roots look spikey and have not yet begun to get long and stringy. If you’re going into a hydroponics system you may choose to let the roots get a little longer before placing them in the system of your choice, but since I grow in soil, this is the perfect time to move them along for my situation.


The Porcupine stage is the perfect time to plant in soil

For my initial clone soil mix, I like to use equal amounts of Promix HP (which is Peat Moss, Perlite, Mycorhizal fungi, and dolomite lime) and Coco Coir. The Promix contains an initial soluble nutrient charge, so there is no need to provide any additional nutrients just yet.

This clone mix offers the perfect amount of nutrient value and drainage for fresh clones

I use small seedling cups, place a little mix in the bottom, hold the clone in the centre, and backfill up to the top, being careful to not damage the delicate roots. Once full to the top I saturate to run-off with reverse osmosis water that has 0.3 EC of a cal-mag product added (210ppm using the 7 scale).

Be gentle when backfilling with soil

Once planted, water thoroughly with a light dose of cal-mag enriched water

When all the clones are planted I place them in a plastic flat tray and put them back on top of the cloning machine, raising the lights up 6 inches or so to accommodate for the extra height gained.

For the first week, keep the newly planted clones in the exact same environment

I’ll keep the clones in this environment for about one week to allow them to adapt to their new shoes before placing them under more intense lighting conditions and beginning their feeding regime. Usually it will be just a matter of two to three days before you’ll see fresh roots peaking out of the bottom of their small containers.

The money shot! A successfully rooted clone!

Once the clones have rooted and are ready for the first dose of nutrients, I’ll apply a low dose of organic bloom nutrients that contains liquid kelp, with an N-P-K of 2-4-4 (such as General Organics Bio Thrive Bloom). I also like to supplement with a soluble bacterial and fungal inoculant which will stimulate root growth (Advanced Nutrients Piranha and Tarantula are good options here) plus a tiny shot of organic cal-mag and little molasses. Total EC of this initial feeding should be around 0.8 EC, or 560ppm on the 7 scale.


Generally speaking I’ll only keep them in these small seedling containers for about fourteen days before I transplant them into larger vegging containers filled with my organic soil mix and then it’s off to the races.


Follow the Recipe

Cloning can be one of the most frustratingly hair-pulling aspects of cannabis cultivation, but if you follow these instructions I guarantee you will overcome this challenge and be poppin’ roots in no time. Just treat these directions as a step-by-step recipe - changing nothing - and you will win.


Now go forth and create your clone army dear reader.


Special Note From Professor Sprout: If you have found this article and my DIY cloning machine plans helpful, please share this blog with your friends. We're not on facebook or twitter, so we rely on people like you to spread the word for us Cheers! PS


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