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Open Access Open Badges Methodology article

Generalized linear mixed model for segregation distortion analysis

Haimao Zhan and Shizhong Xu*

Author affiliations

Department of Botany and Plant Sciences, University of California, Riverside, CA 92521

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Citation and License

BMC Genetics 2011, 12:97  doi:10.1186/1471-2156-12-97

Published: 11 November 2011



Segregation distortion is a phenomenon that the observed genotypic frequencies of a locus fall outside the expected Mendelian segregation ratio. The main cause of segregation distortion is viability selection on linked marker loci. These viability selection loci can be mapped using genome-wide marker information.


We developed a generalized linear mixed model (GLMM) under the liability model to jointly map all viability selection loci of the genome. Using a hierarchical generalized linear mixed model, we can handle the number of loci several times larger than the sample size. We used a dataset from an F2 mouse family derived from the cross of two inbred lines to test the model and detected a major segregation distortion locus contributing 75% of the variance of the underlying liability. Replicated simulation experiments confirm that the power of viability locus detection is high and the false positive rate is low.


Not only can the method be used to detect segregation distortion loci, but also used for mapping quantitative trait loci of disease traits using case only data in humans and selected populations in plants and animals.