In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and what defines a genetic marker?

There are many different KINDS of genetic markers as defined by wikipedia, RFLP, SNP and many more. But when you click these, you get a technique not a sequence. So I'm confused as to whether markers are techniques to find DNA sequences or if they are literally DNA sequences? If they are literally DNA sequences, are they sequences that everyone has? Example of RFLP:

In molecular biology, restriction fragment length polymorphism, or RFLP (commonly pronounced “rif-lip”), is a technique that exploits variations in homologous DNA sequences.

  • $\begingroup$ Is there something missing from Wikipedia that's confusing you? en.wikipedia.org/wiki/Genetic_marker and the links on that page seem quite sufficient to me. $\endgroup$
    – Amory
    Jun 3 '15 at 13:52
  • $\begingroup$ @WYSIWYG the OP is trying :) I asked that they break their question into smaller ones and they've done so. Paze, WYSIWIG has a point though, what is it you don't understand about markers? The first line of the WP article seems clear enough: "A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species." What more do you need? $\endgroup$
    – terdon
    Jun 3 '15 at 14:07
  • $\begingroup$ I made some edits to my question. Hopefully it is clearer now. $\endgroup$
    – Paze
    Jun 3 '15 at 14:25
  • $\begingroup$ Can look ask, lf you had a genetic marker say DYS392=11 and someone else had DYS392=12 because there is only one point difference between the markers will they be related to say race or ancestry ? $\endgroup$ May 3 '18 at 9:01

As hello_there_andy (and also the Wikipedia page) has indicated, genetic markers are DNA sequences that can be used to distinguish individuals (can also be tissues, cells, etc.).

Linkage of a phenotype with genetic markers is used to identify regions of the genome that are likely causative for that phenotype, as hello_there_andy says, but there is nothing inherent to how a marker is chosen that says it has to be linked to any phenotype. Markers are typically chosen for an analysis because they are easy to measure and track, individuals differ at the locus (so you know that if your phenotype of interest segregates perfectly with the marker, it's unlikely to be chance), and they cover the genome (or the region of the genome you already know is linked) appropriately, among other things.

  • $\begingroup$ You put it concisely, but please be careful of using jargon like "Linkage", I will reward you upon replacing jargon with concrete analogies or clear definitions $\endgroup$ Jun 4 '15 at 10:13
  • $\begingroup$ @hello_there_andy I added a link to the Wikipedia page for linkage analysis. As genetic linkage is the topic of entire lectures in undergraduate genetics, I don't think I can summarize it in a few sentences, but that should be a starting point for the OP if he/she has further questions. $\endgroup$
    – blep
    Jun 4 '15 at 16:41

Genetic markers are sequences of DNA that tend to co-occur with some biological property, in a population.


E.g. Imagine you have 200 individuals in a population. 100 individuals have some sequence GGGCCCGGGCCC at some locus (position on the genome), and those 100 individuals have blue eyes. The remaining 100 individuals have AAATTTAAATTT, at the same locus and happen to have other eye colors (green, brown, etc). Then GGGCCCGGGCCC is a marker for the biological property that is "blue eyes".

Other biological properties with associated markers can include the following: (i) predisposition to having a certain disease, e.g. Alzeimers, (ii) high intelligence, (iii) and even the presence of another gene, that is you can have markers for the biological property that is "presence of gene X".

Markers of genes vs. the genes themselves

One often finds that markers for certain biological properties are the genes themselves. But this is not obvious unless one sequences the entire genomes of several individuals of a population, and doing so is expensive. It is cheaper to rely on screening for markers.

One marker to many properties, many markers to one property

You do not always have to have one marker per biological property, there may be several markers scattered across the genome that are all associated with some biological property. You can also have a marker associated with several biological properties.


A genetic marker is, by empirical definition, something that you can unequivocally place on a genetic map. A genetic marker may be an allele of a known gene that confers either a dominant, or a recessive phenotype. Alternatively, a genetic marker could be either a restriction fragment length polymorphism--whose segregation can be detected by either a Southern blot or a PCR experiment, or a single nucleotide polymorphism--whose segregation could be detected by a PCR experiment, or by DNA sequencing.

If two genetic markers segregate independently after a genetic cross the we say that they are unlinked--by which we mean they map to separate chromosomes. If two genetic markers do not segregate independently after a genetic cross (i.e., a mating) then we say they are linked--by which we mean the map to the same chromosome.

Knowing nothing about chromosomes, or DNA, it is still possible, given enough genetic markers, to construct a genetic map for an organism. All of the markers that map as if they are linked to each other are said to form a "linkage group". When there are enough genetic markers to identify all of the linkage groups then the number of different linkage groups will equal the number of chromosomes (this assumes one crossover per chromosome during meiosis).

It is important to remember that chromosomes can only be seen with a microscope, cytologically, typically after fixation, and staining, whereas linkage groups, and genetic maps, do not require, or rely on, chromosomes. A genetic map, made up of different genetic markers, is an abstraction. In some cases a genetic marker can actually be placed on the physical map of a chromosome--for example, in a species with a sequenced genome--this allows us to coordinate the genetic map with the physical map (for that locus).


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