What are Cannabis Genotype, Phenotype, and Chemotype?

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Added 14 March 2023

Before growers figured out how to grow cannabis, the species grew out in the open without any human intervention. The plant naturally adapted to specific conditions during that time, depending on its location.

For example, Indica varieties of cannabis grew to possess better cold resistance and high vigor, whereas Sativa varieties evolved to grow well in tropical conditions with high humidity levels. 

But when growers figured out how to use this evolutionary aspect of cannabis, they started breeding cannabis to possess specific traits they desired the most. We have come far in the last couple of decades.

Nowadays, even a hobby grower can easily invent a new strain by breeding two different strains — the new strain will possess the traits the grower desires the most. Sounds exciting, doesn't it?

If you want to go down the path of breeding cannabis, you will come across three terms: genotype, phenotype, and chemotype. Genotype is the genetic boundary of the plant, phenotype refers to the traits a specific plant exhibits, and chemotype indicates the plant's cannabinoid properties. 

This guide takes you deeper into the three terms, how they relate to each other, and how you can use them to grow your favorite cannabis strains. Who knows, maybe you can invest in the next best cannabis strain. 

Read on to learn everything about cannabis genotype, phenotype, and chemotype. 

Cannabis Genotype and Phenotype

Cannabis Genotype and Phenotype

When growing cannabis, two factors influence how your plant grows — its potency, shape, color, and other traits — namely genetics and environment. This is where genotype and phenotype come into play.

Cannabis genotype and phenotype are closely related, so we will look at the two concepts together. 

Cannabis Genotype

Genotype is essentially the genetic composition of your cannabis plant, which is responsible for defining how the plant grows. It allows your plant to exhibit a range of possibilities in terms of growth, potency, color, shape, etc. 

This genetic code is stored in the DNA of all living beings, including the cannabis plant, and it carries crucial information or instructions for the plant. However, the genotype is never rigid — it merely defines a range of how the plant can grow — but the plant can never go out of this range. 

Genotype defines the boundaries of the plant, but another factor that influences its growth is the environment. When you get involved in the genetics of the cannabis plant, genotype comes in handy to understand the limitations of the cannabis plant and not how it will actually grow, since the environment plays a significant role as well. This brings us to phenotype.

Cannabis Phenotype

As mentioned earlier, the growth environment of the plant affects how the plant grows. Even if you grow two cannabis plants of identical genotypes, both plants will grow entirely differently in different environments. This is the plant's phenotype.

A phenotype can be defined as a genotype that is expressed by the plant based on the growth environment. When the plant grows, the environment influences the growth by pulling out specific phenotypes.

Simply put, a phenotype is the plant's genotype being expressed in its appearance. 

The Phenotype Formula

A Blueberry cannabis plant generally grows purple buds outdoors, but the buds may not turn purple when you grow the same strain indoors. This is caused by the difference in temperature of both grow setups. In an outdoor garden, the low temperature can hamper chlorophyll production, and the anthocyanins in the buds produce the purple hue.

Just a quick word on anthocyanins:

Anthocyanins are nothing but water-soluble pigments responsible for the colors of many plants including cannabis. So, the purple, blue, red, and green hues on cannabis plants you see? That’s due to anthocyanins. Belonging to the class of flavonoids, they are natural compounds that also offer many therapeutic properties. 

The cannabis plant’s trichomes produce anthocyanins. Trichomes are small resinous glands found in the buds, stems, and leaves of the plant. Although trichomes are present in every cannabis plant if it’s grown well, they are found in large quantities in strains exhibiting blue or purple hues. 

Anthocyanins do much more than just make the cannabis plant look pretty — they protect the plant from environmental stresses and UV rays. Plus, they serve as antioxidants and protect the plant's cells from oxidative damage.

Apart from their protection, they offer a number of health benefits to humans including their ability to relieve inflammation and pain. However, we still need a lot of research to be done on the role of anthocyanins and how they can help humankind. 

So, coming back to phenotypes…the Blueberry strain carries a genotype or genetic information that can produce purple buds; the environment influences the color, too. So, the phenotype of an outdoor Blueberry plant is purple buds, while the same for an indoor Blueberry is green buds. 

