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I get that in a single gene locus, an individual can have RR, Rr, or rr as the two alleles for that gene. R is "wild type" because it is the allele occurring most frequently. r is the allele that is not WT.

RR and Rr show dominant phenotypes, whereas rr shows the recessive phenotype.

But what's the difference between r and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where _ is a null allele, my questions are below:

  • R _ would produce the same as Rr, correct or not?
  • r _ would produce the same as rr, correct or not?
  • _ _ would produce the same as rr, correct or not?
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To add to Remi b's answer - this question is confusing because 'null' and 'recessive' are terms emerging from two very different levels of analysis. The concept of 'recessive' existed before we knew what genes were, or how they worked. It just describes the patterns of inheritance you see in a gene's effects.

The concept of a 'null' allele however came later, and explicitly describes how an allele works - by destroying gene activity. So 'null' is molecular concept, 'recessive' is an abstract genetic concept. It so happens that null alleles are very often recessive, because usually one working copy of a gene is fine. But the two terms are describing genetics at very different levels.

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    $\begingroup$ That makes sense. Why scientists don't change the nomenclature? $\endgroup$
    – Noob
    Feb 10, 2020 at 17:06
  • $\begingroup$ Because both levels of genetics are still very much in use. We often want to talk about molecules, but if we have a family tree, or an association study, or a mathematical model of inheritance, we also want to talk about the effects of mutations while remaining agnostic about the molecules. $\endgroup$
    – Dermot Harnett
    Feb 18, 2020 at 10:41
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Good question +1. Unfortunately, the mechanisms by which dominance work is relatively poorly understood and it is likely that the mechanism differs from one locus to another.

You might want to have a look at the posts

or some papers such as

I don't think one can make any general prediction about the phenotype of R_, r_ or __ without having a priori knowledge of the biological pathway (incl. allele interaction (see Llaurens et al. (2009)) and gene interaction network) by which this particular locus is affecting the phenotype. It is tempting to say that R_ is alike Rr or RR, and r_ is alike rr but this is not necessarily true.

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Basically, a recessive allele leads to formation of a product that has a low activity or no activity, which is complemented in the presence of the dominant allele (there can be effects related to dosage, in some cases). This can be easily understood in terms of an enzyme; a dominant allele would code for an enzyme with full activity whereas the recessive allele codes for one with a reduced activity. There are further complexities but this is a simple example.

A null allele however results in zero activity of the gene. This may be because of many reasons:

  • The allele may produce a non-functional protein (for e.g. an enzyme with mutated active site such that it cannot carry out the catalysis)
  • The geneic region of the allele may be transcribed but not translated (loss of ORF)
  • There may be no transcription at all (deletion of DNA sequences critical for transcription)

In cases where there is no dosage effect, a null allele is always recessive but the converse is not true.

  • R _ would produce the same as Rr, correct or not?
  • r _ would produce the same as rr, correct or not?
  • _ _ would produce the same as rr, correct or not?

The first two these assumptions are true for a simplistic case (no dosage effects). Since, r is a hypomorphic allele (by assumption) i.e. it has a reduced activity whereas _ has zero activity, _ _ may not have the same phenotype as rr. Only in cases where there is a threshold on the activity leading to phenotype, can a low activity allele/genotype (activity below threshold) lead to same phenotype as the null allele.

If we add further complexities, R _ or r _ may not be functionally equivalent to Rr or rr respectively. Even RR may behave functionally different than Rr. This would happen because of altered gene dosage (expression level) and reduced expression level of the functional product can cause a change in the net activity. (Also see: Can difference in the expression potential of alleles lead to dominance?)

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  • $\begingroup$ It is not true that a null allele is always recessive. R_ can have a different phenotype from RR if gene dosage matters. $\endgroup$
    – Jack Aidley
    May 11, 2016 at 15:37
  • $\begingroup$ @JackAidley True. I have mentioned gene dosage. I also clarified that when dosage matters then even heterozygotes would behave differently from the homozygotes. Basically the concept of dominant/recessive alleles somewhat breaks down when dosage is important. I have clarified all these exceptions. However, the null allele may still be considered recessive because the presence of R will at least partially complement it. I added a statement to explicitly mention this. $\endgroup$
    – WYSIWYG
    May 11, 2016 at 17:00

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