Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations

Berg Arthur, He Qiuling, Shen Ye, Chen Ying, Huang Minren and Wu Rongling
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Berg Arthur: Pennsylvania State University and Beijing Forestry University
He Qiuling: Nanjing Forestry University
Shen Ye: Nanjing Forestry University
Chen Ying: Nanjing Forestry University
Huang Minren: Nanjing Forestry University
Wu Rongling: Pennsylvania State University and Beijing Forestry University

Statistical Applications in Genetics and Molecular Biology, 2010, vol. 9, issue 1, 24

Abstract: Multiallelic markers, such as microsatellites, provide a powerful tool for studying the genetic structure and organization of an outcrossing population. However, statistical methods of analyzing multiallelic markers in current literature are limited in scope due to the complexity of the multiple alleles. We present a closed-form EM algorithm framework to estimate trigenic linkage disequilibria coefficients of three multiallelic markers and present joint and separate statistical hypothesis tests of different linkage disequilibria. Linkage disequilibria analysis with three multiallelic markers is shown to be considerably more powerful than a two marker analysis or a three marker analysis that treats the multiallelic markers as biallelic markers. A three multiallelic marker model was used to analyze marker data from Lycoris longituba, a tulip-like ornamental plant in China, where each marker consisted of two to four distinct alleles. This algorithm will be useful for studying the pattern of genetic variation for outcrossing populations.

Keywords: EM algorithm; linkage disequilibrium; multiallelic marker; natural population; trigenic disequilibrium (search for similar items in EconPapers)
Date: 2010
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DOI: 10.2202/1544-6115.1528

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