evaluation in American Angus Daniela Lourenco S. Tsuruta, B. - - PowerPoint PPT Presentation
Issues in commercial application of single-step genomic BLUP for genetic evaluation in American Angus Daniela Lourenco S. Tsuruta, B. Fragomeni, Y. Masuda, I. Pocrnic, I. Aguilar, J.K. Bertrand, D. Moser, I. Misztal University of Georgia
Daniela Lourenco
University of Georgia
July, 2016
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82,000 112,000 132,000 152,000 220,000 50,000 100,000 150,000 200,000 250,000 Number of Genotypes # Genotyped Animals
American Angus
07 2014 01 2015 07 2015 10 2015 07 2016
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CORE animals randomly sampled from genotyped population
0.97 0.99 0.99 0.99 5k 10k 15k 20k
Correlation (GEBV,GEBV_APY)
Growth Traits – 82k CORE invert NON-CORE
GAPY −1
Misztal et al., 2014
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Pocrnic et al., 2016 Misztal, 2016
5000 10000 15000 90 95 98 99 3654 6166 10605 14555 Number of Eigenvalues % of Variance
AAA – 82k
3654, 0.96 6166, 0.98 10605, 0.99 14555, 0.99 0.90 0.92 0.94 0.96 0.98 1.00 2000 4000 6000 8000 10000 12000 14000 16000 COR (GEBV,GEBV_APY) NUMBER OF EIGENVALUES
AAA - 82K
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CORE invert NON-CORE
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Adapted from Legarra et al., 2007
Computing time BLUP = 8h ssGBLUP = 12h
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Scenario Description of parameters rounds hours correlation with genomic pcg rounds alpha beta traditional 40
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40 0.9 0.1 488 108
100 0.9 0.1 81 43 0.999 2 100 0.85 0.15 62 32 0.999 3 200 0.9 0.1 24 25 0.999 4 200 0.85 0.15 19 19 0.999
𝐈−𝟐 = 𝐁−𝟐 + 𝟏 𝟏 𝟏 (α𝐇 + β𝐁𝟑𝟑)−𝟐– 𝐁𝟑𝟑
−𝟐
Working on OMP – 30% faster
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di = SNP weight = I
𝑣
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Diag(CZZ+) = PEV Traditional 𝑀𝐼𝑇𝑣𝑣
𝑗𝑗 =
1 (λ + 𝑒𝑗
𝑠 + 𝑒𝑗 𝑞)
𝑠and 𝑒𝑗 𝑞are approximated
(Misztal and Wiggans, 1988)
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𝑗𝑗 =
𝑠 + 𝑒𝑗 𝑞 + 𝑒𝑗 )
𝑒𝑗
𝑠
𝑒𝑗
𝑞
𝑒𝑗
?
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𝑒𝑗
= 1 + ℎ2 ∗ 𝐹𝑇𝑁 ∗ 𝐻 − 𝐵22 ∗ 𝐵𝑑𝑑𝑄𝐵
𝑠 and 𝑒𝑗 𝑞
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𝑒𝑗
= λ
𝑗≠𝑘 𝐵𝑑𝑑𝑄𝐵 𝑑𝑝𝑣𝑜𝑢(𝜀) +≈ 𝑗≠𝑘 𝑗𝑘(𝑒𝑗
𝑠 + 𝑒𝑗 𝑞)
𝑑𝑝𝑣𝑜𝑢(𝜀)
Approximation 1 Approximation 2
3’24” 0’12”
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