Incorporating kernelized multi-omics data improves the accuracy of genomic prediction View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-09-20

AUTHORS

Mang Liang, Bingxing An, Tianpeng Chang, Tianyu Deng, Lili Du, Keanning Li, Sheng Cao, Yueying Du, Lingyang Xu, Lupei Zhang, Xue Gao, Junya Li, Huijiang Gao

ABSTRACT

BackgroundGenomic selection (GS) has revolutionized animal and plant breeding after the first implementation via early selection before measuring phenotypes. Besides genome, transcriptome and metabolome information are increasingly considered new sources for GS. Difficulties in building the model with multi-omics data for GS and the limit of specimen availability have both delayed the progress of investigating multi-omics.ResultsWe utilized the Cosine kernel to map genomic and transcriptomic data as n×n\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${n}\times {n}$$\end{document} symmetric matrix (G matrix and T matrix), combined with the best linear unbiased prediction (BLUP) for GS. Here, we defined five kernel-based prediction models: genomic BLUP (GBLUP), transcriptome-BLUP (TBLUP), multi-omics BLUP (MBLUP, M=ratio×G+(1-ratio)×T\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\boldsymbol M=\mathrm{ratio}\times\boldsymbol G+(1-\mathrm{ratio})\times\boldsymbol T$$\end{document}), multi-omics single-step BLUP (mssBLUP), and weighted multi-omics single-step BLUP (wmssBLUP) to integrate transcribed individuals and genotyped resource population. The predictive accuracy evaluations in four traits of the Chinese Simmental beef cattle population showed that (1) MBLUP was far preferred to GBLUP (ratio = 1.0), (2) the prediction accuracy of wmssBLUP and mssBLUP had 4.18% and 3.37% average improvement over GBLUP, (3) We also found the accuracy of wmssBLUP increased with the growing proportion of transcribed cattle in the whole resource population.ConclusionsWe concluded that the inclusion of transcriptome data in GS had the potential to improve accuracy. Moreover, wmssBLUP is accepted to be a promising alternative for the present situation in which plenty of individuals are genotyped when fewer are transcribed. More... »

PAGES

103

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    http://scigraph.springernature.com/pub.10.1186/s40104-022-00756-6

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    http://dx.doi.org/10.1186/s40104-022-00756-6

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1151163237

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/36127743


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        "description": "BackgroundGenomic selection (GS) has revolutionized animal and plant breeding after the first implementation via early selection before measuring phenotypes. Besides genome, transcriptome and metabolome information are increasingly considered new sources for GS. Difficulties in building the model with multi-omics data for GS and the limit of specimen availability have both delayed the progress of investigating multi-omics.ResultsWe utilized the Cosine kernel to map genomic and transcriptomic data as n\u00d7n\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${n}\\times {n}$$\\end{document} symmetric matrix (G matrix and T matrix), combined with the best linear unbiased prediction (BLUP) for GS. Here, we defined five kernel-based prediction models: genomic BLUP (GBLUP), transcriptome-BLUP (TBLUP), multi-omics BLUP (MBLUP,\u00a0M=ratio\u00d7G+(1-ratio)\u00d7T\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym}\n\t\t\t\t\\usepackage{amsfonts}\n\t\t\t\t\\usepackage{amssymb}\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\boldsymbol M=\\mathrm{ratio}\\times\\boldsymbol G+(1-\\mathrm{ratio})\\times\\boldsymbol T$$\\end{document}), multi-omics single-step BLUP (mssBLUP), and weighted multi-omics single-step BLUP (wmssBLUP) to integrate transcribed individuals and genotyped resource population. The predictive accuracy evaluations in four traits of the Chinese Simmental beef cattle population showed that (1) MBLUP was far preferred to GBLUP (ratio\u2009=\u20091.0), (2) the prediction accuracy of wmssBLUP and mssBLUP had 4.18% and 3.37% average improvement over GBLUP, (3) We also found the accuracy of wmssBLUP increased with the growing proportion of transcribed cattle in the whole resource population.ConclusionsWe concluded that the inclusion of transcriptome data in GS had the potential to improve accuracy. Moreover, wmssBLUP is accepted to be a promising alternative for the present situation in which plenty of individuals are genotyped when fewer are transcribed.", 
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