What Is Background Ld?

Question

[Aabha]

Can anybody explain about the term "background LD" and its usefulness in in LD mapping?

Answer 1

[Genotepes]

Hi,

from what I understand, the background LD is the LD between physically distant markers that is not caused by any kind of population mixture and/or admixture.

Besically LD can be caused by :

• close physical distance between markers (hence very low recombination rate). It decays very quickly with recombination rate / physical distance.
  

• genetic mixture : arises between loci independently of their physical position, just because correlations of allele frequencies in the origin populations. For instance if two SNPs have fixed alleles in two population and the fixed alleles are the ancestral ones in the first population while the fixed alleles are the derived ones in the second population, there will be high correlation between markers (irrespective of their position) when the two populations are mixed. Not depending on recombination rate.

• genetic admixture : it is more about physically linked loci. This is basically the result of population mixture generations several generations after the mixing event (so that the LD between physically very distant SNPs is broken, but not the LD between moderately distant). Still depending on recombination rate.
  

• background LD : it is a "within population" process that extends few cM apart but at shorter distance - usually - than admixture LD. It looks similar to the admixture LD although it does not account for any kind of admixture.

This kind of LD can produce spurious population clustering results (because it looks like admixture LD).

Here is a paper that can help.

http://www.nature.com/hdy/journal/v99/n4/full/6801010a.html

Answer 2

[Damian Kao]

Basically it's the question whether genetic loci are linked because they are selected for or are they linked because they come from common ancestors. Background LD is anything that will cause spurious linkages not due to selective pressure.