We ran a GWAS on farm animals using thousands of individuals and a QTL was found for a specific trait (complex trait).
But I know it is not so easy fine mapping the causative mutation(variation) due to the density of chips(only 50K, for the animals not so dense like human chips).
And next, we resequenced several genes in this QTL-genomic region(3 Mb) just using a DNA panel (16 individuals) and hundreds of SNPs were detected.
Finally, only a few missense SNPs were selected and typed but non-significant.
Now, I am concentrating on one gene which the two most significant markers are within one of introns, we genotyped the unique missense mutation (non-significant) and 1 promoter SNP which highly linked with the second top marker and of course it is significant but have't reach the higher level compared top marker.
So we propose this promoter SNP is not the causative one and we have to continue seeking.
I knew it is hard to find a true causative mutation but we might quite close. Thus the next step we may select some of putative SNPs for genotyping and I am still confusing about it.
Someone who works for GWAS especially animals can give some hint or better ideas to do it well.
Thanks a million.