Joint parameter estimation in the QTL mapping of ordinal traits

With the rapid development of statistical genetics, the deep researches of ordinal traits have been gradually emphasized. The data of these traits bear relatively less information than those of continuous phenotypes, therefore it is more complex to map the quantitative trait loci (QTL) of ordinal traits. In this paper, the multiple-interval mapping method is considered in the genetic mapping of ordinal traits. By combining threshold model and statistical model, we build a cumulative logistic regression model to express the relationship between the ordinal data and the QTL genotypes. In order to make the interval mapping more straightforward, we treat the recombination rates as unknown parameters, and then simultaneously obtain the estimates of QTL positions, QTL effects and threshold parameters via the EM algorithm. We perform simulation experiments to investigate and compare the proposed method. We also present a real example to test the reasonableness of the considered model and estimate both model parameters and QTL parameters. Both results of simulations and example show that the method we proposed is reasonable and effective.