Exact Distribution of Linkage Disequilibrium in the Presence of Mutation, Selection, or Minor Allele Frequency Filtering

Frontiers in Genetics

Rohan L. Fernando¹  Jiayi Qu²  Hao Cheng²  Stephen D. Kachman³  Dorian Garrick⁴ 

[1] Department of Animal Science, Iowa State University, Ames, IA, United States;Department of Animal Science, University of California, Davis, Davis, CA, United States;Department of Statistics, University of Nebraska Lincoln, Lincoln, NE, United States;School of Agriculture, Massey University, Wellington, New Zealand;

关键词: linkage disequilibrium;    effective population size;    mutation rate;    selection;    minor allele frequency filtering;   

DOI  :  10.3389/fgene.2020.00362

来源: DOAJ

【 摘 要 】

Linkage disequilibrium (LD), often expressed in terms of the squared correlation (r2) between allelic values at two loci, is an important concept in many branches of genetics and genomics. Genetic drift and recombination have opposite effects on LD, and thus r2 will keep changing until the effects of these two forces are counterbalanced. Several approximations have been used to determine the expected value of r2 at equilibrium in the presence or absence of mutation. In this paper, we propose a probability-based approach to compute the exact distribution of allele frequencies at two loci in a finite population at any generation t conditional on the distribution at generation t − 1. As r2 is a function of this distribution of allele frequencies, this approach can be used to examine the distribution of r2 over generations as it approaches equilibrium. The exact distribution of LD from our method is used to describe, quantify, and compare LD at different equilibria, including equilibrium in the absence or presence of mutation, selection, and filtering by minor allele frequency. We also propose a deterministic formula for expected LD in the presence of mutation at equilibrium based on the exact distribution of LD.

【 授权许可】

Unknown