Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.02.0013.
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies.
本文介绍了 AlphaSim，这是一个用于模拟动植物育种计划的软件包。AlphSim 具有高度的灵活性，能够模拟育种计划的多个方面。AlphSim 通过一系列步骤模拟育种计划：（i）模拟单倍型序列和系谱；（ii）将单倍型放入系谱的基础世代中，并选择单核苷酸多态性（SNP）和数量性状核苷酸（QTN）；（iii）分配 QTN 效应，计算遗传值，并模拟表型；（iv）将单倍型放入预热世代中；（v）进行选择并模拟新的世代。该程序在历史人口结构和多样性、近期系谱结构、性状结构和选择策略方面具有灵活性。它集成了双单倍体（DHs）和基因编辑等生物技术，允许用户模拟多个性状和多个环境，指定重组热点和冷点，指定基因丛林和沙漠，进行基因组预测，并应用最优贡献选择。AlphSim 还包括重启功能，通过暂停模拟过程，可以增加其灵活性，以便更改参数或导入外部创建的系谱、试验设计或以前模拟数据的分析结果。通过组合这些选项，用户可以模拟具有几个世代、随时间变化的人口结构和不同的繁殖决策的简单或复杂的繁殖计划。总之，AlphSim 是一个灵活且计算效率高的软件包，用于模拟生物技术增强的繁殖计划，旨在快速、低成本、客观地进行繁殖技术的计算机模拟比较。
