Comparing sire and dam estimates of heritability: jackknife and likelihood approaches

Three estimates of heritability are available from the half-sib pedigree design: the sire, dam and genotypic estimates. Because of its significantly smaller standard error, the genotypic estimate is preferred provided that there are no non-additive effects that inflate the estimate. I present two methods to test for such effects: these are a t-test of the paired sire and dam pseudovalues from the jackknife procedure and the likelihood ratio test from the animal model. Both methods are shown to be valid tests for significant dominance and/or maternal effects. SPLUS coding for the implementation of the jackknife method is provided. Unless sample sizes are very large, the power of the tests is low and hence caution is advised in the use of the genotypic estimate following a nonsignificant test. An approximate power analysis can be done using the data from the jackknife method but the estimated power is typically a substantial underestimate of the true power and its use is not recommended.