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Additional file 5 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
journal contribution
posted on 2022-09-25, 15:24 authored by Roger Ros-Freixedes, Martin Johnsson, Andrew Whalen, Ching-Yi Chen, Bruno D. Valente, William O. Herring, Gregor Gorjanc, John M. HickeyAdditional file 5: Figure S4. Genomic prediction accuracy by density of preselected whole-genome sequence variants in the prediction model.
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Biotechnology and Biological Sciences Research Council Innovate UK Svenska Forskningsrådet Formas Genus plc
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statistically significant associationsgenome sequence dataeight complex traitsdifferent numerical sizesallele substitution effectsstandard marker arraysequenced 6931 individualsaround 80k individualsrobust across traitsline training sets8 million variantsline genomic predictionsstandard marker arraysperform genomic predictionscale wgs datalargest training setslarger training setslarge pig datasetgenomic predictions comparedgenomic predictions basedmarker arrays couldgenomic prediction comparedgenomic predictions withinpreselected wgs variantstraining setsgenomic predictionsmarker arraysgenomic predictionvariants preselectedpreselected variantsgenomic diversity100 individualswgs comparedwgs basedlargest advantageacross breeds04 comparedprediction accuracywgs providesusing wgsused bayesrpopulation mustoptimised pipelineslimited potentiallarger improvementsidentify scenariosgenerally smallcurrent implementationscould improvecarefully evaluatedaverage improvedassociation tests
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