How Do I Germinate Cannabis Seeds and Transplant Clones?

Clones vs Seedlings

Clones and seedlings may seem very similar, but there are some differences between the two starting points. First of all, seedlings (small plants sprouted from seed) have a taproot. This is a central dominant root that tends to grow straight down and proliferate the branching root structures that explore the growing medium. Clones do not have a taproot; instead, they immediately begin producing a fibrous branching root structure. I would argue that the taproot is most important in outdoor grows due to the higher degree of anchoring and stem support that it can provide in windy weather.

Secondly, seeds all have unique genotypes while clones have the same genotype as the mother plant they were cut from. Truly stable seed lines produce plants with phenotypes so similar that they could be mistaken for clones, but usually in the Cannabis industry, a given seed pack for a strain may produce multiple different phenotypes. Sometimes this can be desirable if you are phenotype hunting for a unique plant to grow or breed with, but at least in large scale production, uniformity is usually preferred because it simplifies the growing, harvesting, and processing techniques

How Do I Germinate Seeds?

There are many ways to skin this particular cat. First of all, it is important to consider the environmental conditions required for germination.


While some small seeds without much of a starch reserve require light to germinate, it appears that light actually inhibits the germination of Cannabis seeds. This is likely due to the red light sensing system by light-sensing proteins called phytochromes. In general, far-red light can penetrate further into soil than red light due to the longer wavelength. Plants often utilize the ratio of far red light to red light as a way to sense depth in soil. For Cannabis, it appears that it requires a low far red/red ratio (no to minimal light) in order to germinate. However, pure darkness is unnecessary in my experience. In fact, it is a bit of a balancing act because after germination, your seedlings require light or they will not begin to produce chlorophyll and will continue to etiolate (grow and stretch in search of light to begin photosynthesis). Therefore, you will need to check your seedlings frequently so if you germinate in complete darkness, you can quickly introduce your newly sprouted seedlings to light.

Moisture and Humidity

Seedlings require water uptake in order to trigger germination. The media they are in contact with should be moist, and the humidity should be kept high but ventilated to help prevent microbial growth. In general, this translates to around 70-90% humidity. However, I don’t generally keep track of the humidity of the air in my germination area. Humidity is ensured to be high by enclosing the germination medium with a ziploc bag with holes cut in it.


I like to follow the rule of thumb: keep the temp in the 70s throughout the day and night. Don’t let temperatures dip below 70F and don’t let temperatures rise above 80F. In Celsius, this translates to approximately 21-27C. In practice, it is okay if it gets warmer, though I certainly would avoid letting temperatures get above 30C (86F). However, high heat can inhibit germination and encourage microbial growth. Also, dipping below 70F does not ensure failure, but may not be as efficient at germinating seeds.

I will only cover 2 germination methods. This is because in my opinion, they are simple, effective, and I have experience in both.

Method 1: Wet Paper Towel.

Get a paper towel and soak it in water (it is probably ideal if you get sterile, deionized water, though I generally use tap water and it works just fine). Squeeze out the paper towel so that it is damp but not wet. Place your seeds on the damp paper towel, and fold the paper towel one time over the seed. Place the folded paper towel in a gallon size plastic bag.

Option 1: Poke a few holes in the plastic bag (I like to use sharpened pencils, it has a good size for holes), blow into the bag to ensure it’s not collapsed on the paper towel, seal the bag, and place it in a dark, warm place. Check daily for germination and make sure to keep the paper towel moist. If it gets too dry, just use a spray bottle to spritz the inside of the bag and paper towel.

Option 2: Don’t poke any holes, exchange the air inside by sucking the air out the bag and blowing back into it to inflate it. Seal the bag, place it in a cool, dark place, and exchange the air in the bag once to twice/day and check frequently for germination.

Transplanting Germinated Seeds

After germination, I like to wait until the taproot is about an inch long. After this, pick it up by the seed coat with tweezers or a very gentle touch. Don’t touch the taproot. take your soil or growing medium, moisten it using appropriately pH’d water (around 6.5 for soil) and prepare a a hole deep enough to place the germinated seed in with the taproot facing down and the seed coat barely below the soil line. Place the seed in so that the taproot is straight down and so that the tip of the taproot is not bent or hooked when you plant it.

Method 2:

Plant your seed directly in a seed starter (I like to use coco coir with a bit of mycorrhizal fungi sprinkled in).

