Improved reliability of genomic evaluations
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G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD [email protected] G.R. Wiggans Council meeting April 2010 (1) Improved reliability of genomic evaluations
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Improved reliability of genomic evaluations. What is reliability. Squared correlation of PTA with true breeding value Increases with amount of relevant information Initially derived from the inverse of coefficient matrix Approximation needed as number of genotyped animals got large. - PowerPoint PPT Presentation
Transcript of Improved reliability of genomic evaluations
G.R. WiggansAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD
[email protected]. WiggansCouncil meeting April 2010 (1)
Improved reliability of genomic evaluations
G.R. WiggansCouncil meeting April 2010 (2)
What is reliability
Squared correlation of PTA with true breeding value
Increases with amount of relevant information
Initially derived from the inverse of coefficient matrix
Approximation needed as number of genotyped animals got large
G.R. WiggansCouncil meeting April 2010 (3)
Change implemented in April Initial approximation assumed all
animals received the same amount of information from genomics
Genomic relationship of each animal with the predictor animals routinely calculated
These relationships weighted by reliability and summed now are basis for calculating contribution of genomics to Reliability
G.R. WiggansCouncil meeting April 2010 (4)
Reliability for young HO Bulls
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52 5354 55 5657 58 5960 61626364 6566 67 6869 70 7172 73 7475 76 7778 79
Milk REL
Nu
mb
er
of
Bu
lls
N = 15,226
G.R. WiggansCouncil meeting April 2010 (5)
Reliabilities for HO born ≥ 2005No Traditional
EvaluationWith Traditional
Evaluation
Trait Male Female Male Female
N 15226 7536 752 3191
Milk (lb) 73.9 73.7 85.8 77.9
Protein (lb) 73.9 73.7 85.8 77.8
PL (mo) 64.0 63.6 70.1 67.0
SCS 69.7 69.5 78.1 73.0
DPR (%) 61.6 61.2 66.5 64.6
PTAT 70.4 70.1 78.3 74.5
Sire CE 64.9 61.7 80.8 63.5
Daughter CE 60.2 59.0 69.5 61.8
Sire SB 59.8 58.7 66.2 59.6
Daughter SB 58.3 57.6 64.9 59.6
Net Merit ($) 68.6 68.3 77.8 72.0
G.R. WiggansCouncil meeting April 2010 (6)
Bulls First Traditional Eval. Jan., 2010
Genomic
August January
Trait N PTA REL PTA REL Diff PTA
Milk 703 533 76.3 475 83.4 -58
Protein 703 17.6 76.3 17.0 83.6 -0.6
PTAT 471 1.0 70.4 1.0 77.5 0.0
Traditional
August January
Trait N PA REL PTA REL Diff PTA
Milk 703 657 42.0 478 74.9 -179
Protein 703 22.1 42.0 17.0 74.9 -5.1
PTAT 471 1.0 40.9 0.9 65.1 -0.1
G.R. WiggansCouncil meeting April 2010 (7)
Cows First Traditional Eval. Jan., 2010
Genomic
August January
Trait N PTA REL PTA REL Diff PTA
Milk 594 772 74.4 845 75.4 73
Protein 570 25.5 74.4 29.4 75.1 3.9
PTAT 294 1.7 69.4 1.8 71.6 0.1
Traditional
August January
Trait N PA REL PTA REL Diff PTA
Milk 594 774 35.6 943 51.1 167
Protein 570 26.2 35.2 32.9 49.8 6.7
PTAT 294 1.6 36.8 1.7 48.9 0.1
G.R. WiggansCouncil meeting April 2010 (8)
Adapting to more genotypes
Calculating Genomic Matrix may be too time consuming with many 3K genotypes
May sum the allele content of predictor population
Reliability then based on sum of reliabilities of trad PTA and fraction of alleles in common with predictor population
G.R. WiggansCouncil meeting April 2010 (9)
Conclusions
Contribution of genomics to reliability calculated individually
Based on relationship to predictor population and their Rel of Trad PTA
Mode Rel is 74-75 for bulls without a trad evaluation
