There is a closed population with 350 animals and no control over mating. For an association study have been picked 50 male animals from this herd. Some of detected SNPs did not appear in any individual with a heterozygous genotype. I would like to know is the inbreeding condition can be a reason for that? If so how?
Hi Mohammadfazel
maybe the SNP you detected are not really SNP, but errors due to the technique. did you test by sequencing the DNA in which you detected the SNP?
an other way would also be to dig in several database (as UCSC, http://genome.ucsc.edu) to see if what you detected is referenced somewhere.
fred
perhaps the population that you used to detect the snps is different from the population which your 52 animals came from. If there has been severe inbreeding in the 52 sample animals then they may not be representative of the whole population.
If you are measuring all snps in one amplimer using sequencing then if one primer sits over a fifth snp then you may only be amplifying one haplotype and if all of the snps are in linkage disequilibrium then you may only get one haplotype on sequencing. Sometimes in this situation you can see a small second peak in the sequencing electropherogram if the background is very low. Possibly also Frederick is correct in his answer above
Did you test if there's any deviation from Hardy Weinberg Equilibrium?
Segun
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