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Mixed Model Sire Evaluation with Dairy Cattle—Experience and

Genetic Gain

R. W. Everett and J. F. Keown

J Anim Sci 1984. 59:529-541.

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MIXED MODEL SIRE EVALUATION WITH DAIRY CATTLE-
EXPERIENCE A N D G E N E T I C G A I N 1

R. W. Everett 2 and J. F. Keown

Cornell University, Ithaca, NY 14853

Summary
semen distribution organizations. In 1982 there
Mixed model dairy sire evaluations have were 34 AI organizations recorded as members
been available to farmers since 1970. Major of the National Association of Animal Breeders,
refinements in the single trait evaluation system 12 of which produced 13.3 million units of
include the incorporation of the relationship dairy semen.
matrix among animals evaluated and expanding Evaluation of the genetic merit of AI sires
the model to include the sires of the mates. was done initially by the USDA's Bureau of
These refinements primarily increased the Dairy Industry using daughter-dam comparisons.
accuracy of evaluations of sires with few The introduction of high-speed electronic
daughters. Multiple trait sire evaluation is equipment by Dairy Herd Improvement (DHI)
discussed. The primary advantages include record centers allowed for investigations of
increased accuracy of evaluation on sires with complex sire evaluation procedures. In 1954, C.
few daughters and increased accuracy of R. Henderson introduced the herdmate com-
evaluation on sires with missing observations on parison method of evaluating sires along with
one or more traits. Transforming of data to the concept of "repeatability," which regresses
reduce heterogeneous error variances is dis- average deviations for the number of daughters.
cussed. Accurate evaluation of sires and the The herdmate comparison accurately evaluated
heavy use of superior artificial insemination AI sires under the conditions of no genetic
sires has resulted in a genetic gain of 31 kg of progress and random use of all bulls. Use of
milk/yr from 1957 through 1982 in the more accurate pedigree selection, heavy use of
Northeast dairy cattle population. proven sires and the technical breakthrough of
(Key Words: Sire Evaluation, Best Linear frozen semen invalidated the assumptions of
Unbiased Prediction.) the herdmate comparison. Frozen semen
allowed dairymen to choose among many bulls
| ntroduction as service sires and resulted in nonrandom use
Artificial insemination (AI) was introduced of bulls.
in the United States in New Jersey in 1938 by
Professor E. J. Perry of Rutgers University. By Best Linear UnbiasedPrediction
1948, there were 963 farmer cooperatives
artificially inseminating 7% of the 25,000,000 Evaluation of AI sires by herdmate com-
dairy cows on farms in the United States parison was questioned by dairymen because of
(Hirsch and Hedges, 1949). Of these AI co- the tendency of evaluations on superior bulls to
operatives, only 91 were engaged in pro- decrease on subsequent evaluations. As genetic
ducing semen, and the remaining 872 were progress occurred, the merit of a sire decreased
relative to the sires of his daughter's herdmates.
This caused sires to decrease in subsequent
evaluations as shown in figure 1 for a particular
sire. At the same time it was found that the
l Invited paper, presented at the Symposium on competition of all bulls was not equal. Differ-
"Changes and Challenges in the Dairy Cattle Industry" ences in milk yield in level of competition of a
a t the 1983 Annu. Meet. Amer. Soc. of Anim. Sci.,
Pullman, WA. group of popular sires is shown in table 1. The
2Dept. of Anim. Sci. herdmate comparison underevaluated sires with
Received September 7, 1983. positive competition and overevaluated sires
Accepted February 2, 1984. with negative competition.
529
JOURNAL OF ANIMALSCIENCE,Vol. 59, No. 2, 1984
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530 EVERETT AND KEOWN

