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Genomic Selection using Low-Density SNPs




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1 Christian-Albrechts-University of Kiel Institute of Animal Breeding and Husbandry David Habier Napapan Pyiasatian Jack Dekkers Rohan Fernando Habier et al. 2009 Genetics 182: 343 - 353 Genomic Selection using Low-Density SNPs Faculty of Agriculture and Nutritional Science Estimate marker effects Genotype for >50,000 SNPs Phenotype Genotype for >50,000 SNPs Predict BV from marker genotypes at early age Genotype for >50,000 SNPs Training data Training data Training data Predict BV from marker genotypes at early age Genomic selection Genetic Evaluation using high-density SNPs Meuwissen et al. 2001 0.6 0.7 0.8 0.9 1 3 4 5 6 7 8 Generation A cc ur ac y 2 3 Need Low- (<380) vs. High-density panel for routine implementation ?? $50 vs. $250 per animal ?? ‘Standard’ approach to developing Low-density panels: • Select the ‘best’ SNPs from the HD-panel • Trait and population specific Proposed approach: use well-spaced Low-density SNP genotypes on selection candidates to ‘fill in’ missing HD SNP genotypes Introduction Implementation of GS Original principle of Genomic Selection (GS) High-density (HD) SNP genotypes used for both • Estimation of marker effects (training) • Prediction of GS-EBV for selection candidates Not feasible for many species 4 Outline ? Introduction – What is ELD-GS? ? Methods ? Published results ? Unpublished results ? Criteria for loss of accuracy ? Factors affecting loss of accuracy of ELD-GS ? Precision of PDMs ? Simulations – Results ? Conclusions & outlook 19 37 Simulations – Population With Historic LD 1500 males + 1500 females Real pedigree (13 generations) 4 pedigree generations start Random mating (N=100) Generation - 50 Random mating (N=500 ) Generation -1050 38 Linkage disequilibrium Historic LD – Real pedigree 20 39 Accuracy of GEBVs Historic LD – real pedigree (8 chromosomes & 8cM) Mutation rate was high with 0.005 95% of QTL are segregating with MAF 0.27 90% of QTL have MAF > 0.05 40 Genomic Selection can be implemented with low-density SNP genotyping of selection candidates • Loss in accuracy limited: < 3.5% after 1 generation < 8 % after 2 generations with 300 equally spaced SNPs (10 cM) • Loss in accuracy ~ independent of # QTL and # traits • Lower rate of fixation of panel SNPs with selection ? slower accuracy decline • Cost effectiveness needs to be analyzed • Depends on costs of Low- vs. High-density genotyping $40 ???? $180 • Optimal implementation needs to be further analyzed • Which individuals to genotype – HD / LD Discussion & Conclusions 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 4 5 6 7 Generation A cc ur ac y






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