A general likelihood approach to trait-based multipoint linkage analysis in large groups of half-sibs and super sisters

The idea of trait-based linkage analysis in half-sibs is extended by comparing the frequency of parental marker haplotypes in animals with different phenotypes. This article first presents the likelihood of observing different classes of paternal haplotypes in a half-sib family, where only family members of a certain phenotype (e.g., affected) are genotyped and are fully informative. The likelihood function is then generalized to multiple phenotypic categories. A linear predictor allows for discontinuous as well as for continuous phenotypes and other explanatory variables. Finally, how to incorporate not fully informative offspring and how to analyze super sister families are shown. Maximum-likelihood estimates of all parameters can be found by a Newton-Raphson algorithm, which mimics an iteratively weighted least-squares procedure. The method allows for any multilocus feasible mapping function and, among others, for situations with selective or nonselective genotyping, single or multiple traits, and continuous or categorical traits. No parameters are required to describe the mode of inheritance and the method copes with virtually any family size. Fields of applications are therefore mapping experiments in species with a high reproductive capacity, such as cattle, pigs, horses, honey bees, trees, and fish.