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Conclusions: In general, we observed a low statistical power (high false discovery rates and small number of significant SNPs) for non additive genetic effects compared with additive effects for both traits which could be an artefact of higher dependence on linkage disequilibrium between markers and causative mutations or smaller size of non additive effects relative to additive effects. The results of our study suggest that individual non additive effects make a small contribution to the genetic variation of milk yield and fertility. Although we found no individual mutation with large dominance effect for both traits under investigation, a contribution to genetic variance is still possible from a large number of small dominance effects, so methods that simultaneously incorporate genotypes across all loci are suggested to test the variance explained by dominance gene actions..

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