Testing candidate gene effects on milk production traits in dairy cattle under various parameterizations and modes of inheritance

Graphical representation of simulated effects of SNP for various modes of inheritance when . Left diagram: additive mode of inheritance (Am); additive and dominance mode of inheritance (ADm). Right diagram: additive mode of inheritance with pairwise additive-by-additive epistasis.

Coverage of the simulated additive SNP effect by the estimated 95% confidence intervals for the 5 simulated SNP. Black circles represent SNP with no epistatic relationship; gray circles represent SNP with epistatic relationship. The samples of 250 individuals were generated under the true (simulated) ADEm mode. (A) Graphs relate to the additive SNP effect of ; (B) graphs relate to the additive SNP effect of . Am=additive mode; AEm=additive-by-additive epistases; ADm=additive and dominance mode; ADEm=additive and dominance mode with pairwise additive-by-additive epistases. See main text for definitions of parameterizations (Cp, KZ_∞p, AC₁p, and AC₂p).

Estimates and 95% confidence intervals of additive effects of SNP marking butyrophilin (BTN1A1), DGAT1 (diacylglycerol acyltransferase 1), LEP (leptin), and LEPR (leptin receptor) genes. For each gene, the 2 dots in the same color represent effects based on additive mode of inheritance (left dot) as well as on additive and dominance mode with pairwise additive-by-additive epistases (right dot) estimated with AC₁p parameterization (see main text for definition). Grey dots represent Holstein-Friesian cows; black dots represent Jersey cows. Estimates were multiplied by (−1) to retain correspondence with other parameterizations.