AlphaSim: Software for Breeding Program Simulation
AlphaSim: Software for Breeding Program Simulation
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DOI：
10.3835/plantgenome2016.02.0013
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发表时间：
2016-11-01
期刊：
影响因子：
4.2
通讯作者：
Hickey, John M.
中科院分区：
文献类型：
--
作者：
Faux, Anne-Michelle;Gorjanc, Gregor;Hickey, John M.
本文介绍了 AlphaSim，一个用于模拟植物和动物育种程序的软件包。 AlphaSim 能够以高度的灵活性模拟育种计划的多个方面。 AlphaSim 通过一系列步骤模拟育种程序：（i）模拟单倍型序列和谱系； (ii) 将单倍型放入谱系的碱基生成中，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) 将单倍型放入老化代中； (v) 进行选择并模拟新一代。该计划在历史种群结构和多样性、近期谱系结构、性状结构和选择策略方面具有灵活性。它集成了双单倍体（DH）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，执行基因组预测，并应用最佳贡献选择。 AlphaSim 还包括重新启动功能，通过允许暂停模拟过程来更改参数或导入外部创建的谱系、试验设计或先前模拟数据的分析结果，从而提高其灵活性。通过组合这些选项，用户可以模拟简单或复杂的育种程序，其中包括几代、可变的种群结构和随时间变化的育种决策。总之，AlphaSim 是一个灵活且计算高效的软件包，用于模拟生物技术增强育种计划，旨在对育种技术进行快速、低成本和客观的计算机模拟比较。
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.