Association test between haplotypes and longitudinal traits in complex pedigrees

Evaluating the association of candidate genes with longitudinal traits would be a useful method to study the genetic basis of complex traits. Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNP, and have been considered as a more informative format of data in association analysis. In this study, we extended the random regression model to allow analysing haplotype effects in a longitudinal framework and then performed a hierarchical Bayesian method to estimate parameter values. We assessed the performance of the proposed approach and demonstrated its validity and power with simulation. The power of our method was also demonstrated by an example of Meishan pigs, in which one haplotype affecting the total number of piglets born was detected using our method, whereas it cannot be detected using the conventional single SNP-based model. Additionally, the model is flexible to be extended to model a complex network of genetic regulation that includes the interactions between different haplotypes and between haplotypes and environments.