LD r^2 in clonal tetraploids

Question

[Adrian Pelin]

Hello,

I was wondering if r^2 is measured the same way in tetraploids as it is in diploids? I have what I believe is a clonal population of tetraploids but when I measure LD, it seems like average r^2 = 0.5. When I think about it, it is normal for some bi-alleic SNPs to have 4 haplotypes if the organism is indeed tetraploid, but that leads to low LD.

Adrian

[SS]

Hi Adrian,

Did you get any further information on how to calculate LD in tetraploids?

Sanjeev

[Adrian Pelin]

No not really. What I can tell you is that methods using only 2 loci don't work, since in a tetraploid you can have all 4 combinations. I had populations of spores sequenced so I ended up using MLE to get haplotype frequencies and then compute r^2 between all possible pairs of SNPs using plink.