J. B. ColeJ. B. Cole1,*1,*, P. M. VanRaden, P. M. VanRaden11, and C. , and C. M. B. DematawewaM. B. Dematawewa22

1Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD2Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg

2007

Estimation of yields for long lactations using best prediction

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Best PredictionBest PredictionVanRaden JDS 80:3015-3022 (1997), 6VanRaden JDS 80:3015-3022 (1997), 6thth WCGALP XXIII:347-350 (1998) WCGALP XXIII:347-350 (1998)

• Selection IndexSelection Index Predict missing yields from measured yields.Predict missing yields from measured yields. Condense test days into lactation yield and Condense test days into lactation yield and

persistency.persistency. Only phenotypic covariances are needed.Only phenotypic covariances are needed. Mean and variance of herd assumed known.Mean and variance of herd assumed known.

• Reverse predictionReverse prediction Daily yield predicted from lactation yield and Daily yield predicted from lactation yield and

persistency.persistency.

• Single or multiple trait predictionSingle or multiple trait prediction

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

HistoryHistory

• Calculation of lactation records for milk (M), fat (F), protein (P), and somatic cell score (SCS) using best prediction (BP) began in November 1999.

• Replaced the test interval method and projection factors at AIPL.

• Used for cows calving in January 1997 and later.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

AdvantagesAdvantages

• Small for most 305-d lactations but larger for lactations with infrequent testing or missing component samples.

• More precise estimation of records for SCS because test days are adjusted for stage of lactation.

• Yield records have slightly lower SD because BP regresses estimates toward the herd average.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

UsersUsers

• AIPL: Calculation of lactation yields and data collection ratings (DCR). DCR indicates the accuracy of

lactation records obtained from BP.• Breed Associations: Publish DCR

on pedigrees.• DRPCs: Interested in replacing

test interval estimates with BP. Can also calculate persistency. May have management applications.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Restrictions of Original Restrictions of Original SoftwareSoftware

• Limited to 305-d lactations used since 1935.

• Changes to parameters requires recompilation.

• Uses simple linear interpolation for calculation of standard curves.

• It is not possible to obtain BP for individual days of lactation.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Enhancements in New Enhancements in New SoftwareSoftware

• Lactations of any length can be modeled. Lactation-to-date and projected yields.

• The autoregressive function used to model correlations among test day yields was updated.

• Program options set in a parameter file.• Diagnostic plots available for all traits.• BP of individual daily yields, test day

yields, and standard curves now output.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Data and EditsData and Edits

• Holstein TD data were extracted from the national dairy database.

• The edits of Norman et al. (1999) were applied to the data set used by Dematawewa et al. (2007). 1st through 5th parities were

included. Lactation lengths were at least 250 d

for the 305 d group and 800 d for the 999 d group.

Records were made in a single herd. At least five tests were reported. Only twice-daily milking was reported.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Summary StatisticsSummary Statistics

First Later

Records 171,970 176,153

Length (d) 362 369

Pct > 305-d 23.9 27.5

Pct > 500-d 3.3 3.4

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Correlations among test day Correlations among test day yieldsyields

Norman et al. JDS 82:2205-2211 (1999)Norman et al. JDS 82:2205-2211 (1999)

• An autoregressive matrix accounts for biological changes, and an identity matrix models daily measurement error.

• Autoregressive parameters (r) were estimated separately for first- (r=0.998) and later-parity (r=0.995) cows.

• These r were slightly larger than previous estimates due to the inclusion of the identity matrix.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Modeling Long LactationsModeling Long Lactations

• Dematawewa et al. (2007) recommend simple models, such as Wood's (1967) curve, for long lactations.

• Curves were developed for M, F, and P yield, but not SCS. Little previous work on fitting lactation

curves to SCS (Rodriguez-Zas et al., 2000).

• BP also requires curves for the standard deviation (SD) of yields.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Modeling SCS and SDModeling SCS and SD

• Test day yields were assigned to 30-d intervals and means and SD were calculated for each interval. First, second, and third-and-later

parities.• Curves were fit to the resulting

means (SCS) and SD (all traits).• SD of yield modeled with Woods

curves.• SCS means and SD modeled using

curve C4 from Morant and Gnanasankthy (1989).

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Mean Milk Yield (1Mean Milk Yield (1stst parity) parity) (kg)(kg)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

SD of Milk Yield (first parity) SD of Milk Yield (first parity) (kg)(kg)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Mean Somatic Cell Score (1Mean Somatic Cell Score (1stst parity)parity)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Mean Somatic Cell Score(3+ Mean Somatic Cell Score(3+ parity)parity)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

SD of Somatic Cell Score (1SD of Somatic Cell Score (1stst parity)parity)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

SD of Somatic Cell Score (3+ SD of Somatic Cell Score (3+ parity)parity)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Uses of Daily EstimatesUses of Daily Estimates

• Daily yields can be adjusted for known sources of variation. Example: Daily loss from clinical

mastitis (Rajala-Schultz et al., 1999).• This could lead to animal-specific

rather than group-specific adjustments.

• Research into optimal management strategies.

• Management support in on-farm computer software.

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Mean Milk Yield (kg)Mean Milk Yield (kg)

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

Accounting for Mastitis Accounting for Mastitis LossesLosses

ADSA 2007 – Best prediction and long lactations Cole et al. 2007

ConclusionsConclusions

Correlations among successive test days may require periodic re-estimation as lactation curves change.

Many cows can produce profitably for >305 days in milk, and the revised BP program provides a flexible tool to model those records.

Daily BP of yields may be useful for on-farm management.