318
where
295
273 Yijk~ = the ~th first lactation .daughter
250 record of the kth sire in the jth sire
227 group initiated in the ith herd-year-
204 season,
182 la = the overall mean,
" 159 9e ~ J hys i = the fixed effect of the ith herd-year-
x 136 season,
114 gj = the fixed effect of the jth AI sire
91 group,
68 Sjk = the random effect of t h e kth AI sire
45 in the ith AI sire group assuming the
56 57 58 59 6O 6l 62 63 ratio Oe/O2s is 15.0 and
YEAR
eijk~ = the random error with mean zero and
Figure 1. Average deviation from herdmates of variance o~.
daughters of Woosterdale Imperial Dean (bpT =
regression of production on years).
Herd-year-seasons were absorbed into the
sire equations, AI sire groups were formed and
equations were solved b y Gauss-Seidel iteration.
Henderson (1966) proposed a mixed model The evaluation for a sire was ~j + Sjk. There
procedure that simultaneously evaluated sires were assumed to be differences among AI studs
and adjusted for fixed effects and competition in genetic merit. In addition, genetic trends
of sires. The procedure had the properties of would cause differences between years within
best linear unbiased prediction (BLUP) and was an AI stud. Therefore, groups were defined as
commonly called the "direct sire comparison." AI bulls entering an AI stud in a given year.
Miller (1968) did the basic groundwork of Use of model (1) restricted the data to
estimating sire effects, age correction factors, lactations on AI daughters and comparisons of
herd effects, cow effects and genetic and AI bulls within a herd-year-season. The elimi-
environmental trend. That allowed for a reduc- nation of non-AI records used in the herdmate
tion in the size of the sire evaluation model by comparison and the use of BLUP caused
preadjusting lactation records for certain fixed considerable changes in sire rankings as shown
effects prior to fitting the sire evaluation in table 1. Kingpin's evaluation, for example,
model. The first Northeast AI Sire Comparison changed 483 kg of milk, 227 kg because of the
(NEAISC) was published in June 1970. The average level of his AI competition and 256 kg
model assumed for the preadjusted daughter because of the elimination of non-AI herdmates.
records was: Composition and level of AI competition
changes irregularly over time. The average merit
Yijk~ = gt + hys i + gj + Sjk + eijk~, (I) of bulls entering AI service is not necessarily a

TABLE 1. EXAMPLE OF DIFFERENCES IN GENETIC LEVEL OF HERDMATES


OF SIRES DAUGHTERS (KG OF MILK)

Sire evaluation Average level


Herdmate of sires No. of
Sire name BLUpa comparison of herdmates daughters

Robbie 544 410 159 33


Plebe 454 451 -113 465
Astronaut 249 529 -159 121
Kingpin 181 664 --227 521
Sherry 113 34 181 46
Maple -136 137 -249 35

aBest linear unbiased prediction.


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MIXED MODEL SIRE EVALUATION 5 31

-- M~N OF ENTERING ~LLS is shown in table 2. The purpose of the work in


273 -- WEIGHTED M~N ~ BULLS U~D i~
table 2 was to determine the adequacy of CR in
227 7 /
estimating changes in evaluations with added
information. The first column indicates changes
in evaluations even with no additional daughters.
This occurs for several reasons:

--45 it~ ,/ 1) Solutions are obtained by iteration, and as


~-91 ,'/'-'/ a result, exact solutions are never obtained.
m -136 \ /
N -182 / 2) Sires may change groups if additional sires
-227 are added to the system because groups are
51 53 55 57 59 61 63 65 67 69 71
predefined to be a constant size and sires
YEAR USED
are allocated to groups in sequence by
Figure 2. Comparison of average evaluation of bulls birth date. A nonoAI proven bull entering
entering service in .a year and weighted mean of all
bulls used that year. AI at 7 yr of age will cause group changes.
3) Pedigree information may change because
of the addition of a paternal half brother
or the addition of a bull with the same
good indicator of the genetic merit of semen maternal grandsire.
used. The disparity between semen usage and 4) Changes in evaluations of sires of contem-
sire's average genetic merit is shown in figure 2. poraries with added information can cause
In 1954, 1955 and 1966, there was heavier use a change in the evaluation of a sire with
of poorer bulls. Data for figure 2 are from no additional daughters.
BLUP estimates made in retrospect, which may
In table 2, the typical change in an NEAISC
indicate that dairymen did not have sufficiently
evaluation with additional daughters given the
accurate information on which to base their
number of daughters in a previous evaluation i.s
selection decisions.
illustrated. Sires with larger numbers of daugh-
ters change little with added information
Confidence Range
compared with sires with fewer daughter s . It
The accuracy of NEAISC sire evaluations are was concluded that CR was a conservative
expressed in terms of confidence range (CR), an estimate of expected changes in sire evalua-
A A.
estimate of the standard error of gl +. Sjk. tions with additional daughters.
Because it is impossible to invert the large Incomplete and complete lactations are used
number of absorbed equations, the CR on each in the NEAISC. As shown in table 3, a close
bull was estimated by o2X~e/Skk, where Skk is relationship exists between sire evaluations
the diagonal element of the absorbed equations using incomplete records and subsequent
corresponding to the kth AI sire. evaluations with completed records. An average
The stability of NEAISC evaluations with absolute change of .41 CR and a correlation of
added daughters was studied in retrospect and .90 to .94 indicates that sire evaluations com-

