Genetic Recombination

Chris Gaynor

2025-09-04

This article provides an overview of the biology of genetic recombination and how it is modeled within AlphaSimR. I will first provide a brief review of meiosis with special emphasis on how process differs between diploid and autopolyploid species. I will then discuss genetic maps before concluding with an overview specific models used to simulate genetic recombination.

Meiosis

Usual process of diploids, two copies of each chromosome, one from mother and one from father

Chromosome doubling, sister chromatids

Chromosome pairing in meiosis I, bivalent pair or tetrad

Chiasma form which may result in crossovers

Homologous pairs split

Sister chromatids split in meiosis II to produce haploid

Meiosis in Polypoids

There are two primary types of polyploids: autopolyploids and allopolyploids.

Allopolyploids, such as wheat, have multiple genome copies that come from different species.

Meiosis and recombination proceeds similarly to diploids.

Autopolyploids have multiple copies of the same genome. This

Genetic Maps

Recombination Models

Recombination Models in Autopolyploids

Introduction including basic details of inheritance

Review meiosis Stages of meiosis Chromosome pairing Chiasma (crossovers) Crossover interference Segregation Diploids first and then polyploids Centromeres for polyploids

Review genetic maps Development of maps in Morgan’s fly lab Haldane mapping function Kosambi mapping function

Recombination models Count-location model Gamma model Gamma sprinkling model

Recombination tracking in AlphaSimR