Genetics Research

Paper

Radial basis function regression methods for predicting quantitative traits using SNP markers

NANYE LONGa1 c1, DANIEL GIANOLAa1a2, GUILHERME J. M. ROSAa2, KENT A. WEIGELa2, ANDREAS KRANISa3 and OSCAR GONZÁLEZ-RECIOa4

a1 Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA

a2 Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA

a3 Aviagen Ltd, Newbridge, Midlothian EH28 8SZ, UK

a4 Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain

Summary

A challenge when predicting total genetic values for complex quantitative traits is that an unknown number of quantitative trait loci may affect phenotypes via cryptic interactions. If markers are available, assuming that their effects on phenotypes are additive may lead to poor predictive ability. Non-parametric radial basis function (RBF) regression, which does not assume a particular form of the genotype–phenotype relationship, was investigated here by simulation and analysis of body weight and food conversion rate data in broilers. The simulation included a toy example in which an arbitrary non-linear genotype–phenotype relationship was assumed, and five different scenarios representing different broad sense heritability levels (0·1, 0·25, 0·5, 0·75 and 0·9) were created. In addition, a whole genome simulation was carried out, in which three different gene action modes (pure additive, additive+dominance and pure epistasis) were considered. In all analyses, a training set was used to fit the model and a testing set was used to evaluate predictive performance. The latter was measured by correlation and predictive mean-squared error (PMSE) on the testing data. For comparison, a linear additive model known as Bayes A was used as benchmark. Two RBF models with single nucleotide polymorphism (SNP)-specific (RBF I) and common (RBF II) weights were examined. Results indicated that, in the presence of complex genotype–phenotype relationships (i.e. non-linearity and non-additivity), RBF outperformed Bayes A in predicting total genetic values using SNP markers. Extension of Bayes A to include all additive, dominance and epistatic effects could improve its prediction accuracy. RBF I was generally better than RBF II, and was able to identify relevant SNPs in the toy example.

(Received May 25 2009)

(Revised March 06 2010)

Correspondence:

c1 Corresponding author. Nanye Long, Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA. e-mail: nlong@wisc.edu

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