I do not seem to understand the concept of Quantitative Trait Loci(QTL's), can anyone explain it to me in detail? Reading the wikipedia article helped somewhat, but I do not understand it well.

What I understand:

-quantitative traits = a number(quantity) of phenotypes(traits) that vary

-To "make" a QTL, one must "map" the phenotypical traits to the genes that they are believed to propagate.

-This is done by AFLP-PCR, or Amplified fragment length polymorphism, according to wikipedia at least. This process cuts the genomic DNA into pieces and then amplifies the target region with primers via PCR. Then it is visualized using some type of gel technique?

-I am not sure how this gel data then allows the mapping of phenotypes to genes. I know gel electrophoresis can help to identify the length of a gene or region of a gene if using a ladder to compare.

  • $\begingroup$ I would disagree with your definition of "quantitative traits" and instead describe it as traits that are quantiative instead of qualitative. Eg, height is a quantitative trait whereas presence or absence of hairs is a qualitative trait $\endgroup$
    – C_Z_
    Apr 24, 2015 at 15:17

1 Answer 1


When we say that something is a genetic marker we mean that we can establish its linkage to a chromosome AND that we have some way of discerning, or detecting, how the marker has segregated after meiotic recombination (this definition is only valid for diploid species that undergo sexual reproduction).

So, for example, in the fruit fly, Drosphila melanogaster, the white gene is linked to the X chromosome. Wild-type flies have red eyes, a mutation in the white gene yields flies with white eyes. You can use genetic crosses (matings) to (a) show that the white gene is linked to only one of the four fly chromosomes, and (b) if you have other genetic markers on that chromosome you might be able to construct a genetic map showing the order and distance of the linked genes.

You can also use a DNA fragment from a chromosome as a genetic marker--if you have an assay that lets you track the fragment after meiotic recombination. A Southern blot, using a labeled probe is one way to accomplish this (e.g. a Restriction Fragment Length Polymorphism or RFLP). PCR that lets you detect a RFLP or a SNP serves the same function, and is much quicker than a Southern Blot (and requires less DNA starting material).

A QTL is just one of these "molecular" genetic markers that shows linkage to the trait you are assaying. So, for example, if you had RFLPs or SNPs sprinkled all along the human chromosomes, and if you had a way to detect the segregation of all those markers after meiotic recombination, then you could use DNA from a family with lots of kids of varying heights, where one parent was tall, and the other parent was short, to see if any of your genetic markers were segregating, or linked to the phenotype of height in the children (this example assumes that height in humans is a quantitative trait).

  • $\begingroup$ If I may paraphrase you a bit, so the concept of a genetic marker is valid only for organisms that can do crossing over, or meiosis, since crossing over events allow for exchange of genetic material, and the closer a gene for a trait lies on a chromosome, the tighter the linkage will be. This means then that when looking for a genetic marker, we are looking at linkage? And also, therefore QTL's are simply a type of genetic marker, an gene in the chromosome to be studied for linkage to a chromosome? And then this is done by adding a probe that would fluoresce when examined? $\endgroup$
    – Ro Siv
    Apr 25, 2015 at 1:35
  • $\begingroup$ Haploid organisms, like bacteria, and their viruses also have genes and DNA, and therefore have genetic markers. It is just that they don't have meiosis. You can still construct genetic maps, I was just trying to be precise. I think your understanding is correct. There are only two things to emphasize. The QTL is probably not the gene you are interested in, it is probably not even a gene, it is a proxy for the gene, because it is a hopefully tightly linked marker; you would still have to do further work to find the gene. Also you may want to ask how a Southern blot works. $\endgroup$
    – mdperry
    Apr 25, 2015 at 1:50
  • $\begingroup$ Thank you, i think I know how a southern blot works, but do you have any suggestions for a image that would sum up the concept of QTL? I feel like learn better from images in general. Also as an aside, cant bacteria do some type of homologous recombination, i remember reading about it but maybe it was just my imagination. $\endgroup$
    – Ro Siv
    Apr 25, 2015 at 5:10
  • $\begingroup$ @RoSiv Yes they can, for example a phage genome can be integrated in the bacterial genome through recombination. This is done through recombination att-loci (att for attachment). Of course this is only one example. en.wikipedia.org/wiki/Site-specific_recombination $\endgroup$
    – Wolgast
    Apr 25, 2015 at 6:27

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