This means that while the Blueberry strain has a genotype that can grow buds that can turn blue, only an outdoor environment influences the expression. For the outdoor plant, purple buds are the phenotype. 

You can consider the phenotype of your cannabis and how it expresses itself using this formula:

Generally, the environmental factors that affect the phenotype expression of your cannabis plant include:

As a result, an experienced grower can easily manipulate the factors mentioned above to bring out a specific phenotype in their cannabis plant. 

What is Pheno-Hunting?

What is Pheno-Hunting?

To grow the best plants based on your preferences, you must look into pheno-hunting. What is it? Pheno-hunting is nothing but the process of looking for the best cannabis phenotypes, so you can narrow down the most desirable traits. 

Pheno-hunting usually involves planting multiple seeds from a single mother plant and eliminating any plant that expresses undesirable phenotypes. Once you have narrowed down on plants with the most desired traits, you then clone them to lock in the traits. 

This practice is also beneficial if you want to breed a new strain of cannabis. Here, you can select two different cannabis plants with desirable traits, breed them, and backcross them to create a stabilized line. The resulting hybrid will contain desirable phenotypes of both parent plants. 

Note that pheno-hunting is complex and meticulous, and you need to be committed to the process. Generally, the entire process can take up to at least nine months when you grow multiple plants at the same time. 

Once you grow a few generations of clones, you then switch the plants to bloom, where you will start noticing the desirable phenotypes. 

Step-by-Step Guide on Pheno-Hunting

Pheno-hunting allows you to personalize your cannabis plant unlike you’ve ever done before, but before you even begin, you need to get a few things sorted. Start with the growing space — ensure there is enough room to grow multiple plants, and then move on to pots or containers, lighting systems, air circulation, nutrients, or other peripherals as needed. 

Next, schedule the entire process. You will be growing several generations of plants until you get the desired phenotype. You need at least nine months. Then, follow these steps.

1. Germinate the Seeds

Select the strain you want to grow and sow the seeds. Make sure you label your plants, so you know exactly what is in your garden. If you’re growing multiple strains, use their names or initials and desired phenotypes on the label along with the generation number.

For example, if you are growing Girl Scout Cookies, you can label the plants as GSC1a, GSC2a, GSC3a, and so on. For the clones, you can switch the letter "a" to "b," like GSC1b — this will help you keep track of the clones' mother plants. 

Once the seeds germinate, grow the plants as usual, and within a month or so, they will have grown big enough with true leaves — a sign that they are ready to be cloned. 

2. Clone the Plants

The next step is to clean each plant in your garden to create genetic copies of them, and you can use any method that suits you to clone them. 

But wait, isn't it too soon to clone?

Nope. Cloning at this time will ensure the clones are direct copies of their mother plants. As long as the environmental conditions are similar, the clones will grow identically to the mothers and exhibit the same phenotypes. 

Use a separate area to grow your first generation of clones, and meanwhile, let the mother plants also grow. During this time, you can even manipulate the environmental factors for the clones to check for any new phenotypes that may occur.

3. Switch the Mother Plants to Flowering

Soon enough, the mother plants will be ready to flower — switch the light cycle to 12/12 and wait for the buds to develop. Once they are ready for harvest after 8 to 12 weeks, you can take out the buds and start testing them. 

Note: when you switch to flowering, take out any plants that show male sex organs — you don't want them to pollinate your female plants at all. To avoid this, you can start with feminized seeds.

4. Check for Desired Traits in Your Clones

During this time, your clones should reach their vegetative stage. It's time to observe them and look for any traits you want in the future. You need to check the following characteristics in your clones:

  • Morphology — symmetry, the distance between the nodes, number of bud sites, height, shape, etc.
  • Training — how well do the clones fare with training methods?
  • Growing speed or vigor — do they grow fast or slow?
  • Resistance to factors like heat, humidity, pests
  • Nutrient demands 

5. Look for Desired Phenotypes

Yay! It's time to smoke a lot of doobies. While you do that, ensure you track every trait of the buds, including their flavor and aroma profiles, potency, terpene, and cannabinoid content, et al. 

