Constructing a linkage-linkage disequilibrium map using dominant-segregating markers

Xuli Zhu, Leiming Dong, Libo Jiang, Huan Li, Lidan Sun, Hui Zhang, Weiwu Yu, Haokai Liu, Wensheng Dai, Yanru Zeng, Rongling Wu

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Abstract

The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage-LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage-LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.

Original languageEnglish (US)
Pages (from-to)1-10
Number of pages10
JournalDNA Research
Volume23
Issue number1
DOIs
Publication statusPublished - Aug 2 2015

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All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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