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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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
StatePublished - Aug 2 2015

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Linkage Disequilibrium
Genetic Recombination
Taxaceae
Gymnosperms
Population
Meiosis
Population Genetics
Methylation
Single Nucleotide Polymorphism
China
Seeds
History

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Zhu, Xuli ; Dong, Leiming ; Jiang, Libo ; Li, Huan ; Sun, Lidan ; Zhang, Hui ; Yu, Weiwu ; Liu, Haokai ; Dai, Wensheng ; Zeng, Yanru ; Wu, Rongling. / Constructing a linkage-linkage disequilibrium map using dominant-segregating markers. In: DNA Research. 2015 ; Vol. 23, No. 1. pp. 1-10.
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Zhu, X, Dong, L, Jiang, L, Li, H, Sun, L, Zhang, H, Yu, W, Liu, H, Dai, W, Zeng, Y & Wu, R 2015, 'Constructing a linkage-linkage disequilibrium map using dominant-segregating markers', DNA Research, vol. 23, no. 1, pp. 1-10. https://doi.org/10.1093/dnares/dsv031

Constructing a linkage-linkage disequilibrium map using dominant-segregating markers. / Zhu, Xuli; Dong, Leiming; Jiang, Libo; Li, Huan; Sun, Lidan; Zhang, Hui; Yu, Weiwu; Liu, Haokai; Dai, Wensheng; Zeng, Yanru; Wu, Rongling.

In: DNA Research, Vol. 23, No. 1, 02.08.2015, p. 1-10.

Research output: Contribution to journalArticle

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T1 - Constructing a linkage-linkage disequilibrium map using dominant-segregating markers

AU - Zhu, Xuli

AU - Dong, Leiming

AU - Jiang, Libo

AU - Li, Huan

AU - Sun, Lidan

AU - Zhang, Hui

AU - Yu, Weiwu

AU - Liu, Haokai

AU - Dai, Wensheng

AU - Zeng, Yanru

AU - Wu, Rongling

PY - 2015/8/2

Y1 - 2015/8/2

N2 - 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.

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