Date post: | 17-Jan-2016 |
Category: |
Documents |
Upload: | ashley-simpson |
View: | 215 times |
Download: | 0 times |
G.R. Wiggans* and P.M. VanRadenAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, MD
G.R. WiggansADSA 2010 (1)
Improved reliability approximation for genomic evaluations in the United States
Abstr.617
G.R. WiggansADSA 2010 (2)
Reliability (REL)
Measure of amount of information in an evaluation
Squared correlation between EBV and true breeding value
May be expressed as daughter equivalents (DE = k*Rel/(1-Rel), where k = variance ratio)
Diagonal element of inverse of coefficient matrix
Approximation used when computing inverse is too time consuming
G.R. WiggansADSA 2010 (3)
Approximation of REL
Time to compute inverse increases cubically with number of genotyped animals
When inversion discontinued in 2009, all animals given same contribution from genomics
Genomic relationship (G) with predictor animals measures information contributed
REL of predictor animal evaluation used for weighting
G.R. WiggansADSA 2010 (4)
Approximation procedure
Convert traditional reliability to DE
Remove contribution from parents
Convert back to reliability for weighting genomic relationship
Sum weighted relationships across predictor animals (∑Gw). Similar to genomic future inbreeding
G.R. WiggansADSA 2010 (5)
Conversion of ∑Gw to reliability
August 2009 reliabilities from inverse converted to DE and genomic contribution (DEg) extracted
DEg predicted from ∑Gw for 3 Holstein groups
8,353 bulls with traditional evaluations
3,559 cows with traditional evaluations
16,135 animals without traditional evaluations
G.R. WiggansADSA 2010 (6)
Conversion of ∑Gw (continued)
Straight line fit well except for low ∑Gw
Floor set at 30 DEg
Slopes and floor differ by breed
Applicable across traits because same k used to calculate DEg
G.R. WiggansADSA 2010 (7)
Coefficients to predict DEg
Breed Floor Bulls* Cows*
Young animals*
*HolsteinJersey
20 0.058 0.056 0.051 10 0.088 0.086 0.072
Brown Swiss
6 0.122 0.122 0.085 *Traditional evaluation
**No traditional evaluation
G.R. WiggansADSA 2010 (8)
Genotyped Holsteins
Date
Young animals**
All animal
sBulls* Cows* Bulls Heifers
04-09 7,600 2,711 9,690 1,943 21,94401-10 8,974 4,348 14,061 6,031 33,41402-10 9,378 5,086 15,328 7,620 37,41204-10 9,770 7,415 16,007 8,630 41,82205-10 9,958 7,940 16,594 9,772 44,26406-10 9,958 8,122 17,507 10,713 46,30007-10 9,963 8,186 18,187 11,309 47,645 *Traditional evaluation
**No traditional evaluation
G.R. WiggansADSA 2010 (9)
REL for 18,187 young Holstein bulls
0500
100015002000250030003500400045005000
60616465666768697071727374757677787980
REL (%) for mlk yield
Bu
lls (
no.)
G.R. WiggansADSA 2010 (10)
REL (%) for Holsteins born ≥2005
Trait
Young animals**
Bulls* Cows* Bulls HeifersMilk 87 80 76 76Protein 87 79 76 76Productive life 72 68 65 64Somatic cell score 80 74 71 71Daughter pregnancy rate
68 65 62 62
PTA type 79 74 70 70Service-sire calving ease
82 71 72 70
Daughter calving ease 74 68 67 66Service-sire stillbirth 66 60 59 58Daughter stillbirth 67 62 59 59Net merit 79 73 70 70Animals, n 1,262 4,487 18,117
11,171
*Traditional evaluation**No traditional evaluation
G.R. WiggansADSA 2010 (11)
G matrix
Computing time increases by (number of SNP)*(number of genotyped animals)2
Options for calculating genomic relationships Get faster computer Run program in parallel Compute relationships before evaluations Calculate only for new animals; store old ones Calculate based only on SNP from 3K chip Use Eigenvalues & Eigenvectors to reduce
processing
If G used to calculate EBV greater precision needed
G.R. WiggansADSA 2010 (12)
Genotype quality and reliability
Problems – greater with imputation
Missing genotypes Genotype incorrect
Remedies
Discount for missing SNP genotypes Consider if parents were genotyped Discount uniformly for 3K chip
G.R. WiggansADSA 2010 (13)
Implementation of 3K chip
Chip expected to ship this week
2,882 usable SNP, plus 14 on Y Chromosome
Unofficial evaluations expected Sept. 7
Large initial use expected
New genotyping laboratories
G.R. WiggansADSA 2010 (14)
Conclusions
Improved REL approximation implemented April 2010
REL reduced for animals less related to predictor population MN control-line bulls Foreign bulls
Approximation relies on G matrix
Modification planned to account for loss in accuracy from imputation
G.R. WiggansADSA 2010 (15)
Brought to you by AIPL Staff