Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs.

ABSTRACT: A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny. It, however, overlooks the fact that the underlying likelihood function may have two maxima. The magnitudes of the maxima depend on the maternal allele frequencies at the investigated marker pair. Which maximum the algorithm converges to depends on the chosen start values. We present a stepwise procedure in which the relationship between the two modes is exploited.

SUBMITTER: Hampel A 

PROVIDER: S-EPMC5996054 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature