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Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations

Author

Listed:
  • 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)

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.

Suggested Citation

  • Berg Arthur & He Qiuling & Shen Ye & Chen Ying & Huang Minren & Wu Rongling, 2010. "Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-24, February.
    • Handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:16
    DOI: 10.2202/1544-6115.1528
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    References listed on IDEAS

    as
    1. Li Qin & Wu Rongling, 2009. "A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-27, February.
    2. Hössjer Ola & Hartman Linda & Humphreys Keith, 2009. "Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-46, September.
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    1. Hou, Wei & Liu, Tian & Li, Yao & Li, Qin & Li, Jiahan & Das, Kiranmoy & Berg, Arthur & Wu, Rongling, 2009. "Multilocus genomics of outcrossing plant populations," Theoretical Population Biology, Elsevier, vol. 76(1), pages 68-76.

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