Estimation of Linkage Disequilibria in Diploid Populations with Multilocus Dominant Markers

Analysis of population structure and organization with DNA-based markers can provide important information regarding the history and evolution of a species. Linkage disequilibrium (LD) analysis based on allelic associations between different loci is emerging as a viable tool to unravel the genetic basis of population differentiation. In this article, we derive the EM algorithm to obtain the maximum likelihood estimates of the linkage disequilibria between dominant markers, aimed to study the patterns of genetic diversity for a diploid species. The algorithm was expanded to estimate and test linkage disequilibria of different orders among three dominant markers \textcolor{red}{and can be technically extended to manipulate an arbitrary number of dominant markers. The algorithm is validated by a real example for population genetic studies of hickory trees, native to the southeastern China, using dominant markers.} Extensive simulation studies were performed to investigate the statistical properties of this algorithm. \textcolor{red}{The precision of our estimates of linkage disequilibrium between dominant markers were compared between that between codominant markers.} Results from simulation studies suggest that three-locus LD analysis can increase the power for LD detection as compared with two-locus LD analysis. The algorithm will be useful for studying the pattern and amount of genetic variation within and among populations.

Key Words: Codominant Marker, Dominant Marker, EM algorithm, Linkage Disequilibrium, Natural Population

Online ISS 1091-6490
Copyright 2008 by the Genetics Society of America
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