TABLE 2. AVERAGE ABSOLUTE CHANGE (KG OF MILK) IN BLUPa SIRE EVALUATIONS


WITH ADDED DAUGHTERS

Average
No. of confidence Number of new daugnt~rs-L'--
daughters range 0 1 to 20 21 to 50 51 to 100 100+

1 to 20 222 31 109 192 292 215


21 to 50 196 15 64 109 131 259
51 to 100 150 11 44 70 95 156
101 to 500 84 10 24 42 50 71
~501 38 9 15 21 18 25

aBest linear unbiased prediction.


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532 EVERETT AND KEOWN

TABLE 3. RELATIONSHIPS AMONG SIRE EVALUATIONSCOMPOSED OF INCOMPLETE


AND COMPLETE RECORDS

Mean change in confidence range --.03 CR


Avg. absolute change .41 CR
Largest change 1.41 CR
282 kg of milk
Correlation between sire evaluations with incomplete records
and complete records .90 -- .94
Correlation between first crop complete and
last crop complete evaluations .86

18 adjustment factors for days nonpregnant or


z_ t6 days carried calf. The days carried calf adjust-
ments were applied to AI first lactation records
~,o ,~ and sires were evaluated using adjusted and
unadjusted records. A comparison of sire
0 w 8
evaluations from days carried calf adjusted
and unadjusted records is shown in table 4. The
standard deviation and maximum absolute
change decreases with increasing number of
2
daughters. Days carried calf effect is assumed to
l.S 1.25 1.0 ,75 .5 -25 O -.25 -.5 -.7~-I.O -I.25-1.S -I.75 be an environmental effect because heritability
MILK CR CHANGI[S in Holsteins was estimated to be .027 (Schaeffer
Figure 3. Frequency distribution of changes in sire et al., 1973). Adjustments for days carried calf
evaluations with at least 20 completed daughters to all essentially were independent of sires' genetic
daughters with complete records.
merits for milk production. Adjusting for days
carried calf especially is important in evalua-
tion of young sires so bulls truely superior in
posed of incomplete records are good predictors genetic merit are returned to heavy service.
of evaluations composed of completed records.
Use of DHI-AP Records
The largest change was 282 kg of milk, which
was equivalent to 1.41 CR for a young sire with The alternate morning and evening sampling
first-crop daughters. The distribution of changes (DHI-AP) concept was introduced in DHI by
on AI bulls with at least 20 daughters is shown Putnam and Gilmore (1968). It consists of
in figure 3. The correlation between evaluations sampling morning and evening milkings in
of first-crop completed records and second-crop alternate months with lactation estimates
completed records was .86. composed of 1/60th sample compared with the
Schaeffer et al. (1973) analyzed production traditional DHI sample of 1/30th. With the
records of daughters of AI sires and estimated rapid growth of DHI-AP sampling, DHI-AP

TABLE 4. EFFECTS OF ADJUSTING RECORDS FOR DAYS NONPREGNANT ON SIRE EVALUATIONS

Minimum daughters per sire


Item 1 25 50 100 200

No. of sires 1,140 617 449 310 203


Average change (kg of milk) .02 -.15 -1.08 .78 .58
SD of change (kg of milk) 55 46 41 38 33
Maximum absolute change
(kg of milk) 419 254 189 170 104

