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I am trying to understand what exactly a phenotype is to try and understand a genetics database. (Ie I don't really know very much about genetics at all)

I've been reading through wikipedia on what a phenotype is and from what I can gather it is an observable trait which may be impacted by a specific gene.

What I would like to know is if you were looking for the presence of a phenotype such as red hair, would characteristics like not red hair and carrier of red hair also be phenotypes?

For example the following table is named Phenotype,

| Code |   Description    |
| RR   | Red Hair         | this makes sense with my understanding of phenotype
| RN   | Red Hair Carrier | this doesnt
| NR   | Red Hair Carrier | this doesnt
| NN   | No Red Hair      | this doesnt

The whole code column looks like it represents a gene not a phenotype

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up vote 5 down vote accepted

I agree with one of Alan's comments when he says:

"I think this comes down to whether you include being a carrier of a genetic "condition" a part of your phenotype. It's almost a question of semantics"

To expand on this, I would say there are two major definitions of phenotype, and both are employed by geneticists depending on the context. Definition one is a bit more naive, and I tend to use it when teaching or trying to explain phenotype to a layman: anything you can observe is a phenotype. Under this definition, having red hair is a phenotype, not having red hair (or, more directly, having black, brown, blonde, etc. hair) is a phenotype, but carrying the recessive gene for red hair is not a phenotype. I can observe without checking your genome that you do or don't have red hair, I cannot tell without checking your genome that you have one copy of the recessive gene for red hair.

Definition two is more complete, and I tend to use it more in a lab research setting: anything that is the OUTCOME of a genotype can be defined as a phenotype. Again, red hair and not red hair (meaning brown, black, blonde, etc) are outcomes defined by the genotype. However, depending on the context (let's say I'm interested in understanding heritable potential and not the color of hair) I'd say that the phenotypes would be 1) the ability to pass on red hair to progeny (outcomes of genotypes RR, RN, RN in your example), and 2) lack of ability to pass on red hair to progeny (outcome of genotype NN in your example). In both cases, the phenotype is the outcome of the underlying genes, I just have to make sure I frame my scientific context appropriately.

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I think you are correct, "phenotype" really should be what you observe, or measure in the organism, and genotype is what the underlying genetics is, either inferred, or experimentally determined.

Keep in mind, Mendelian genetics makes for great homework exercises, but there are a million more phenotypes that don't fit the Mendelian paradigm than there are ones that do. Hair color is a phenotype, but it has a lot more genetic components than the simple "one gene, two alleles, one completely dominant over the other" model that Mendel found applied to his 7 phenotypes.

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Thanks that's what I though, obviously the data is a little different to what's above but it demonstrates the point. – Luke McGregor Jan 29 '14 at 19:13

You say it yourself: The phenotype is the observable trait. So this means if you have red hairs, your hair phenotype is red. The most likely reason for it, the mutation of the melanocortin-1-receptor, is the underlying genotype. Or: The phenotype of mouse coat color is black, white, brown, speckled, whatever. That what you see, the reasons for that can be (and are) completely different between different mouse strains.

The first column of the table is the genotype and showing that red hair is a recessive trait (without naming a gene, but this doesn't matter), the second only is a representation of the first and makes actually no statement about the actual phenotype.

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Thanks that half answers what i was after, im really interested in the counter case, what shouldn't be a phenotype. I have a table in a database called phenotype which has things like carrier of red hair and no red hair these dont really match what i have read and understand a phenotype to be but its really hard to tell as ive only just read some wikipedia articles. are these phenotypes? – Luke McGregor Jan 29 '14 at 7:28
I am not sure, if I understand your problem: You are thinking about comparing red hair carrier to not red hair? Simply speaking: Hair color is a phenotype, as is skin color (or the color of your eyes). The reason for it (the genes underlying and causing your hair, eyes, skin to have the color it has) is the genotype. Can you show this table? – Chris Jan 29 '14 at 8:30
i added the table into the question, does this make a bit more sense? – Luke McGregor Jan 29 '14 at 9:17
I think this comes down to whether you include being a carrier of a genetic "condition" a part of your phenotype. It's almost a question of semantics. – Alan Boyd Jan 29 '14 at 17:04
I depends on the definition. I learned a quite strict one (actually what you see), so this doesn't fall under phenotype. – Chris Jan 29 '14 at 17:07

The table in your question is a derivative of a punnett square, which shows how different dominant Vs recessive alleles go on to inform phenotype in a logical way; In this case R is dominant red and r is recessive red.

RR = red : rr = not red : rR / Rr = carrier of red. Red is the phenotype expression (for red hair).

A carrier can pass on either the (R)ed or the (r)ed during meiosis, whereas a totally dominant (R) or totally recessive (r) will pass on just one type, to be combined with the other contributing parent chromosomes during meiosis 1. I hope this helps.

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Hmmmm... no, that is not what a Punnet square does. A Punnet square gives you the expected outcome of a specific crossing. In any case the table in the question has nothing to do with it, aside from having some genotypes written in it... – nico Jan 30 '14 at 21:07

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