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This question may seem illogical to some, but I seriously have this doubt. I searched google for some proofs but they were extremely complex and I couldn't understand anything.

I was just wondering whether we really have recessive allele or not? Is it like there are only dominant allele present, and when dominant allele isn't present we consider it recessive.

Is it like there is a place reserved for dominant allele and if that place is empty it turns out to be recessive.

Although this thought is vague but then if you take this example, it probably would make sense: Let's say there are two allele : T and t for tall and short respectively. Now, because TT, Tt, tT are tall, they all lead to the formation of specific hormone due to the presence of dominant allele. But the plant with genotype tt is short, hence the "extra" hormone for "excessive" tallness is missing in tt plant because the dominant gene isn't present. Can we say that that place for two allele (dominant allele) is actually empty in the plant with genotype tt?

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This is a good question. Firstly, let's get the terminology straightened out: The terms recessive and dominant are not actually used to describe genes, but rather alleles. The term allele is used for alternative forms of the same gene.(1) Many genes have two or more alleles, and some genes have alleles that can be described as dominant or recessive.

It is also useful to be familiar with the terms genotype and phenotype. Genotype refers to the form of the genetic material (DNA), while phenotype refers to the observed effect of the genotype.

Secondly, it's important to realize that the concept of "dominant" and "recessive" is a human-made abstraction. The concept of dominant and recessive genes were invented (or discovered, if you like) before we reached a good undertanding of how genetics works at the molecular level. Thus, genetics in the early days had a much cruder understanding of how different phenotypes depend on the genotype.

The dominant/recessive concept is useful in cases where there is a limited number of possible allele pairs and one or several alleles can mask the effect of other alleles. This is a very limited set of cases. Many genes have many different alleles, and it's hard to account for all of them. Many alleles also do not have a clear observable effect, in which case any "masking" effect is not prominent. To quote Wikipedia (2):

The most common basis of dominance and recessiveness is that the dominant allele codes for a functional protein and the recessive allele for a mutant, non-functional protein.

A further important point is made in the following passage:

Dominance is not inherent to an allele. It is a relationship between alleles; one allele can be dominant over a second allele, recessive to a third allele, and codominant to a fourth. Dominance should be distinguished from epistasis, a relationship in which an allele of one gene affects the expression of an allele at a different gene.

Let's consider your example: A single gene with two different alleles, T and t. Let's assume the T allele codes for a more powerful version of the growth hormone than the t allele, or that the t allele produces a non-functional hormone. Furthermore, we assume that production of the T hormone from a single allele is enough to make the plant grow tall, and that production of T or t from a second allele has no further effect. Then, we can say that the T allele masks the effect of the t allele. However, as you can probably imagine, one allele fully masking the effect of another is rather rare. So recessive/dominant allele pairs are rather the exception than the norm.

Thus, the that place for the two alleles in the genome of the plant is definitely not empty. Note that a mutation could in principle cause one of the genes to be deleted in its entirety from one of the chromosomes of the plant during reproduction. The "place" for the gene on that chromosome would then indeed be empty. This has nothing to do with how dominance and recessiveness usually works, except that a recessive gene could become expressed if the dominant allele is deleted.

So, at the molecular level there is no concept of recessive or dominant alleles. Some genes have allele pairs that can be described as dominant/recessive in relation to each other, most others do not. The effect of different combinations of alleles determines whether the relationship between the alleles is described in terms of dominant/recessive.

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Yeah, I used wrong term gene over here. Thanks. But question still remains unanswered. –  Harshal Gajjar Mar 8 at 16:42
    
OK. I'm working on a bit more elaborate explanation. –  jarlemag Mar 8 at 16:46
    
Do we seriously have recessive allele or is it just the dominant one? Is it like when dominant allele isn't present we consider it (the allele's placeholder) to be recessive. This is want I am searching for. :) –  Harshal Gajjar Mar 8 at 16:46
    
I expanded my answer. Does it answer your question now? –  jarlemag Mar 8 at 17:12
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Great answer. I sometimes wonder if the usual way Mendelian genetics is taught causes more confusion than it's worth. People don't seem to get that that paradigm is only helpful for a small percentage of our observations, even though it spawns a huge number of easy-to-grade homework assignments –  swbarnes2 Mar 8 at 22:12

I'm having real difficulty understanding the original question. We know that a diploid organism has two copies of a gene because we can sequence them, and if they are different alleles we can point to the difference in their sequences. Then through genetic crosses we can follow the two alleles and look at the association between genotype and phenotype, thus deciding on the nature of any dominance.

Also we can create a mutation in a gene by inserting another piece of DNA with its own associated phenotype (drug resistance for example). In this situation we would normally see a dominant phenotype associated with the undisrupted gene, but we would know that the recessive (disrupted) allele was also present because of the associated drug resistance. Certainly this is done all of the time in yeast genetics.

I think the problem is that you are treating genes as abstract entities in some sort of 19th century theoretical framework, disregarding over a century of genetic studies and, as @jarlemag has so eloquently explained, the physical reality of genes (as DNA sequences).

Final thought: the situation that you are describing (a "space") does exist in the special case of males for X-lined genes, where only one allele is present. This is the explanation for the genetic properties of sex-linked diseases like haemophilia.

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