ArticleG3 (Bethesda, Md.)2025
GOplan: an R package for animal breeding program design via integrating Gene Flow and Bayesian optimization methods.
Qianqian Huang, Lei Zhou, Yahui Xue, Heng Du, Yue Zhuo, Ruihan Mao, Yaoxin Liu, Tiantian Yan, Wanying Li, Xiaofeng Wang and 1 more
Abstract read
In one paragraphArticle in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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11 authors.
Qianqian HuangState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Lei ZhouState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0000-0003-4080-0435 Yahui XueState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Heng DuState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0000-0001-6655-2033 Yue ZhuoState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0000-0003-3662-8038 Ruihan MaoState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Yaoxin LiuState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Tiantian YanBeijing Breeding Swine Center, Beijing 100194, China.
Wanying LiState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0009-0003-4654-9736 Xiaofeng WangBeijing General Station of Animal Husbandry, Beijing 100107, China.
Jianfeng LiuState Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Funding
Beijing Municipal Commission of Science and Technology Z211100004621005Chinese Universities Scientific Fund 2023TC196Earmarked Fund for China Agriculture Research System CARS-pig-35National Natural Science Foundations of China 31972563National Science and Technology 2023ZD0404403-04Talent Development Program of China Agricultural University
6 · The paper itselfAbstract
The design of breeding programs is crucial for maximizing economic gains. Simulation provides the most efficient measures to test these programs, as real-world trials are often costly and time-consuming. We developed GOplan, a comprehensive and user-friendly R package designed to develop animal breeding programs considering pure-bred populations and crossbreeding systems. Compared with other traditional simulators, it has mainstream crossbreeding frameworks that streamline modeling and use Gene Flow and Bayesian optimization methods to enhance breeding program efficiency. GOplan includes 3 key functions: runCore() to evaluate the effects of nucleus breeding programs, runWhole() to predict economic outcomes and the production performance of crossbreeding systems, and runOpt() to optimize crossbreeding structures for greater profitability. These functions support breeders in better planning and accelerating breeding goals. Additionally, the application of Bayesian optimization algorithms in this study provides valuable insights for developing new optimization algorithms in the future. The software is available at https://github.com/CAU-TeamLiuJF/GOplan.
Indexed as
BreedingGene FlowSoftwareAlgorithmsAnimalsBayes TheoremComputer SimulationModels, GeneticBayesian optimizationbreeding program evaluationGene Flow
Identifiers
PMID39657014
PMCPMC11797026
What Socratic holds
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LicenceCC BY
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