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MIXED MODEL SIRE EVALUATION 533

TABLE 5. COMPARISON OF MILK REPORTED'VERSUS MILK SOLD PER COW


ON TEST DAY FOR NEW YORK STATE HOLSTEIN HERDS

Standard
Type of No. of Average no. Milk reported (kg) deviation
test herd tests of cows/herd -- milk sold/cow (kg of milk)

DHI 29,232 65.6 .39 -+ .01 1.03


DHIR 2,638 62.1 .57 -+ .02 1.06
DHI-AP 10,227 60.2 .49 -+ .01 1.20
OS 5,239 45.4 .32 -+ .01 1.08

records were evaluated as a source of infor- considered official by breed associations, was
mation in sire evaluation. A comparison of milk the least accurate. Standard supervised DHI
sold vs milk r e p o r t e d for four testing plans used and supervised DHI-AP were intermediate to
in New Y o r k State Holstein herds is shown in OS and D H I R in accuracy. Sire evaluations
table 5. O w n e r / s a m p l e r (OS), where the dairy- c o m p o s e d of traditional records (DHI and
man records all p r o d u c t i o n w i t h o u t supervision, D H I R ) correlated highly with sire evaluations
was ranked the m o s t accurate testing plan using c o m p o s e d of DHI-AP records (table 6). This
the criterion of m o s t accurately measuring milk provided sufficient evidence for the inclusion of
s o l d / c o w b y the farm, and Dairy Herd Improve- DHI-AP in the N E A I S C in 1975.
m e n t Registry (DHIR), where all p r o d u c t i o n
i n f o r m a t i o n is r e c o r d e d b y a supervisor and is Relationship Matrix
The greatest technical advance in m i x e d
m o d e l sire evaluation was the d e v e l o p m e n t of a
simple m e t h o d for c o m p u t i n g the inverse o f a
TABLE 6. CORRELATIONS AMONG HOLSTEIN n u m e r a t o r relationship m a t r i x (A -1) b y C. R.
SIRE EVALUATIONS USING AM-PM a AND Henderson (1975a,b,c, 1976a). The m o s t
TRADITIONAL RECORDS (DHI interesting aspect o f Henderson's discovery was
AND DHIR) b
that A -1 can be calculated for a large p o p u l a t i o n
in a m a t t e r of seconds f r o m a list of animals
No. of Kg of and their sires and dams, whereas A m a y be
Item sires Milk Fat quite difficult to obtain. F o r N E A I S C evalua-
tions, A -1 is obtained f r o m a list of bulls, sires
All sires 769 .982 .886 and maternal grandsires (Henderson, 1975c)
Active sires 464 .983 .873 using the values in table 7. Elements of A -1 are
a . .
s u m m e d over bulls. For a particular bull,
Mdkmgs recorded per month. elements of A -1 in table 7 are multiplied by
b 9 9 . 2 2
Consecutwe mdkmgs recorded per month. Oe/O s. F o r example, a bull with a k n o w n sire

TABLE 7. SIMPLE METHOD FOR THE CALCULATION OF A-1 FOR A KNOWN PROGENY (p),
SIRE (s) AND MATERNAL GRANDSIRE (g) BY ADDING VALUES TO MATRIX LOCATIONS,
ASSUMING NO INBREEDING
;z =

s known s known s unknown s unknown


Matrix location g known g unknown g known g unknown

(p, p) 16/11 4/3 16/15 1/1


(p, s), (s, p) -8/11 --2/3
(p, g), g, p) --4/11 -4115
(s, s) 4/11 1/3
(s, g), (g, s) 2/11
(g, g) 1/11 1/15

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534 EVERETT AND KEOWN

TABLE 8. SIRE (S) AND MATERNAL GRANDSIRE (MGS) PEDIGREE COMBINATIONS


USED IN CALCULATING A -1 FOR HOLSTEINS

No. of Percentage of sires with


Sire model sires S + MGS S MGS Neither

NEAISC-1968 a 3,242 65.0 16.6 2.8 15.6


NEAISC-1978 b 3,488 62.7 17.1 3.0 17.2

aNEAISC-1968 model: Y~kl = ~ + hysi + gj + Sjk + eijkl.


