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Linkage disequilibrium under polysomic inheritance.

Kang Huang1,2, Derek W Dunn1, Wenkai Li1

  • 1Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China.

Heredity
|January 5, 2022
PubMed
Summary
This summary is machine-generated.

This study extends linkage disequilibrium (LD) measures to polyploids, enabling effective population size (Ne) estimation in diverse organisms. Results show polyploid Ne estimation requires similar sample sizes and loci as diploids.

Keywords:
Effective population sizeLinkage disequilibriumMating systemPolysomic inheritanceRecombination frequency

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Area of Science:

  • Population genetics
  • Genomics
  • Quantitative genetics

Background:

  • Linkage disequilibrium (LD) describes non-random allele associations at different genetic loci.
  • Current LD methods are limited to diploid organisms.
  • LD is crucial for gene mapping and effective population size (Ne) estimation.

Purpose of the Study:

  • To extend LD measures to include polysomic inheritance in polyploid organisms.
  • To derive equilibrium values for LD coefficients (r² and [Formula: see text]) under various mating systems and ploidy levels.
  • To assess the feasibility of estimating Ne in polyploids using unphased genotypes.

Main Methods:

  • Derivation of equilibrium LD coefficients for polysomic inheritance.
  • Mathematical modeling for monoecious and dioecious mating systems.
  • Simulation of Ne estimation using unphased genotypes in polyploids.

Main Results:

  • Developed extended LD measures applicable to polyploids.
  • Derived formulas for LD equilibrium under different ploidy levels and mating systems.
  • Demonstrated that Ne estimation in polyploids requires comparable sample sizes and loci to diploids.
  • Identified using 0.5 for recombination frequency as a primary source of bias in Ne estimation.

Conclusions:

  • The extended LD measures provide a framework for analyzing population genetic structure in polyploids.
  • Ne estimation in polyploids is feasible with similar genomic data requirements as in diploids.
  • Accurate recombination frequency values are essential for reliable Ne estimation in polyploid populations.