Option 1 is to buy seed starter coco coir pellets. All that is required is to wet the pellets with properly pH’d sterile water. They will expand and will have a small hole in the center for you to place your seed. After planting your seed, gently cover it up. This will provide both light and local humidity around your seed. Cover the pellet loosely with an open plastic bag to help retain moisture and leave it on a windowsill or under artificial light. This will ensure that once the seed germinates under the soil which is dark and humid, it will sprout above the ‘soil’ line, remain in a humid environment in the plastic bag , and will also be exposed to light so that the seedling can begin photosynthesis. I do not like to use peat moss or peat-based pellets such as Jiffy pellets. First of all, coco coir is far more environmentally friendly because peat is a nonrenewable resource, unlike coco coir. I stay away from rock wool for the same reason, coco coir is just a more responsible consumer choice for the environment. Secondly, peat is extremely acidic and may affect nutrient uptake early in a plant’s life as compared to coco coir. For all seed starting mixes, I like to make about a quarter of the volume perlite. Seedlings do not uptake water well and you want good soil aeration to avoid damping off and root rot diseases. If you use premade pellets, you will not have this option.

Option 2 is to fill a small, 2-3 oz plastic cup with coco coir, moisten it and make a hole for the seed yourself, and sow your seed. Follow the same directions as outlined for the pellets.

What do I do now that my seedling has germinated?

Now that you have a germinated seedling, you will notice two small ‘leaves’ that are kind of oval-shaped. These are known as cotyledons, and can actually help provide your plant with nutrients that were stored in the seed until the plant can feed on fertilizer or nutrients in soil depending on your growing style.


You will want to provide your plant with enough light to not stretch out. You can get away with using even a 60W single CFL ‘grow’ bulb for a seedling, but I tent to keep my seedlings under a 300W LED panel. I like to keep the light source about a foot from the top of my seedling.


Go ahead and keep the temperatures in the 70s (Farenheit). This is a great range for Cannabis growth and isn’t as conducive to disease development as warmer temperatures.


You will want to slowly lower the relative humidity. Keeping the same level of humidity as for germination will prove to be too conducive to disease development especially seedling damping off and root rots. Go ahead and keep the plastic bag over the seedling at first, and slowly increase the amount of time each day that it is not under the plastic bag. In general, I like to leave the bag off the seedling at night after it sprouts and during the day, reduce the time it is under the bag by an hour each day until the second set of true leaves are visible, then remove it altogether.

Moisture and Feeding

Seedlings require more moisture that mature plants but you also want to avoid root rots. Therefore, I like to use a spray bottle to mist the soil every day without soaking it. This should be done until the second set of true leaves are visible, then begin your normal watering schedule. Your seed starter mix should not have fertilizer in it. Your plant should have all the nutrients it needs from the cotyledons and all the energy it needs from photosynthesis. However, after the first true leaves are fairly large and the second set of true leaves are barely visible, I will sometimes include a Nitrogen dominant fertilizer at 1/4 strength in the spray bottle and lightly mist until slightly damp (I only ever do this once before transplanting, and only if the leaves are looking light). I tend to use liquid fertilizers (you can find conventional or organic fertilizers depending on your fancy).

Transplanting Your Seedling

By the time the second set of true leaves have grown in, your seed starter plug should be colonized by roots. Or, if you purchased a clone, it is likely already rooted in a rock wool cube. Take a pot approximately 10x the volume of your rooting medium, fill it with the planting medium of your choice (soil or soilless medium[if soilless, it is a good idea to do a light feeding (1/4 strength) as well at this point]). Water the medium in your new pot before transplanting and allow it to drain to field capacity. Make a crater in the center of your moistened medium deep enough to completely cover the seedling medium. I like the lowest nodes on the plant to be about 1-2″ above the soil line after planting. Place in your rooting plant, fill in the crater, smooth it out, and lightly pack in the planting medium around the stem of your plant. Water the pot once more to ensure the soil settles in, allow it to drain capacity.

Congratulations, you have germinated your seed and/or transplanted your clone/seedling. That was pretty easy, right?

How Do I Select Which Cultivar (Strain) to Grow?

A cultivar is a cultivated crop variety that has been produced from selective breeding. In the Cannabis world, cultivars have long been called ‘strains’, similar to wine grape cultivars being referred to as ‘varietals’. The term strain generally refers to unique genotypes of microorganisms, but has been somewhat co-opted by the Cannabis industry.

