Genetic markers in casein (CSN1S1) and thyroglobulin (TG) genes have previously been associated with fat distribution in cattle. Determining the nature of these genetic associations (additive, recessive, or dominant) has been diffi cult, because both markers have small minor allele frequencies in most beef cattle populations. This results in few animals homozygous for the minor alleles. Selection to increase the frequencies of the minor alleles for 2 SNP markers in these genes was undertaken in a composite population. The objective was to obtain better estimates of genetic effects associated with these markers and determine if there were epistatic interactions. Selection increased the frequencies of minor alleles for both SNP from0.10). Additive, dominance, and epistatic SNP association effects were estimated from genotypic effects for adjusted fat thickness and predicted meat tenderness. Adjusted fat thickness showed a dominance association with TG SNP (P \u3c 0.06) and an epistatic additive CSN1S1 Γ additive TG association (P \u3c 0.03). For predicted meat tenderness, heterozygous TG meat was more tender than meat from either homozygote (P \u3c 0.002). Dominance and epistatic associations can result in different SNP allele substitution effects in populations where SNP have the same linkage disequilibrium with causal mutations but have different frequencies. Although the complex associations estimated in this study would contribute little to within-population selection response, they could be important for marker-assisted management or reciprocal selection schemes
