@PlantAWG Let’s talk about Plant Names!
What’s the right terminology?
What’s an ecotype?
What’s a genotype?
What’s a cultivar?
What’s a strain?
What’s a line?
What’s a mutant?
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Ecotypes are plants collected from a defined ecological region.
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Genotypes are a description of …? hmmm.
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Phenotypes describe some characteristic of the plant, which can be traced to its genotype.
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Lines are bred populations of virtually identical plants. It can refer to asexually propagated plants, or plants that reproduce by seed.
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Strains are designated groups of offspring that have similar traits. Strains can be produced through traditional breeding or by genetic mutation.
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Varieties are groupings of plants with similar characteristics that usually produce true to seed.
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Cultivars are lines that are developed and maintained by horticulturalists. These lines are not true to seed.
Let’s talk about Arabidopsis thaliana!
The most frequently grown ectoypes for spaceflight research have been: Landsberg erecta (Ler-0), Columbia (Col-0), and Wassilewskija (Ws).
We use the term Ecotype to describe each of these because they were collected from ecologically distinct communities.
When you make a mutant from a specific ecotype, you’ll want to note that as well!
What are your thoughts on this topic?
Do you have any pet peeves about naming that you want to bring up?
What happens when we start ingesting data for “Red Robin” cultivar of Solanum lycopersicum?
Genus, species, cultivar… what happens when we need to keep going?
And why do we only capitalize genus, not species?
Are there other naming conventions that we should consider when curating in the repository?
Dang, that Botanical Latin textbook sitting on my shelf at home might actually come in handy for these sorts of discussions.
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Here’s the very thorough breakdown that Sam Gerbre and Kris Peach put together for the repository.
These are all currently linked to an ontology.
Strain (default)
EFO Definition: "A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics."EFO Definition: “A population of organisms that is genetically different from others of the same species and possessing a set of defined characteristics.”
Ecotype (linked as synonym to strain in search)- EFO Definition: “A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler” * Unfortunately I can also show you publications that refer to A. thaliana Landsberg erecta (Ler) as a genotype and as a strain.
Cultivar (linked as synonym to strain in search)- EFO Definition: “A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.”
Variety (linked as synonym to strain in search)- NCIT Definition (EFO has not entry for variety): “In botanical nomenclature, a rank below subspecies but above forma.”
Accession (linked as synonym to strain in search)- EDAM Definition: A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.
Genotype (linked as synonym to strain in search)- EFO Definition: “Information, making the distinction between the actual physical material (e.g. a cell) and the information about the genetic content (genotype). The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.”
NCIT Definition: “The genetic constitution of an organism or cell, as distinct from it’s expressed features or phenotype.”
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Sorry for the late reply but am trying to get caught up on this new system. @botanynerd Are we confining this to plants only or are these definitions meant to be for a broader set of organisms? It gets dicey as you move out of plants (and animals) I think.
Great question. I was specifically attempting to address plants.
The distinctions between variety, ecotype, and cultivar were my primary concern at the time that I made this post.
@kristen.peach is probably the person who has the latest and greatest perspective on the topic. I recommend chatting with her.
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Hi @botanynerd @ben.sikes Happy to chat about this. At OSDR we describe the additional organism modifiers (variety, ecotype, strain, cultivar) using the language provided by the data submitter. For example, if the data submitter calls “Wasselewskija” an ecotype we would call it an ecotype, or if they wanted to call it a strain or a variety they could. Our protocol is to accept whatever language the data submitter used in their submission. And if the data submitter does not provide a categorization we refer to the definitions listed for each category in the ontology (posted above by Christina) to make a decision. However, as you can tell by reading the definitions they are quite fuzzy and disagreement about how to apply them is widespread (at least for plant model organisms).
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Hi, My specialization is in agriculture, and we broadly use all these terms for plants. For us, when a certain plant species contains all the basic and desired traits/ phenotypes and is fully authorized/ registered to be used publicly, it’s called a variety of that species. For strains, of the same species, if the genotypes/ phenotypes vary and show diversity, each of the diverse individual plants would be called a strain of that species. So all these strains have slightly different genotypes from each other. when we are setting up an experiment, we call each of these different strains with slightly different genotypes a ‘Line’. Cultivars are those varieties, which are legally recognized and authorized to be openly grown in the environment, after varietal registration. I hope this helps.
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