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G1 and G1' are an allelomorphic pair, so their interaction would fall under dominance, overdominance or underdominance.
Thus, a secondary objective of this study was to compare BSAM to the additive model under dominance when SNP effects must be estimated.
Under dominance and without retraining, genomic selection based on the dominance model is superior to the additive model and the breed-specific allele model to maximize crossbred performance through purebred selection.
The analysis including the main child and maternal effects from locus 1, a main effect from locus 2 and the two-locus M×O and M×M interactions under dominance or codominance will be referred to as a full model, while the analysis restricted to a subset of these effects will be referred to as a reduced or restricted model.
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However, over- and under- dominance is a rare phenomenon in GAS [ 6].
If the fitness of the complete network was lower than the average of the homozygotes (e.g. if the dominant allele was deleterious) the effect was counted as under-dominance (see below).
The collapse of hybrid fitness is caused by both under-dominance and epistatic incompatibility.
The one-sided z-test for under-dominance (h < -1 or k < 0or) is statistically significant (P = 0.02).
In the model, under-dominance and epistatic incompatibility both contribute to the observed collapse in hybrid fitness.
Otherwise, dominance (including over- and under-dominance) is present and the direction of dominance depends on the value of h.
We calculated the relative strength of the effects of dominance, over-dominance and under-dominance; see Methods for details on the calculation of each of these effects.
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