Hi All

I am running GWAS in maize population which was tested under water stress. I found that the many significant markers are heterozygous which has three alleles (e.g. C, T, C:T). Do these marker provide spurious assoication as there are three alleles?.

Another point can be also detected in allele effects. some of markers have two alleles with negative sign and the other is positive such as (C= -1.5, T= - 2, T:C=0|). So, which one should considered to increase the trait. I think such marker is not useful for marker-assisted selection and design promising markers via KASP.

Some studies dealt with heterozygous loci as missing and then filter markers again to avoided rara alleles. In my case, I did the same thing, I will lose many markers after filtering.

what do your recommend? proceed the GWAS with heterozygous loci or treating them as missing data.