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.

A unified DNA sequence and non‐DNA sequence mapping model of complex traits

“…Tests were based on Zhu et al . 's () sparse linkage map comprising of eight linkage groups, with markers shown in group 9 being those that are unlinked with the map. Horizontal lines are the 5% critical thresholds for three models each determined from 1000 permutation tests.…”

“…These complementary advantages can be combined if linkage mapping and association analysis are unified into an organizing framework. Several studies have used this unified model to infer population history and perform QTL mapping in a variety of species, such as maize (Lu et al ., ), Euphrates poplar (Zhu et al ., ), coniferous T. grandis (Zhu et al ., ) and the canine (Liu et al . ).…”

“…The unified model contains information from both linkage and linkage disequilibrium analyses and, therefore, reduces the likelihood of spurious detection (Wu and Zeng, ). When two or more than two markers are analyzed, the unified model can simultaneously estimate the recombination fraction and linkage disequilibrium by which a linkage‐linkage disequilibrium relationship map can be constructed (Zhu et al ., , ). From such a map, we can infer the evolutionary history of each significant QTL.…”

“…Zhu et al . (, ) implemented the EM algorithm to estimate haplotype frequencies at a pair of markers from an OP family design.…”

“…Zhu et al . (, ) modified this design by capitalizing on multiallelic markers, such as microsatellites, and dominant markers for linkage analysis. Wu et al .…”