Home > Agriculture, Genomic Selection, Linux, phasing, Shell, SNP > Evolutions of LD across generation

Evolutions of LD across generation

A classical way to present LD is ploting LD structure (with e.g. Haploview) anyway, while giving us a good overview of the LD in a certain population, this does not give any hints on how this structure evolve across generations.

So I decided to write for fun a little script, looking over 50 non overlapping generations the LD plot obtained by Haploview.

The population contain 1000 individuals per generation. The marker map have 100 markers spanning 7cM.

I then split my simulated genotypes file according to generations. And for each of them generate a LD plot.

And last but not the least I merged all the plot to obtain an animated gif with ImageMagick.

And here is the result !

A very funny thing is to see how fast some SNP are fixed (I made no assumption on MAF in founders population). I tested several scenario, with varying selection pressure . The one used here is rather simple :

  • Generations 1 to 5 use 100 males 500 females,
  • Generations 6 to 10 use 50 males/250 females,
  • Generations 11 to 15  10 males/200 females,
  • Generations 16 to 50  20 males/200 females.

While no LD is supposed at generation 1, we can see pretty fast that LD is created, and once pattern are observed they remain stable for a while.

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