Genet. Sel. Evol. 39 (2007) 39-53
DOI: 10.1051/gse:2006030

Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle

Joaquim Casellas^a, Jesús Piedrafita^a and Luis Varona<sup>b

a</sup>  Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
^b  Àrea de Producció Animal, Centre UdL-IRTA, 25198 Lleida, Spain

(Received 21 October 2005; accepted 3 July 2006 ; published online 11 January 2007)

Abstract - The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.

Key words: Bayes factor / genetic groups / beef cattle / weaning weight / Bruna dels Pirineus

Correspondence and reprints: Joaquim.Casellas@uab.es

© INRA, EDP Sciences 2006