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AlphaSim: Software for Breeding Program Simulation.

Anne-Michelle Faux, Gregor Gorjanc, R Chris Gaynor

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    AlphaSim is a flexible software for simulating plant and animal breeding programs. It enables in silico comparison of breeding technologies, enhancing efficiency and reducing costs.

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    Area of Science:

    • Plant and animal breeding
    • Quantitative genetics
    • Bioinformatics

    Background:

    • Breeding programs require sophisticated tools for simulation and optimization.
    • Evaluating new breeding technologies in silico is crucial for efficiency and cost-effectiveness.

    Purpose of the Study:

    • To describe AlphaSim, a flexible software package for simulating plant and animal breeding programs.
    • To highlight AlphaSim's capabilities in integrating advanced biotechnologies and diverse breeding strategies.

    Main Methods:

    • AlphaSim simulates breeding programs through sequential steps including haplotype and pedigree simulation, QTN effect assignment, phenotype simulation, and multi-generational selection.
    • The software allows flexible parameterization of population structure, trait architecture, and selection strategies.
    • It integrates doubled-haploids, gene editing, genomic predictions, and optimal contribution selection, with restart functionalities for user convenience.

    Main Results:

    • AlphaSim provides a flexible platform for simulating complex breeding programs with variable structures and decisions over time.
    • The software supports the simulation of multiple traits, environments, and advanced genetic features like recombination hotspots and gene deserts.
    • It facilitates in silico comparison of biotechnology-enhanced breeding programs.

    Conclusions:

    • AlphaSim is a computationally efficient software package for simulating advanced breeding programs.
    • It enables rapid, low-cost, and objective in silico evaluation of breeding technologies and strategies.
    • The software's flexibility supports diverse research needs in plant and animal breeding.