XSim version 2: simulation of modern breeding programs

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dc.citation.issue4
dc.citation.volume12
dc.contributor.authorChen CJ
dc.contributor.authorGarrick D
dc.contributor.authorFernando R
dc.contributor.authorKaraman E
dc.contributor.authorStricker C
dc.contributor.authorKeehan M
dc.contributor.authorCheng H
dc.contributor.editorde Koning D-J
dc.coverage.spatialEngland
dc.date.accessioned2024-04-17T01:29:35Z
dc.date.accessioned2024-07-25T06:39:49Z
dc.date.available2022-03-04
dc.date.available2024-04-17T01:29:35Z
dc.date.available2024-07-25T06:39:49Z
dc.date.issued2022-04-04
dc.description.abstractSimulation 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 article, we present XSim Version 2 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 XSim Version 2 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, XSim Version 2 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 XSim Version 2 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, XSim Version 2 will serve as a modern simulator bridging the gaps between theories and experiments with its flexibility, extensibility, and friendly interface.
dc.description.confidentialfalse
dc.edition.editionApril 2022
dc.format.paginationjkac032-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/35244161
dc.identifier.citationChen CJ, Garrick D, Fernando R, Karaman E, Stricker C, Keehan M, Cheng H. (2022). XSim version 2: simulation of modern breeding programs.. G3 (Bethesda). 12. 4. (pp. jkac032-).
dc.identifier.doi10.1093/g3journal/jkac032
dc.identifier.eissn2160-1836
dc.identifier.elements-typejournal-article
dc.identifier.issn2160-1836
dc.identifier.numberjkac032
dc.identifier.pii6542309
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70636
dc.languageeng
dc.publisherOxford University Press on behalf of Genetics Society of America
dc.publisher.urihttps://academic.oup.com/g3journal/article/12/4/jkac032/6542309
dc.relation.isPartOfG3 (Bethesda)
dc.rights(c) 2022 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectbreeding programs
dc.subjectgenetic evaluation
dc.subjectsimulation
dc.subjectAnimals
dc.subjectBayes Theorem
dc.subjectComputer Simulation
dc.subjectGenomics
dc.subjectModels, Genetic
dc.subjectReproduction
dc.titleXSim version 2: simulation of modern breeding programs
dc.typeJournal article
pubs.elements-id452750
pubs.organisational-groupOther
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