bNEAISC-1978 model: Yijklmn = I~ + hysi + gj + ~k + thgl + lhSlm + eijklmn"

and u n k n o w n m a t e r n a l grandsire has f o u r filled maternal grandsire o f t w o or m o r e AI bulls


subclasses: evaluated. Therefore, nearly all of the sires and
maternal grandsires that are non-AI are classified
as u n k n o w n . The c o m p o s i t i o n of the pedigree
c o m b i n a t i o n s used in calculating A -1 are shown
-2/3 a/V in table 8. The sire m o d e l described in (1) has
15.6% o f the bulls classified f r o m u n k n o w n
The inclusion of A-1 in the N E A I S C reduced sires and maternal grandsires. These bulls
the need for grouping sires and increased the required r e t e n t i o n of groups in the m o d e l so
accuracy o f evaluations b e t w e e n bulls in that their evaluations w o u l d n o t be regressed to
different AI studs and in different generations. the base p o p u l a t i o n of bulls generated by
A c c u r a c y o f y o u n g sire evaluations especially A-1.
was i m p r o v e d b y the proper utilization of Utilization of A -1 in the N E A I S C changed
pedigree i n f o r m a t i o n supplied by A -1 . However, the concept and c o m p o s i t i o n of group solutions,
grouping of bulls was still necessary because o f as shown in table 9 for Holsteins. With sires
a lack o f pedigree i n f o r m a t i o n on s o m e AI assumed unrelated, sires' solutions theoretically
bulls. F o r example, the sire or maternal grandsire sum to zero within a group. Sires no longer
of an AI bull m a y be identified but will be averaged zero within a group w h e n A -1 was
classified as u n k n o w n if t h e y are n o t one of the utilized. In fact, if the c o m p l e t e relationship
AI bulls evaluated or are not the sire and(or) matrix were k n o w n , all group solutions w o u l d

TABLE 9. GROUP SOLUTIONS a FOR HOLSTEINS ASSUMING SIRES UNRELATED (MODEL 1)


AND WITH KNOWN RELATIONSHIPS (MODEL 2)

Milk (kg)
Group Model 1 Model 2

1 -121 -36
2 -21 8
3 -27 -1
4 -27 -23
5 13 8
6 I1 -28
7 37 -10
8 272 124
9 267 154
10 322 209
11 322 115
12 279 121

asires are assigned to groups of constant size in sequence by birth date. Model is: Yijkl = ~ + hys/+ gj + Sjk +
eijkl"
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MIXED MODEL SIRE EVALUATION 535

TABLE 10. TIES BETWEEN AI SIRES IN NEAISC A-1

Breed
Item Ayrshire Guernsey Holstein Jersey Brown Swiss

Number of sires 136 425 2,320 375 136


Ties
<50 118 305 869 240 130
51 to 100 16 95 539 115 6
101 to 200 2 25 539 20
201 to 400 267
401 to 700 92
>700 14
Most ties 111 180 981 176 72
Least ties 2 2 2 2 2
Average ties
for 10 youngest sires 27 29 56 30 18

be near zero and grouping would be less critical. The sparseness and composition of the
The exact composition of group solutions with equations solved are described in table 11. For
A -1 in the model is given by Quaas and Pollak the NEAISC A -1 described in (1), 3,272 sires in
(1981) and Pollak and Quaas (1983). 30 groups resulted in 3.8% filled subclasses.
The equations for the NEAISC A -1 with Calculation of A -1 resulted in 305 base sires
herd-year-seasons absorbed form a sparsely defined as sires or maternal grandsires with no
filled, diagonally dominant matrix. Ties between progeny that had at least two sons or grandsons
bulls as measured by the number of nonzero with progeny.
elements are summarized in table 10. Of the
Maternal Grandsire Model
2,320 Holstein sires evaluated, 869 had direct
comparisons with 1 to 50 other bulls, 539 bulls A common question from dairymen on sire
had direct comparisons with 51 to 100 other evaluation concerned bulls' evaluations dropping
bulls, and 14 bulls had greater than 700 direct with the addition of second-crop daughters. A
comparisons. One bull had direct ties with 981 second-crop daughter is a daughter conceived
other bulls. Of primary concern is the number after her sire has a progeny test evaluation and
of comparisons for the typical young sire. For has been returned to heavy A1 service. Although
the Holstein breed, the 10 youngest sires changes with added daughters were within the
averaged 56 ties with other bulls, which is expected CR, as shown in table 4, there was
sufficient for a valid ranking of the young sires. concern that certain popular bulls had a greater
Ties described in table 10 are composed of tendency to decrease. Research on Holsteins
relationships due to A -1 and direct comparisons showed a tendency for positive assortative
of sires within herd-year-seasons. mating while model (1) assumed random