While there are some Cannabis breeders that truly pursue the production of stabilized genetic lines with unique phenotypic properties, in my opinion, most of the Cannabis strains on the market are produced quickly and have not undergone a long enough selective breeding process to stabilize the lines. Many strains on the market are a result of breeders simply crossing the best sellers of a given season in order to cash in on the hype of particular genetics. This results in most of the products on the market being unstable polyhybrids that have not undergone rigorous breeding on a large enough scale to select phenotypes for traits such as disease resistance that are commonly overlooked.

This is my list for the most important aspects in selecting genetics for your grow:

  1. The most important aspect to consider in microgroweries is whether or not you enjoy the effects of the strain you are growing.
    1. For example, some of my favorite strains of all time have Cherry Pie genetics including GDP and Purple Punch. I tend to get anxiety with sativa-dominant (cerebral) strains and prefer strains with more sedating effects. I also really enjoy strains with high CBD and moderate THC.
  2. Secondly, it is extremely important to choose strains that have been released by reputable breeders that place importance on stable genetics (particularly when growing from seed). If you are purchasing clones, it is important to know that the genotype does not have a strong propensity for hermaphroditism and has phenotypic traits that are favorable.
  3. In an indoor grow, some of the most important phenotypic traits to look for besides the effect of the strain are:
    1. Flowering time (In general, strains that are closer to ‘indica’ on the cannabis spectrum are ready to harvest quickly as compared to plants that are considered more ‘sativa’). I tend to select strains that can finish in approximately 8-10 weeks after the start of flowering. If you are buying seed, one should consider the possibility of growing an ‘autoflowering’ strain. I will go into a bit more detail on autoflowering Cannabis a bit later on.
    2. Yield (Plants that produce large and dense colas are generally preferable when growing on a small scale).
    3. Stature (Height, bushiness, the degree that the plant stretches in flower, and density of branching are all important factors to consider.)
    4. Cannabinoid profile and potency (This may be a very important factor to some. While cannabinoid profile is important to me, I tend to not select my strains on the basis of THC levels simply because most of the strains on the market are too strong for my personal preference, and I do not care much about maximizing THC).
    5. Other metabolite profiles of your plant: Terpenes and flavonoids are important to consider. Terpenes are mainly responsible for the odor of the strain you are growing, but many are psychoactive and influence the effects of the strain you are growing.
    6. Resistance to disease and pests: Different strains have different levels of resistance to various diseases and insect pests. For example, if you have had trouble with powdery mildew in the past, it would be useful to avoid strains that are particularly known for powdery mildew susceptibility.
      1. In my last grow, I had three strains in one grow tent (Dream Queen, Purple Punch, and Venom OG). I had a whitefly infestation occur, and I noticed an obvious difference in whitefly populations on the different strains. Dream Queen had very few whiteflies, while Venom OG seemed to have the most.
      2. For Powdery Mildew, it appears that the most resistant strains have Afghani heritage, please see my post on PM under pest and disease profiles for strain recommendations.
      3. For bud rot, it appears that the most resistant strains are equitorial sativas. Please see my post on bud rot under pest and disease profiles for strain recommendations.

As you can tell, indoor growing really lends itself to strains that have classically been considered ‘indica heavy’ and have a short, bushy stature, quick finishing time. Although plants with a more ‘sativa’ phenotype can be grown indoors, they tend to be more difficult because they are more lanky, they tend to have a longer internodal spacing, they stretch a lot during flower, buds tend to be less dense, and the time to finish can be quite long. However, there are techniques to help keep these plants more manageable such as training. Do not let yourself be deterred if you are set on growing such a strain.

If you are new to Cannabis and do not have a firm grasp on your strain preference, I would do the following to select a strain to grow:

  1. Look for local vendors selling cannabis clones and look through their offerings. Select at least a few of the strains (some indica dominant strains, some sativa dominant strains, and some hybrid strains).
  2. See if there are any dispensaries in your region selling flower of your selected strains and purchase a small amount of each of the selected strains.
  3. Sample the flower on different days and select the one with the effects you enjoy the most for purchasing clones. Often times, the dispensaries in the region may not have the flower of the strain you want to sample. In that case, it might be worth doing some searching for the offerings of local dispensaries and only selecting strains that you can purchase clones for.

