How important is it to determine linkage in a set of microsatellite markers? I am using a set of markers developed from a closely related species. The ssr markers were gleaned out of genomic sequence via algorithm, but as far as I know the genome has not been annotated to chromosomes or scaffolds.
I have 20-24 markers that work on my organism but I am wondering how important it is to determine linkage in these markers.
I should add that these markers will be used to determine population diversity.
@Vicky:
It will be nice to know that your 20 to 24 ssr loci are actually spread evenly in every chromosome. However, for genetic diversity, it should not be a requirement to know the chromosome location of the evaluated ssr loci.
For the genetic diversity analysis, you should consider to use ssr loci having more alleles per ssr locus and having alleles that are easy to score. Therefore, you should do primer selection first to identify ssr loci having as many easily readable alleles as possible.
If it is possible, use as many such ssr loci as possible. Otherwise, use as many as twice the number of n haploid chromosomes. Assuming your loci is distributed randomly among the chromosomes, you will evaluate two loci for each chromosome.
However, the final decision depend on your available resources since the more ssr loci you evaluate, the more funding you will require. Good luck
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