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When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions.

Foll and Gagiotti (2008)

Typically reading from Foll and Gagiotti (2008), they list give two examples of markers of each type

  • Codominant markers
    • SNP
    • microsatellite
  • Dominant markers
    • RFLP
    • AFLP

reddit

This reddit post indicates that RFLP are codominant markers (unlike stated in Foll and Gagiotti (2008)).

wageningenur

On wageningenur.nl (random website I never heard of before), they define dominant and codominant markers based on gene expression suggesting that the terms dominant and codominant used for markers have the same definition than those used for allelic effects on the phenotype (dominance, recessivity, overdominance, etc..).

Questions

  • What are the definitions of dominant and co-dominant genetic markers?

  • Can you please offer examples for each type and explain why they fit in one or another category?

  • Do the terms dominant and codominant have the same definition when used to describe a marker and when used to describe allelic effects on the phenotype (dominance, recessivity, overdominance, etc..)?

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  • $\begingroup$ So does it make any sense to say that SNPs are codominant while RFLP are dominant (or vice-versa)? Thanks $\endgroup$ – Remi.b May 23 '16 at 15:46
  • $\begingroup$ I don't think that would be right. RFLP is a technique which may in certain circumstances differentiate SNPs as well. It is a low resolution technique. Now SNP is just a physical feature on the DNA: it is not a phenotypic marker; more of a genotype you can say. However SNPs may be in a non-geneic region and affect the phenotype. SNPs create allelic variants (let's also consider any region that affects the phenotype as a part of the allele i.e. include the promoter/enhancer etc). These alleles can be dominant, co-dominant or recessive. It does not make sense to say SNPs are codominant. $\endgroup$ – WYSIWYG May 25 '16 at 5:14
  • $\begingroup$ I would agree but these terms I used over and over. See a search on Google Scholar with the terms "codominant dominant marker". $\endgroup$ – Remi.b May 25 '16 at 5:31
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From wikipedia

If the genetic pattern of homozygotes can be distinguished from that of heterozygotes, then a marker is said to be co-dominant.

This definition seems to be different from the one used to explain allelic effects. For example, as you would know a SNP is basically a feature of the DNA sequence. It is more of a genotype rather than a phenotype. Markers are supposed to be phenotypes (can be a molecular phenotype too for example a marker for stem cells etc). SNPs do create allelic variants but they may or may not contribute to different phenotypes. Consequently, the allelic variants may exhibit dominance or co-dominance with respect to each other. So, going by the definition used in classical genetics, you cannot call SNP as a "dominant"/"co-dominant" marker.

That is a weird usage of the terminology but people have done it so the deed cannot be undone. I would avoid future usage of such misleading terms. Having said that SNP would fit the definition of a "co-dominant marker" if it is observed by DNA sequencing .

Personally, I would consider RFLP a technique and not a marker per se. RFLP can be used to differentiate SNPs but sometimes it may not even resolve different strongly visible phenotypes (its efficacy basically depends on the polymorphism at restriction sites). Heterozygotes however, would have a different band pattern compared to homozygotes. So it should be a "co-dominant" marker.

AFLP, as far as I know is simply PCR amplification of restriction fragments. It would be "co-dominant" for the same reasons. However, just a PCR based screen would not differentiate between homozygotes and heterozygotes and would thus be a "dominant" marker. Now again, these are techniques and not, in a true sense, "markers" whereas SNPs and microsatellites are actual DNA features. So these cannot be even compared. A technique, depending on its resolution, can be "dominant" or "co-dominant" as per these definitions.


For general interest

I would want to reiterate that these definitions, for some reasons mentioned above, are quite flawed and are therefore misleading (they may have been okay at certain point of time but are obsolete now). Please avoid their usage in your papers and reports and if possible point these flaws out, so that they do not propagate.

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