6. Eliminate the Plants with Undesirable Phenotypes

Once you have tested both the mother plants' buds and clones, you must purge any plants with undesirable phenotypes. Yes, this is a difficult task — who wants to toss good cannabis plants — but it’s necessary. 

That doesn't mean you have to toss them in the trash, though. You can simply move the plants to a different grow space or give them to your friends!

7. Sow, Grow, Repeat

By now, you must have narrowed down your desired phenotype. What's next? You can create a new set of clones from the first generation clones — the second generation will be identical to the first one. Don't forget to label them!

You can also switch your first-generation clones to flowering and harvest their buds. 

If you want to further expand your scope, you can subject some clones from the first generation to different environmental conditions to check how they turn out. 

You have found the traits you desire most in a clone plant. If you want an endless supply of it, you need to keep cloning the same plant. On the other hand, if you're going to experiment with breeding, you can use the same steps mentioned above to find the desired traits in another strain. 

Once you have two clones of different strains with desired phenotypes, you can breed them. You'd have to follow these steps:

  1. Create an inbred line for each parent plant to create a line of homozygote plants — you can do this by self-pollinating the plants. This inbred line is also known as IBL. 
  2. Choose plants that perform the best and keep self-pollinating them until the plants in one generation turn out to be identical to one another. Here, you will create multiple generations of self-pollinated plants, which are referred to as S1, S2, S3, and so on. Over time, after multiple generations, the plants’ traits will be locked in. 
  3. Once you have two pure lines with locked-in traits, you can cross-breed them to create a heterozygote offspring — this is your F1 hybrid.

Do note that creating F1 hybrids is a long and meticulous process. The steps listed above only give you a rough idea of the process. If you want to create your own strain, you need to do a lot of research and take up the project only if you’re willing to spend a lot of time, effort, and money on it. 

The results will be worth it. Using this technique, you can invent a new strain that is stable and will not lose the desired traits when reproduced. Imagine having a strain that tastes like your favorite variety while having the desired THC levels of another strain!

What is Cannabis Chemotype?

What is Cannabis Chemotype?

While learning more about cannabis, you will come across not only genotypes and phenotypes but also chemotypes. What is a chemotype exactly?

Chemotype refers to the phytochemical composition of the cannabis plant (or any other living organism). For cannabis, the term is used to define the THC: CBD ratio of the plant.  

This approach was first introduced by the Canadian botanist Ernest Small, who suggested three chemotypes. But during his time, cannabis wasn't as potent as it is now, so the study didn't go anywhere. 

But in the 70s, when cannabis was potent enough for scientists to study, they applied Small's approach and solidified his suggested three chemotypes. 

Nowadays, cannabis is categorized mainly in the following chemotypes:

Type 1: THC Dominant

Type 1 chemotype is ideal for recreational users who want to get high — this chemotype is dominant in its THC content but lacks other cannabinoids like CBD. But this can often be misleading for users who choose strains with only high THC content. 

THC tends to work better with other cannabinoids and terpenes, thereby producing the entourage effect. 

Type 2: Balanced Ratio

The next chemotype has a balanced ratio of THC and CBD, which can work for both recreational users as well as medicinal users. Generally, Type 2 cannabis contains a 1:1 ratio of THC and CBD. 

Type 3: CBD Dominant

This is a chemotype that is dominant in CBD, not in THC. Due to low THC levels, this chemotype cannabis is not psychoactive, making it perfect for medicinal users who want to reap the benefits of cannabis without getting high. 

While there are three significant chemotypes for cannabis plants, researchers have also developed other chemotypes for the lesser-known cannabinoids. Here are the new chemotypes:

Type 4: CBG Dominant 

As the name suggests, this chemotype contains high levels of cannabigerol (CBG), often referred to as the mother of cannabinoids. The acid form of CBG, CBGA, is a precursor to CBD and THC, but experts are studying this cannabinoid for its anti-inflammatory benefits.

Type 5: No Cannabinoids

The latest chemotype is Type 5, which does not contain any cannabinoids at all. While it may be a disappointment for most users, cannabis with zero cannabinoid content can serve a different purpose — research and new product development. 

Expect many more chemotypes to come up in the future as experts delve further into the various lesser-known cannabinoids of cannabis. 

