What's the difference between phenotype and genotype?

Phenotype and genotype are terms commonly used in the cannabis industry. Dictionary definitions of these terms may not provide a complete understanding of their roles in cannabis botany, but taking a closer look into how they each apply to the cannabis plant helps navigate the ever-changing world of breeding and cultivation.

At the basic level, the term genome refers to all of the genetic material of an organism, cell, or tissue. Coding DNA translates into proteins while noncoding DNA does not, therefore, not all DNA in the genome influences the development of an organism. Certain consequential sequences of DNA found within the entirety of an organism's genome are considered that organism's genotype. These sequences vary among individuals within the Cannabis sativa L. species.

Related plant species have similar genotypes — the more closely related the plants, the more similar their genotypes will be. When it comes to clones, the genome of one organism is copied, or cloned, meaning the two plants are the exact same genotype. Genomes are only exactly identical in the case of clones, but genotypes may be similar in the case of related organisms.

How can plants with the same genotype display different physical characteristics?

Physical differences between clones are a consequence of exposure to different environmental conditions. This is called phenotypic plasticity. In other words, it is the ability of an organism to adapt to changing conditions of light, air, water, or nutrient levels. This is especially relevant for plants because they are typically stuck in one place and forced to adapt to their surroundings.

cannabis seedling closeup
A plant's phenotype is the way it physically expresses its genetic makeup.
Photo by: Gina Coleman/Weedmaps

The way an organism physically expresses itself via its genetic makeup is its phenotype. All expressed, observable traits associated with an organism are that organism's phenotype. The phenotype is a result of selective gene expression, or the ability to turn genes on or off. Genes may turn on or off depending on environmental conditions, which alter the organism's phenotype. Terpene and cannabinoid profile, height, bud density, and leaf shape are all examples of phenotypic traits that can vary with different growing conditions, even within the same genotype.

For example, in an area with limited sunlight, a plant's leaves that were genetically predisposed to be narrow might start to grow wider and more broad to absorb as much light as possible. A clone of that exact plant, but grown in an area with a wealth of sunlight, may develop slender and more elongated leaves, as it will not need to compete so hard for the light. These plants' abilities to alter their physical traits in order to thrive in their environments is an example of phenotypic plasticity. Plasticity accounts for the physical deviations among clones, which would otherwise be identical due to their shared genotype.

The origins of different cultivars of apples (Granny Smith, Honeycrisp, pink lady, etc.) have been thoroughly documented by the farmers that first bred them. However, the lineage of even the most famous cannabis cultivars, commonly referred to as strains, can be hazy due to the lack of documentation in an industry that still maintains its roots underground.

The story of one well-reputed strain, OG Kush, is a prime example for explaining the difference between genotype and phenotype. OG Kush was bred from cannabis seeds that originated from an accidental pollination of a cultivar called Emerald Triangle by a male Hindu Kush plant. The Floridian grower then brought a cutting to Southern California in the early '90s. The cannabis he perpetuated from clones became very popular. These clones, which had identical genomes and were therefore of the same genotype, were grown in different locations across California and developed different phenotypes after exposure to their particular environments.

Successive interbreeding, while selecting for desirable traits, led each grower to develop different strains: Tahoe OG, SFV OG, Skywalker OG, etc. A grower who prefers diesel aromas, like those found in the strain Chem Dog, or the more piney aromas of Ghost OG, will select the phenotypic trait they desire. Without genetic testing it is hard to say for sure, but the assertion can be made that some of the strains with the “OG”  moniker are phenotypes of the same OG Kush genotype.

How genetic information helps growers

Temperature, humidity, lighting, nutrients, and growth media are all some of the principal influencers that are essential to control how to get the best out of a particular cultivar. However, a host of more subtle environmental conditions that are more difficult to regulate may also affect phenotypic expressions: the level of air circulation, the spectrum of light, trace gases in the air, day and night temperature fluctuations, differences in source water, and so on.

indoor cannabis cultivation
Two plants with the same genetics that grow in different environmental conditions may lead to multiple phenotypes.
Photo by: Gina Coleman/Weedmaps

The particular environmental conditions of an individual's grow room may even lead to the expression of phenotypic traits that were otherwise untapped, creating a product unique to that grower.

Growers who have received a clone from a breeder will receive a plant with the same genotype as the mother. But they will want to inquire closely about the growing conditions the breeder used to get the plant to express the desirable traits they were attracted to if they hope to grow a similar phenotype.

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The information contained in this site is provided for informational purposes only, and should not be construed as medical or legal advice. This page was last updated on September 9, 2020.