I believe that for first time growers, it is best to grow from clone as opposed to seed if you have access to them. The reasons for this include: genetic uniformity between plants and phenotypes that have already been selcted for favorable traits. When you buy seeds, as I mentioned earlier, many strains are not stable and can produce a variety of phenotypes, some of which may be unfavorable. It is best to have a bit of experience in finding trusted breeders before buying seeds. However, with a bit of web searching, you can find some well-reviewed genetics from trusted breeders. If you are buying seeds, I believe autoflowering seeds tend to be the easiest beginner plants to grow; you will not need to change the light cycle to induce flowering, they finish quite quickly, and you do not need to fuss about physical manipulation techniques such as ‘topping’, ‘FIMing’, trellising, or other training techniques. Though historically considered to be of lesser quality, autoflowering Cannabis has come a long way and there are many strains out there that produce high quality flower.

What to Look for in a Clone Nursery

Due to my location, I have only ever bought my clones from one source: Dark Heart Nursery (with the exception of when I was running Ken’s Cut GDP for a while). Dark Heart is a very reputable nursery that puts a lot of care into their strain selection, and most importantly for me, they produce disease-free clones. They have a dedicated Plant Health Department that ensures operating procedures are kept as sterile as possible, and they go through the necessary steps to ensure that their clones are free from known viruses and viroids. The causal agent of cannabis ‘dudding’ disease was discovered and described as the Hop Latent Virus by their plant health department and necessary steps were taken to ensure the viroid was eliminated from all plants [1].

It is important to select your clones from a nursery that takes care to ensure they are providing healthy, disease free clones.

How Do I Select a Reputable Breeder?

In my opinion, if you are not going to test out seeds or cuts from various different breeders, the best way to find reputable breeders is to read forums discussing the topic.

One of my favorite strains of all time that I kept in production for multiple years was Ken Estes’ Granddaddy Purple. I personally do not have a ton of experience with trying a large variety of breeders, but I have also had success with Greenhouse Seeds (I did a few runs of their Bubba Kush).

Purple Punch is a favorite of mine, and though uncertain, breeders at Supernova Gardens claim to have produced this legendary strain. Often times, the breeder of well-known strains are debated and the actual crosses that occurred are unknown as well. In such cases, you generally will grow the strain because it has a reputation of being high quality regardless of the breeder. One such strain I have grown is Dream Queen, though the genetics I grew came from the highly reputable Humboldt Seed Co.

I enjoyed growing Venom OG from Rare Dankness, but as with many ‘OG’ strains, it was a bit lanky and the buds were a bit loose for my liking. However, I enjoyed the diesel odors, rich colors, and effects of this strain. One of the most reliably consistent seed-grown strains I have ever run is Skunk #1 from Sensi Seeds. Though the strength of this strain is mild to moderate, I enjoy the lower THC content, the consistency of the plants, the hard to come by skunky odor, and the yield. Sensi Seeds has a lot of very stable strains that I enjoy, and they don’t seem to play the THC-hunting game or the name game so prevelant in today’s Cannabis culture. Their Big Bud is also a nice strain to grow. It produces well, is not overly powerful, and is very forgiving to the new grower.

I am also a big fan of Barney’s Farm. Though I cannot speak to all of their products, I grew their LSD one time. It yielded well, had no issues to speak of, and I enjoyed the moderately strong but relaxing effects. I would grow this strain again.

In terms of autoflowering plants, I have ever only tried Blueberry Auto by Dutch Passion Seeds. By introducing ruderalis genetics to DJ Short’s legendary Blueberry genetics, they have managed to produce a plant that yields very well, finishes very quickly under long day conditions, and is fairly potent with a nice nose, which can be difficult to achieve with autoflowers.

Aside from the breeders/seed companies mentioned above, popular seed companies in forums include DNA Genetics, Bomb Seeds, Sin City Seeds, Buddha Seeds, Anesia Seeds, and Royal Queen Seeds. These are all companies I see popping up in forums (recently I have seen a lot of praise for Sin CIty, Buddha, and Anesia in particular). I have not tried anything from them.

What is the Takeaway?

There are so many strains out there it can be overwhelming to choose. The bottom line is you should choose a strain that you enjoy consuming, but other factors (mainly yield and finishing time) should come into play in choosing between strains you like. Buy your seeds from a reputable breeder/seed company and buy your clones from nurseries that ensure you are receiving a healthy plant.

If you don’t know where to even begin and don’t want to sample a bunch of cannabis, simply choose any of the companies I have mentioned above and buy a product with positive reviews, go on Leafly and determine if the described effects are desirable to you, and just do it. When it really comes down to it, it’s hard to go wrong.

  1. Warren, J. G., Mercado, J., & Grace, D. (2019). Occurrence of Hop Latent Viroid Causing Disease in Cannabis sativa in California. Plant Disease, 103(10), 2699.

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