TABLE 11. CHARACTERISTICS OF THE ABSORBED BLUPa NORTHEASTERN


ARTIFICIAL INSEMINATION SIRE COMPARISON EQUATIONS
FOR HOLSTEIN SIRE EVALUATION

No. of No. of % filled No. of


Model sires groups subclasses Base sires MGS only

NEAISC-1968 3,272 30 3.8 305


NEAISC-1978 3,520 32 7.4 318 230

aBest linear unbiased prediction.


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536 EVERETT AND KEOWN

mating. To account for bulls having nonran- grandsires in the model (table 11). There is also
dom mates, Quaas et al. (1979) and Everett et an increase in the number of equations to solve
al. (1979) developed the maternal grandsire because of 230 additional bulls that have no
model (NEAISC - 1978). daughters and are only maternal grandsires (AI
sires of mates of AI bulls). In recent years, 66%
Yijk~mn = # + hysi + gj + Sjk + 89 + of the AI first lactation records have identified
89 + eijk~mn, (2) AI maternal grandsires.
Changes in sire evaluations due to model (2)
where are shown in table 12. The changes in sire ranks
and evaluations were large while the rank
Yijk~mn =the nth first lactation daughter correlations between the sires remained near
record of the ruth maternal grand- 1.00. Using the same variance ratio, Oe2/O~, the
sire in the ~th group by the kth sire standard deviation of sire evaluations decreased
in the jth sire group initiated in the in the NEAISC-1978, which indicates positive
ith herd-year-season, assortative mating occurred in the population.
# =the overall mean, Reduction in differences among sires was the
hys i =the fixed effect of the ith herd- result of accounting for maternal grandsires
year-season, when there was positive assortative mating.
gj =the fixed effect of the jth AI sire Because of large differences among AI studs in
group, the genetic merit o f their bulls, it was esti-
Sjk =the random effect of the kth sire in mated that approximately 50% of the positive
the jth AI sire group, assortative mating occurred because dairymen
gs =the fixed effect of the ~th AI sire used the services of one bull stud, and the other
group, 50% was the result of dairymen selectively
S~m =the random effect of the mth AI mating their top cows to the best bulls and
maternal grandsire in the s AI b o t t o m cows to the poorer bulls (Everett et al.,
sire group and 1979).
eijk~mn =the random error.
Stayability
Pedigree combinations used in calculating
A -1 for the NEAISC-1978 are shown in table 8 The concept of stayability, a measure of
and are similar to those of the NEAISC-1968. longevity, was introduced by Everett et al.
Model 2 results in a large increase in percentage (1976a). Stayability is a binominal trait where
filled subclasses because of inclusion of maternal an AI daughter either survives or does not

TABLE 12. RELATIONSHIPS BETWEEN NORTHEASTERN ARTIFICIAL INSEMINATION


SIRE COMPARISON-1968 a AND NORTHEASTERN ARTIFICIAL INSEMINATION
SIRE COMPARISON-1978 b FOR HOLSTEINS

Number of daughters
Item ~1 />100

Number of bulls 2,937 707


Largest change in rank 1,793 105
Average change in rank 129 16
Largest change in kg 437 144
Average change in kg 52 34
Rank correlation .974 .993
Standard deviation
NEAISC-1968 259 308
NEAISC-1978 255 298
a
bYijkl = U + hys/+ gj + Sjk + eilkl.
Yijklmn -- ta + hys/+ g] + sl.k + 89 + 89 + eilklmn.
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MIXED MODEL SIRE EVALUATION 537

