Using LDhat with genotyping by sequencing data and isolated populations

[dosshra]

Hello.
I plan to use LDhat to estimate recombination rate along the chromosomes wild wheat which is a selfer species. The data is composed of ~400 genotypes sampled from ~100 isolated collections sites and genotyped with ~6000 SNP per chromosome. The genotyping was done using restriction enzymes reduced representation libraries (GBS). Therefore, it does not include all of the sequence variation along the chromosome. I have two concerns about violating the assumptions of the analysis:

1. The SNP represent just a small fraction of the actual diversity along the chromosomes. Will it bias the results?
2. The genotypes were collected from isolated sites , dose this violates the analysis assumptions?
   Thank you