Use of reproductive technology to estimate variances and predict effects of gene interactions

Advanced reproductive techniques are creating the large numbers of close relatives needed to study gene interactions. Identical triplets, a set of 26 full sisters, a family of 4215 three-quarter sisters (same sire and maternal grandsire), a family of 76,698 half sisters, and 1.6 million granddaughters of Round Oak Rag Apple Elevation now have lactation records. Similarity of closest relatives might be explained by similar nonadditive as well as additive genetic merit. The 23,015 families of full sisters with mean family size of 3 provide nearly as much information about dominance variation as do the 55,779 families of three-quarter sisters with mean family size of 13; the 79 families of clones provide little information by comparison. Hypothetically, REML analysis of all US Holstein data could provide estimates of dominance and additive x additive variance with standard errors approximately 1% of phenotypic variance, but estimates of any higher order interactions would have standard errors greater than 10%. The tilde-hat approximation proved to be incompatible with animal models but was used for sire-maternal grandsire analysis of 765,868 first lactation records. Dominance variance was estimated as 3.5% of phenotypic variance for milk and 3.3% for fat with standard error of 4.2%. With constant data set size, variances are estimated most precisely if family sizes equal 1 plus ratio of within-family to between-family variance. An animal model evaluation including dominance relationships for 581,670 animals was computed, but gene interactions from distant ancestor pairs were ignored. Mating advice and improved additive predictions, especially for clones, could be obtained by including dominance in models.