Linkage disequilibrium

1. Linkage

https://online.stat.psu.edu/stat555/node/109/

Linkage refers to the probabiity that two segments of DNA are inherited together.
If the segments are on different chromosomes, then the linkage probability is 1/4.

2. Linkage equilibrium

https://online.stat.psu.edu/stat555/node/109/

Two segments are said to be in linkage equilibrium if they are inherited independently.

Under random mating without selection you would expect SNPs on different chromosomes to be unlinked. Linkage equilibrium also occurs when the segments are sufficiently distant on the same chromosome.

3. Linkage disequilibrium

https://online.stat.psu.edu/stat555/node/109/

The loci at the same chromosome have higher probability to be inherited together.

For the loci at the same chromosome:

• If there is no recombination between sister chromosomes:
  The linkage between two loci is indenpendent from the genetic distance (related to the distance within a chromosome) and the linkage equals 1.

• If there is recombination between sister chromosomes:
  The linkage between two loci is negatively correlated with the genetic distance (related to the distance within a chromosome) and ranges from 1/4 to 1.