A two-step approach combining the Gompertz growth model with genomic selection for longitudinal data

We used the Gompertz growth curve to model a simulated longitudinal dataset provided by the QTLMAS2009 workshop and applied genomic evaluation to the derived model parameters and to a model-predicted trait value.

Prediction of phenotypic information from the Gompertz curve allowed us to obtain genomic breeding value estimates for a time point with no phenotypic records. Despite that the true model used to simulate the data was the logistic growth model, the Gompertz model provided a good fit of the data. Genomic breeding values calculated from predicted phenotypes were highly correlated with the breeding values obtained by directly using the respective observed phenotypes. The accuracies between the true and estimated breeding value at time 600 were above 0.93, even though t600 was outside the time range used when fitting the data. The analysis of the parameters of the Gompertz curve successfully discriminated regions with QTL affecting the asymptotic final value, but it was less successful in finding QTL affecting the other parameters of the logistic growth curve. In this study we estimated the proportion of SNPs affecting a given trait, in contrast with previously reported implementations of genomic selection in which this parameter was assumed to be known without error.

The two-step approach used to combine curve fitting and genomic selection on longitudinal data provided a simple way for combining these two complex tasks without any detrimental effect on breeding value estimation.