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The interaction of selection intensity, inbreeding depression, and random genetic drift on short- and long-term response to selection: Results using finite locus and finite population size models incorporating directional dominance

Department of Animal Sciences, Purdue University, W. Lafayette IN 47906

^1. Correspondence: phone: 765-494-8032; E-mail: bmuir{at}purdue.edu.

Abstract

The impact of method of calculating breeding values (best linear unbiased prediction, BLUP, vs individual performance, MASS), selection intensity, and population size on short- (Generation 5) and long-term (Generation 20) response to selection with dominant (heterotic) and additive (nonheterotic) gene action traits was examined using a gene-level simulation program that assumed a finite number of loci and a finite population size with either a completely additive or dominant type of gene action. Results showed that for additive gene action there was a short-term advantage but a long-term disadvantage of increasing selection intensity. In the short term, maximum response for both methods was achieved with a proportion selected of 5%, and selections based on BLUP were always superior to those based on MASS. In the long term, BLUP selections remained superior to MASS, but maximum response for both methods was achieved with a proportion selected of 10%. In contrast, with dominant allele effects, MASS was superior to BLUP in the short term for proportions selected of less than 10% and in the long term for proportions selected of less than 20%. With intense selection the increased accuracy of selection based on BLUP breeding values could not offset negative impacts of associated increased inbreeding. With less intense selection, the increased accuracy of BLUP selection could offset negative impacts of associated increased inbreeding. However, the differences between selection based on BLUP and on MASS breeding values were not as important as optimizing the proportion selected. With dominant gene action in the long term, with a proportion selected of 20%, the superiority of BLUP over MASS was less than 2%, both of which were at least 100% greater than that achieved with a higher selection intensity corresponding to a proportion selected of 5%. This result was due to cumulative inbreeding depression associated with the smaller effective population size with intense selection. In general, the breeding program with the greatest rate of response per unit of inbreeding will give the greatest response in the long term. Breeders should be more concerned with increasing effective population size than with the method of computing expected breeding values.