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I am trying to determine if I can use the word strain correctly as it is presented in the dictionary as "a variety of plant occurring naturally or developed by breeding" or should strain be used only to refer to subtypes of microorganisms such as a virus or bacteria. More specifically, would I be correct if using "strain" to refer to naturally occurring variety in plants?
Yes, you would be correct in referring to a strain of a cannabis plant.
I have seen the term mostly applied to plants and microorganisms but it can also be used to describe genetically identical animals in experimental studies. Check out the Wikipedia article for strain and some of the sources in it where the term is used:
A strain is a low-level taxonomic rank used at the intraspecific level (within a species). Strains are often seen as inherently artificial concepts, characterized by a specific intent for genetic isolation.1 This is most easily observed in microbiology where strains are derived from a single cell colony and are typically quarantined by the physical constraints of a Petri dish. Strains are also commonly referred to within virology, botany, and with rodents used in experimental studies.
More specifically, see this article about cannabis where the term 'strain' is used consistently: https://www.biorxiv.org/content/10.1101/592725v1.full
The word "strain" is colloquially used to describe cannabis, but is usually not used to describe other plants. The following are common terms for differentiating plant sub-species groups which are used by horticulturists, gardeners, evolutionary scientists and farmers.
"Breeding stock" is a breeding term used to identify genetic stocks in a breeding program. Breeding stock names are typically not ones that someone outside the breeding program would be able to identify, as they are used primarily for tracking hundreds to thousands of plants. Think of these as barcodes used to keep track of plants. Examples would be names like "WA38" and "WW_2019_7"
"Cultivar" is used to describe plants that have been released from a breeding program to the used in agriculture. These are typically hybrid plants, or plants with an interesting trait that the breeder selected for.
"Variety" is a tricky term. It is used to describe breeding material once it is released to farmers in the case of most grain crops, and some major horticulture crops, but is also used to describe naturally occurring sub-species populations of plants (see below). In the case of grain, not all breeding material become varieties. To be released as a variety, the breeding stock must exhibit a trait that is desirable and unique from other already released varieties (i.e. different flavor, resistance to disease, drought tolerance, etc.). A good example of varieties at the store would be apples. There are many varieties (Cosmic Crisp, Honey Crisp, Gala, Granny Smith, etc.) but they all still belong to the same species.
"Sub-population" is typically used to describe plant sub-species in the wild. This is a term that you may see in plant evolution papers. If a population of a species of plants becomes separated for a long enough time (we are talking evolutionary time here, i.e. 10's of thousands to millions of years) they may begin to develop novel characteristics. For example, the "Rocky mountain white fur" and the "California white fur" are the same species (meaning they can mate and have viable offspring), but they have traits unique to them. These are also often referred to as varieties.
The above descriptions, while useful, are often imprecise. All describe variation within a species, but the threshold for these designation is often based on easily observable phenotypic traits (i.e. flower color, height, leaf shape, flavor) rather than actually genetic evidence. It also does not help that these words are often interchanged (sub-populations are often referred to as varieties, varieties is sometimes interchanged with cultivar). This makes these terms tricky, and you must know the context they are presented in.
For your use, you can use "strain" and people will know what you are talking about.
For other plants you might find in a garden, you can usually refer to them as "cultivar" or "variety" and people will still know what you are talking about.
These terms have developed colloquial meanings as our understanding of plants and genetics has progressed. They are imprecise by their very nature, as they are attempting to describe differences in species at the sub-species level, and are arguably only describing variation that is interesting to humans. These terms are most useful within the context of a specific discipline, where their meaning is usually more constrained.
Conifers of the Pacific Slope by Michael Edward Kauffmann