Genomic estimated breeding values were calculated in the same way except that SNP genotypes rather than QTL genotypes, and predicted genotypic effects were used.
We assume a diallelic marker with allele A1 with frequency p, and allele A2 with frequency 1 − p = q, and genotypes A1A1, A1A2 and A2A2 with genotypic effects a, d and − a, respectively, (Fisher 1918; Falconer and Mackay 1996).
The genotypic effects of rs11641468 varied with the genotypes of rs2239301 (Additional file 1, Figure S6).
Diploid SNP genotypes were then sampled for each individual, and genotypic effects of 0, α or 2α were assigned to individuals with zero, one or two copies of the first SNP allele, respectively.
Each individual's genotypes for the 37 SNPs were tested for additive genotypic effects.
For the analysis of genotypic effects at each SNP, the common allele homozygous genotype was selected as the comparison group.
We found that pathogen genotype and inoculation day had significant effects on infection efficiency but that host genotype and the interaction term for pathogen and host genotypic effects were not significant (Table 3).
Genotypic effects influenced the TRL development over the growing season, and genotypes of subspecies fastigiata had greater TRL deep in the soil profile.
As exploratory analyses, the role of genotypic effects across various high-risk subgroups was examined both with stratified analyses and by fitting interaction terms into the regression models.
Test for allelic association and genotypic effects was calculated for all three Scandinavian samples separately and combined using a standard chi squared test.
Furthermore, environmental variation may also modify genotypic effects.
