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Improving multibreed genomic prediction for breeds with small populations by modeling heterogeneous genetic(co)variance blockwise accounting for linkage disequilibrium

摘要Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partition-ing the genome into nonoverlapping blocks to model heterogeneous genetic(co)variance in multitrait models can achieve higher joint prediction accuracy.However,the block partitioning method,a key factor influencing model performance,has not been extensively explored.Results We introduce mbBayesABLD,a novel Bayesian MBGP model that partitions each chromosome into nonover-lapping blocks on the basis of linkage disequilibrium(LD)patterns.In this model,marker effects within each block are assumed to follow normal distributions with block-specific parameters.We employ simulated data as well as empirical datasets from pigs and beans to assess genomic prediction accuracy across different models using cross-validation.The results demonstrate that mbBayesABLD significantly outperforms conventional MBGP models,such as GBLUP and BayesR.For the meat marbling score trait in pigs,compared with GBLUP,which does not account for heterogene-ous genetic(co)variance,mbBayesABLD improves the prediction accuracy for the small-population breed Landrace by 15.6%.Furthermore,our findings indicate that a moderate level of similarity in LD patterns between breeds(with an average correlation of 0.6)is sufficient to improve the prediction accuracy of the target breed.Conclusions This study presents a novel LD block-based approach for multibreed genomic prediction.Our work provides a practical tool for livestock breeding programs and offers new insights into leveraging genetic diversity across breeds for improved genomic prediction.

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作者 Weining Li [1] Siyu Li [1] Heng Du [1] Qianqian Huang [1] Yue Zhuo [1] Lei Zhou [1] Jinhua Cheng [2] Wanying Li [1] Jicai Jiang [3] Jianfeng Liu [1] 学术成果认领
作者单位 State Key Laboratory of Animal Biotech Breeding,Frontiers Science Center for Molecular Design Breeding(MOE),College of Animal Science and Technol-ogy,China Agricultural University,Haidian,Beijing 100193,China [1] Institute of Animal Science,Jiangsu Academy of Agricultural Sciences,Nanjing Jiangsu 210014,China [2] Department of Animal Science,North Carolina State University,Raleigh North Carolina 27695,USA [3]
DOI 10.1186/s40104-025-01303-9
发布时间 2026-03-16(万方平台首次上网日期,不代表论文的发表时间)
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