QMSIM

QMSim simulates large-scale genotyping data within complex livestock pedigrees to model genetic architectures and population structures for genetic and breeding studies.

Key Features:

• Two-step simulation process: Simulation is divided into a historical population phase that establishes mutation-drift equilibrium and a recent population phase that generates complex contemporary population structures.
• Versatile genome architectures: Supports genome models ranging from infinitesimal models to single-locus models to represent different genetic hypotheses.
• Efficiency: Optimized for computing time and memory usage to enable large-scale data simulations.

Scientific Applications:

• Genetic architecture studies: Enables exploration of single-gene effects through polygenic traits influenced by numerous loci.
• Population genetics research: Simulates historical and recent dynamics to study mutation, drift, linkage disequilibrium (LD), bottlenecks, and expansions on genetic diversity.
• Breeding program optimization: Predicts outcomes of breeding strategies and simulates potential genetic gain or loss over generations.

Methodology:

QMSim performs a two-step computational simulation: (1) historical population simulation to reach mutation-drift equilibrium and (2) generation of recent population structures reflecting contemporary pedigree and breeding processes.