title: Constructing a linkage-linkage disequilibrium map using dominant-segregating markers.
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.
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Xuli
authors.initials: X
authors.lastname: Zhu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China.
authors.forename: Leiming
authors.initials: L
authors.lastname: Dong
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Libo
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Li
authors.affiliation: National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 10083, China Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.
authors.forename: Lidan
authors.initials: L
authors.lastname: Sun
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China.
authors.forename: Weiwu
authors.initials: W
authors.lastname: Yu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China.
authors.forename: Haokai
authors.initials: H
authors.lastname: Liu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Dai
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Zhejiang 311300, China rwu@bjfu.edu.cn yrzeng@zafu.edu.cn.
authors.forename: Yanru
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA rwu@bjfu.edu.cn yrzeng@zafu.edu.cn.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D003198:Computer Simulation; D005799:Genes, Dominant; D005819:Genetic Markers; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010944:Plants / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers
keywords: linkage; linkage disequilibrium; linkage–linkage disequilibrium map