TABLE 13. GENETIC CORRELATIONS AMONG PRODUCTION,


STAYABIL1TYAND TYPE FOR HOLSTEINS

Trait
Trait 2 3 4 5 6 7 8a

1. Milk .85 .27 .41 .55 .51 .51 -.32


2. Fat .20 .32 .45 .43 .47 -.34
3. 36-stayability .94 .82 .62 .58 -.1i
4. 48-stayability 1.00 .99 .86 -.14
5. 60-stayability 1.00 1.00 -.15
6. 72-stayability 1.00 -.11
7. 84-stayability -.09

aTrait8isPDT.

survive to a given age. Sires are evaluated for Error Variance


stayability using binominal data in model (1).
The resulting sire evaluations measure genetic Nonrandom use of AI bulls within and
differences between bulls for total merit to stay between herds is a symptom of an underlying
in the herd, a composite of all traits for longev- problem pointed out by a dairyman. The
ity. The relationships between stayability and problem is heterogeneous within herd error
other traits are given in table 13 for Holsteins. variances and their effects on genetic evaluations
Under the assumption that 84-mo stayability is (Everett et al., 1982). In table 15, correlations
the ultimate measure of longevity, genetic among herd parameters and the error standard
correlations in table 13 indicate that genes for deviation from information on 7,398 Holstein
longevity can be measured accurately at 48 mo herds are presented. The relationships in table
of age, 3 yr earlier than 84-mo stayability. 15 indicate heavy use of AI and many years on
Genetic correlations with 36-mo stayability DHI are negatively associated with the within
indicate it is not as accurate an indicator of herd-year error variance of milk. Because a
84-mo stayability. Table 13 also indicates a 2 2s is used in evaluating all
constant ratio of Oe/O
consistent moderate genetic correlation between herds, the distribution or variance of estimated
production and stayability as well as consistent genetic merit is in proportion to the error
negative genetic correlations between type and variance. This indicates a lower probability of
other traits. Further evidence of these relation- finding elite cows in herds using AI and being
ships is given in table 14 where Holstein sire on test for many years because the genetic
evaluations are sequenced in quartiles by milk variance within a herd is related to the error
production. The positive relationships with variance. Therefore, dairymen using all the
stayability and negative relationships with type recommended procedures are less likely to have
are evident. cows identified as superior or elite.

TABLE 14. SIRE EVALUATIONS SEQUENCED BY MILK PRODUCTION FOR HOLSTEINS

Quartile
Sire
evaluation 1st 2rid 3rd 4th

Milk, kg 267 20 -158 -427


Fat, kg 7 0 -5 -12
36-stayability 1.8 1.4 1.5 1.0
48-stayability 1.1 .5 .4 -.8
60-stayability .7 -.1 -1.0 -2.5
72-stayability 1.4 .8 -.1 -1.4
84-stayability 1.7 1.0 .1 -1.0
PDT -.77 -.5 -.45 .01

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53 8 EVERETT AND KEOWN

TABLE 15. CORRELATIONS AMONG HERD PARAMETERS FOR HOLSTEINS

Variable
Variable 1 2 3 4 5 6a

1) No. of live cows -.12 .10 .05 .28 .01


2) 96 AI cows .49 .42 -.19 .15
3) Yr on DHI .25 -.34 .03
4) Avg ME milk, kg .24 .27
5) a e milk, kg .06
Mean 69 49 12.3 7,530 920 48

aTrait 6 is average ETA for milk (kg).

