2001ASAS/ADSA 2001 Conference (1)

Simultaneous accounting Simultaneous accounting for heterogeneity of for heterogeneity of (co)variance components in (co)variance components in genetic evaluation of type genetic evaluation of type traitstraits

N. GenglerN. Gengler1,21,2, G.R. Wiggans, G.R. Wiggans*,3*,3, , J.R. WrightJ.R. Wright33, and T. Druet, and T. Druet1,21,2

11 Gembloux Agricultural University, Belgium Gembloux Agricultural University, Belgium22 National Fund for Scientific Research, Brussels, National Fund for Scientific Research, Brussels, BelgiumBelgium33 Agricultural Research Service, USDA, Beltsville, Agricultural Research Service, USDA, Beltsville, MD MD

2001ASAS/ADSA 2001 Conference (2)

USDA Type evaluation

Breeds: Ayrshire Brown Swiss Guernsey Jersey Milking Shorthorn Red and White

15 Linear traits and Final ScoreMulti-trait Model

Canonical Transformation Estimation of missing values

2001ASAS/ADSA 2001 Conference (3)

Heterogeneity of (co)varianceVariances and (co)variances assumed

constant across herds and timeHolstein Association accounts for

heterogeneity in final scoreVariance tends to decrease with

increasing herd average final scoreChanges in appraisal program over

time can be a cause

2001ASAS/ADSA 2001 Conference (4)

Methods of HV estimation

Holstein Association estimates phenotypic variance using combination observed variance predicted variance from model including

– mean final score– registry status– number of appraisals for herd-classification

date

Meuwissen proposed simultaneous estimation of variances and breeding values expected to improve accuracy of both

estimates

2001ASAS/ADSA 2001 Conference (5)

USDA HV adjustment system

Apply Canonical transformation to linear traits

Prepare data for 2 models

score = herd-sire + herd-year-season-parity + parity-time_period-age + parity-time_period-stage

var = mean + parity-group_size + parity-herd_mean_final_score + parity-year-season + herd-year-month

2001ASAS/ADSA 2001 Conference (6)

Variance model

Herd-year-month effect in variance model random

Regression of variances within parity toward population mean (fixed effects)

Method R estimation of variance ratios within each EBV iteration

2001ASAS/ADSA 2001 Conference (7)

Computational requirementsComputational requirements

February 2001 Jersey Evaluation Run

number of rounds

time required

(hr)no HV 42 13

with HV 43 26.5

2001ASAS/ADSA 2001 Conference (8)

Iteration

Time increased due to iteration for variance model estimation of variance ratios

Convergence sensitive to quality of the starting values size of unknown parent groups

Ways of reducing processing time parallel processing using a faster computer limiting iteration for variances

2001ASAS/ADSA 2001 Conference (9)

Correlations between HV-adjusted official evaluations

February 2001 official evaluations2497 Jersey AI bulls born 1980+All correlations .989 or higher

2001ASAS/ADSA 2001 Conference (10)

Change in slope of PTA for Change in slope of PTA for Jersey AI bullsJersey AI bulls

Trait

slope

official

slope

HV adj diff

pct

diff

Dairy form 0.27 0.24 -0.036

-15.4

Rear udder height

0.20 0.17 -0.028

-16.2

Front teat place 0.09 0.07 -0.018

-26.4

Strength 0.08 0.07 -0.007

-10.2

Fore udder attach

0.06 0.05 -0.003

-5.7

Teat length 0.02 0.02 0.004

22.5

Udder Depth -0.05 -0.04 0.010 24.8

2001ASAS/ADSA 2001 Conference (11)

Differences between HV-adjusted and official evaluationStandard deviations & mean absolute

values increased as reliabilities increased to 80% decreased slightly for reliabilities of > 90%

Mean differences largest for bulls born from 1985 through 1994 with lowest mean daughters final scores

2001ASAS/ADSA 2001 Conference (12)

Mendelian sampling

Mendelian sampling evaluation minus mean of parent

evaluations

Jersey cows born from 1984 through 1998 regression of SD on birth year

2001ASAS/ADSA 2001 Conference (13)

Mendelian samplingMendelian sampling

Trait

slope

official

slope

HV adj diff

pct

diff

Foot angle -0.0050 -0.0026 0.0024 51

Rump angle -0.0160 -0.0122 0.0038 76

Rear udder height

-0.0050 -0.0011 0.0039 21

Teat placement -0.0097 -0.0055 0.0042 57

Stature -0.0199 -0.0135 0.0064 68

2001ASAS/ADSA 2001 Conference (14)

Interbull trend validation

Trend tests conducted for Stature Udder support

Comparison first parity v. all parities without recent years v. all data

Trend differences within tolerance

2001ASAS/ADSA 2001 Conference (15)

HV model implementation plans

Jersey - May 2001Other breeds by Feb 2002

2001ASAS/ADSA 2001 Conference (16)

Conclusions

Simultaneous estimation of BV & Variances possible

Requires substantially more computer time

Improves stability of Mendelian Sampling Variance over time

HV adjusted EBV enable more accurate selection decisions