The Problems with the Chemotype Approach

Chemotypes are simple ways to categorize cannabis, and it only focuses on the dominant cannabinoid within a specimen. For cannabis users, this categorization is a terrific way to understand cannabis products without getting into the nitty-gritty of it. 

However, this method does not give the users any insight into the specific cannabinoid profile. A plant with 15% THC and 5% CBD and another with 5% THC and 1% CBD will be classified as Type 1 cannabis. This approach also ignores other aspects of cannabis, like the flavor profile, smoothness, aroma, etc. 

Another drawback of the chemotype approach is that it does not account for the fact that the plants may exhibit different chemical profiles even in a single strain. 

What is the solution to this problem? Chemovars. 

What are Cannabis Chemovars?

What are Cannabis Chemovars?

Cannabis chemotypes are based on cannabinoid ratios, but chemovars are something entirely different. In this approach, the classification of cannabis is a lot more detailed — it describes the dominant cannabinoids and terpenes in a cannabis specimen.

For example, a single strain like Girl Scout Cookies can have multiple chemovars, depending on the plant's genotype and environmental conditions. 

Sounds familiar? Because the "strains" we know now are based on the chemovar approach!

This approach is much more reliable for experts studying cannabis and consumers as it gives a much better insight into the cannabis varieties and their potential effects. 

For a long time, cannabis researchers have been facing a significant challenge where they could only study a single compound at a time instead of the interactions between various combinations. The chemovar approach can help experts study the varieties in more detail.

At the same time, instead of relying merely on cannabinoid ratios, cannabis users can now use chemovars to understand cannabis products better. With this approach, they can better understand cannabis, its flavor and aroma profile, and a lot more, including the entourage effect. 

But does it help a cannabis grower or a breeder? Read on to know more. 

How Does Chemovar Relate to Genotype and Phenotype?

How Does Chemovar Relate to Genotype and Phenotype?

Chemovar and chemotype may seem out of place when discussing the genotype and phenotype of the cannabis plant, but there is more to this relationship than meets the eye. And it gets complex. 

Each cannabis variety has a distinct genotype, which sets the boundaries for phenotypes. The expression of these phenotypes further depends on various environmental factors like temperature, relative humidity, nutrients, and light. 

So, when you grow cannabis plants, even if you have plants of the same genotype, they can express different phenotypes if grown in varying conditions and possess unique chemovars. 

Breeders can selectively breed cannabis plants to produce desired phenotypes as well as chemovars. Here, you need to select plants with the desired phenotypes and chemotypes and cross-breed them — the resulting offspring will have the desired traits. 

While this approach is relatively new, it is crucial for growers and breeders who want to breed new varieties of cannabis to produce the desired results. 

Summary: What are Cannabis Genotype, Phenotype, and Chemotype?

To summarize, as a cannabis grower, you must know all you can about cannabis genotype, phenotype, and chemotype. 

Cannabis genotype helps you understand the limits of cannabis varieties — a cannabis plant will never produce 25% THC if its genotype dictates it to produce only up to 20% THC. 

On the other hand, a phenotype is the expression of various traits based on environmental conditions. Two cannabis plants with identical genotypes can still produce varying phenotypes if they are grown in different environmental conditions. Pheno-hunting and cross-breeding can help you find and breed a new line of cannabis plants with the most desired traits. 

In all this, chemotype comes into play when understanding the plant's chemical makeup and potential effects. But chemotype isn't enough — you need to focus on chemovar. Chemovar helps you know the cannabinoid and terpenoid content of the varieties, helping you narrow down your search for the best plant.

Using phenotypes and chemotypes, you can grow cannabis plants that have the desired physical traits and produce the desired effects, whether you want them to get you super high or super sleepy, depending on what you are going for. 


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very informative article, thanks @NetraManjunath 🙏
Great stuff. Of the many benefits of legalization, it has allowed me to be much more meticulous about cultivation. As an outdoor grower, I've noticed over the last few years that it seems environment and technique have more influence on the end result, and genetics is kind of a starting point for whether or not you can achieve quality. Similar to the idea of terroir that is used in viticulture I guess. Seeds of the same strain from the same batch will even express themselves differently depending on the time of year they are grown.
Very interesting thank you for the article.