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Ideas for continuous genomic evaluation for newly genotyped Walloon Holstein females and males

Ideas for continuous genomic evaluation for newly genotyped Walloon Holstein females and males. S. Naderi 1 , R. R. Mota 1 , S. Vanderick 1 , N. Gengler 1 1 Gembloux Agro-Bio Tech, ULiège , B-5030 Gembloux, Belgium. Current Situation.

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Ideas for continuous genomic evaluation for newly genotyped Walloon Holstein females and males

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  1. Ideas for continuous genomic evaluation for newly genotyped Walloon Holstein females and males S. Naderi1, R. R. Mota1, S. Vanderick1, N. Gengler1 1Gembloux Agro-Bio Tech, ULiège, B-5030 Gembloux, Belgium EAAP 2018 Meeting Dubrovnik

  2. Current Situation • Number of genotyped animals in the Walloon genomic evaluations~ 9,000 • Single-step genomic Bayesian procedure (ssGBayes) • Blending genomic, Walloon and MACE information • Subtract Walloon information contributing to MACE • Delay between genotyping animals and official GEBV Worst case scenario: 4months EAAP 2018 Meeting Dubrovnik

  3. Why preliminary genomic evaluations ? • CulIing animals at calf-hood reducing rearing costs • Time span reduction between DNA sampling and GEBV • An official evaluation generating GEBV and GREL Processing time may increase EAAP 2018 Meeting Dubrovnik

  4. Objectives • Generate preliminary genomic evaluations that are: • Simpler and faster: practical monthly/weekly evaluations • Quite similar to current official routine evaluations EAAP 2018 Meeting Dubrovnik

  5. Possible approches • SNP effect methods using official routine evaluations as source polygenic contributions ??? • Genomic selection index methods correct covariance structures “H” based? EAAP 2018 Meeting Dubrovnik

  6. Decomposition of GEBV PA: parent average YD: yield deviation PC: progeny contribution PP: pedigreeprediction based Young animals GEBVi ≈ w1PA + w2DGV (Lourenco et al., 2015) EAAP 2018 Meeting Dubrovnik

  7. A- Group I: Animalswithout progeny GEBVi ≈ w1PAG + w2DGVi PAi = (GEBVs + GEBVd)/2 GEBV of young bulls without progeny used to derive Wi EAAP 2018 Meeting Dubrovnik

  8. A-Group II: Animalswith progeny GEBVi ≈ w1PAG+ w2DGVi +w3PAC+ w4EBVi PAi = (EBVs+ EBVd)/2 GEBV of ~3000 genotyped animals with progeny used to derive Wi EAAP 2018 Meeting Dubrovnik

  9. Running postGS (solution of previous evaluation) Running own code (Parents average all animals) Requirements of the method • Combined Pedigree • SNP effects (previous evaluation) • Parent average • Proper regression coefficients Regression coefficient derivation SNP sol DGV PAi = (GEBVs + GEBVd)/2 From BOTTOM to the TOP Fill the gaps with GEBV or EBV Regular variance and covariance of vectors of PA ,DGV EAAP 2018 Meeting Dubrovnik

  10. Milk EAAP 2018 Meeting Dubrovnik

  11. Fat EAAP 2018 Meeting Dubrovnik

  12. Protein EAAP 2018 Meeting Dubrovnik

  13. SCS EAAP 2018 Meeting Dubrovnik

  14. Milk Fat Protein SCS EAAP 2018 Meeting Dubrovnik

  15. Genomic selection index based methods • Directly proportional: selection index “H” inversion difficulty • However, as shown by many researchers (e.g. Gengler et al., 1997)  equivalent MME • GEBV of routine evaluation as “data” and heritability close to unity • Extending GEBV for new genotyped animals EAAP 2018 Meeting Dubrovnik

  16. Extending GEBV for new genotyped animals (Ext_GEBV) • New genotyped animals pedigree extraction • Combining with routine pedigree • GEBV from December 2017 routine evaluation as priors  GEBV of new genotyped animals (71 animals) EAAP 2018 Meeting Dubrovnik

  17. Overlapping and relationship of new genotyped animals with animal in routine evaluation EAAP 2018 Meeting Dubrovnik

  18. Extending GEBV for new genotyped animals EAAP 2018 Meeting Dubrovnik

  19. Accuracy of the preliminary evaluation could be improved • Adding new genotyped animals • parent average or missing (the correlation ~0.99, not shown results)  processing time may increase • Adding a specific group of animals • closely linked to routine population • only a group of genotyped animals representing the dimensionality of the genomic information (proven and young) • An official evaluation generating GEBV and GREL EAAP 2018 Meeting Dubrovnik

  20. Conclusion • The correlation between preliminary and official evaluations was not as high as expected (specially for approach B): • Small size of new genotyped animals • Instability of SNP estimates • The proportion of residual polygenic variance in total additive genetic variance (approach B) EAAP 2018 Meeting Dubrovnik

  21. Acknowledgements Thank you for your attention EAAP 2018 Meeting Dubrovnik

  22. Cor(R_GEBV, E_GEBV) for other traits (April 2017) EAAP 2018 Meeting Dubrovnik

  23. Regression (de-regression) coefficient used for Protein • Used to estimate GEBV for new genotyped animals • Used to estimate GEBV for animals with Progeny EAAP 2018 Meeting Dubrovnik

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