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XSim Version 2: Simulation of Modern Breeding Programs

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  • Chunpeng James Chen, Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA
  • ,
  • Dorian Garrick, AL Rae Centre for Genetics and Breeding, New Zealand
  • Rohan Fernando, Department of Animal Science, Iowa State University, IA
  • ,
  • Emre Karaman
  • Chris Stricker, agn Genetics GmbH
  • ,
  • Michael Keehan, AL Rae Centre for Genetics and Breeding
  • ,
  • Hao Cheng, Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

Simulation can be an efficient approach to design, evaluate, and optimize breeding programs. In the era of modern agriculture, breeding programs can benefit from a simulator that integrates various sources of big data and accommodates state-of-the-art statistical models. The initial release of XSim, in which stochastic descendants can be efficiently simulated with a drop-down strategy, has mainly been used to validate genomic selection results. In this paper, we present XSim Version 2 (XSimV2), that is an open-source tool and has been extensively redesigned with additional features to meet the needs in modern breeding programs. It seamlessly incorporates multiple statistical models for genetic evaluations, such as GBLUP, Bayesian alphabets, and neural networks, and it can effortlessly simulate successive generations of descendants based on complex mating schemes by the aid of its modular design. Case studies are presented to demonstrate the flexibility of XSimV2 in simulating crossbreeding in animal and plant populations. Modern biotechnology, including double haploids and embryo transfer, can all be simultaneously integrated into the mating plans that drive the simulation. From a computing perspective, XSimV2 is implemented in Julia, which is a computer language that retains the readability of scripting languages (e.g., R and Python) without sacrificing much computational speed compared to compiled languages (e.g., C). This makes XSimV2 a simulation tool that is relatively easy for both champions and community members to maintain, modify, or extend in order to improve their breeding programs. Functions and operators are overloaded for a better user interface so they may concatenate, subset, summarize, and organize simulated populations at each breeding step. With the strong and foreseeable demands in the community, XSimV2 will serve as a modern simulator bridging the gaps between theories and experiments with its flexibility, extensibility, and friendly interface.

Original languageEnglish
JournalG3: Genes, Genomes, Genetics
Number of pages9
Publication statusPublished - Apr 2022

    Research areas

  • breeding programs, genetic evaluation, simulation, Reproduction, Animals, Computer Simulation, Bayes Theorem, Models, Genetic, Genomics/methods

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