Trilocus disequilibrium analysis of multiallelic markers in outcrossing populations

Arthur Berg, Qiuling He, Ye Shen, Ying Chen, Minren Huang, Rongling Wu

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish (US)
Article number16
JournalStatistical Applications in Genetics and Molecular Biology
Issue number1
StatePublished - 2010

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Molecular Biology
  • Genetics
  • Computational Mathematics


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