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Journal of Animal Science, Vol 76, Issue 9 2263-2271, Copyright © 1998 by American Society of Animal Science

JOURNAL ARTICLE

A bootstrap approach to confidence regions for genetic parameters from Method R estimates

A. Reverter, C. J. Kaiser and C. H. Mallinckrodt
Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, Australia.

Confidence regions (CR) for heritability (h2) and fraction of variance accounted for by permanent environmental effects (c2) from Method R estimates were obtained from simulated data using a univariate, repeated measures, full animal model, with 50% subsampling. Bootstrapping techniques were explored to assess the optimum number of subsamples needed to compute Method R estimates of h2 and c2 with properties similar to those of exact estimators. One thousand estimates of each parameter set were used to obtain 90, 95, and 99% CR in four data sets including 2,500 animals with four measurements each. Two approaches were explored to assess CR accuracy: a parametric approach assuming bivariate normality of h2 and c2 and a nonparametric approach based on the sum of squared rank deviations. Accuracy of CR was assessed by the average loss of confidence (LOSS) by number of estimates sampled (NUMEST). For NUMEST = 5, bootstrap estimates of h2 and c2 were within 10(-3) of the asymptotic ones. The same degree of convergence in the estimates of SE was achieved with NUMEST = 20. Correlation between estimates of h2 and c2 ranged from -.83 to -.98. At NUMEST < 10, the nonparametric CR were more accurate than parametric CR. However, with the parametric CR, LOSS approached zero at rate NUMEST(-1). This rate was an order of magnitude larger for the nonparametric CR. These results suggested that when the computational burden of estimating genetic parameters limits the number of Method R estimates that can be obtained to, say, 10 or 20, reliable CR can still be obtained by processing Method R estimates through bootstrapping techniques.


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