/
Also s h o w n in t a b l e 15 is a positive relation-
ship b e t w e e n m e a n a n d v a r i a n c e o f .24, as well
as a positive r e l a t i o n s h i p b e t w e e n m e a n a n d
average E T A o f .27 ( E v e r e t t et al., 1 9 8 2 ) . T h e s e
results violate t h e a s s u m p t i o n s o f t h e N E A I S C -
w
Q 1/"//
1978 m o d e l . I t was suggested t h a t a log trans-
_z
/ i -- Y~iy ~ pFodM~ (b" .RI251 f o r m a t i o n o f t h e d a t a c o u l d r e m o v e a large p a r t
~_. ,/ -- ~ Her4 w ~ ~ (b,.OO30~
of the relationship between the mean and
/ i we4acnm (b..Og~O~)
variance. T h e r e l a t i o n s h i p b e t w e e n x~ean a n d
9" .-. Leg t m m l m a l 4 t ~ t hat4
ta*~s ( b . - . O ~ O ) variance f o r log t r a n s f o r m e d a n d u n t r a n s f o r m e d
d a t a is s h o w n in figure 4. W i t h i n h e r d o e
544 increases 182.5 kg f o r each 1 , 0 0 0 kg increase in
5443 7~7 907~ 10686
.(Re eaooucT0Oa LEVEL (hg) yearly average p r o d u c t i o n . Log t r a n s f o r m a t i o n
r e d u c e s this to 20 kg p e r 1,000 kg increase in
Figure 4. Relationship between within and across
years production level and error standard dev/ation for yearly average p r o d u c t i o n . Herd p r o d u c t i o n
untransformed and log transformed milk production. levels w i t h i n years b e h a v e d i f f e r e n t l y a n d have

TABLE 16. AVERAGE WITHIN HERD-YEAR STANDARD DEVIATIONS (SD)


AND SIRE EVALUATIONS FOR HOLSTEIN BULLS ENTERING AI
IN DIFFERENT YEARS
=, , ;,, .. .,, _- ~ =:,

Year of entry into AI


Item 1960 1965 1970 1975 1979 All

1. Error SD, kg 788 841 894 980 1,018 898


2. NEAISC milk, kg
x -303 -224 -134 7 91 -162
SD 244 279 299 258 236 305
3. Transformed NEAISC
milk, kg
x -333 -243 -151 5 82 -179
SD 292 319 325 267 243 337
4. Milk change
(2 - 3)
x 30 18 17 2 9 17
SD 54 48 45 32 43 49
5. Number of bulls 64 89 95 113 88 2,078

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MIXED MODELSIRE EVALUATION 539

a slope of .083 compared with .1825. Log because of nonrandom use of bulls across
transformation produces a within year slope of production levels.
-.025, which indicates a large reduction in the Differences among sires and changes in
association between mean and variance both NEAISC evaluations for groups of bulls entering
within and across years by use of log trans- AI service in different years reflect the associa-
formed data. Of course, this would not be a tion between mean and variance. Uniformity of
serious problem in ranking bulls if there was bulls entering service decreased in 1965 and
random use of all AI bulls. 1970; however, this did not influence the
Nonrandom use of AI bulls across herds has standard deviation of milk change, which went
been a problem, and the effect on sire evaluation from 54, 48, 45, 32 to 43 kg and averaged 49
is demonstrated in table 16. Over 1,200,000 kg for all bulls with at least 20 daughters. It
first lactation records on daughters of 5,624 AI appears from figure 4 and table 16 that sire
Holstein sires were used to determine changes evaluations on log transformed data are superior
in NEAISC evaluations resulting from log to sire evaluations on untransformed data
transformed and untransformed records. In log because of the strong association between mean
transformed data, natural logarithms of produc- and variance. Beginning in 1984, NEAISC
tion records were modeled using the NEAISC 9evaluations will be calculated on the log trans-
model (2). Antilogs of solutions were obtained formed production records of the daughters.
at the production level of the base year of
1978. Within herd-year standard deviations and Multiple Trait NEAISC
sire evaluations are given in table 16 for bulls Testing individual cow milk samples for
with at least 20 daughters that entered AI protein was initiated by New York DHI in
service in 1960, 1965, 1970, 1975 and 1979. 1978. Interest in protein sire evaluations
Besides reranking bulls, log transformation increased, and the multiple trait BLUP described
produced greater differences among bulls than by Henderson and Quaas (1976) and Henderson
occurred with untransformed data. In 1960, (1976b) was the method of choice. Multiple
bulls entering service averaged - 3 0 3 kg com- trait NEAISC allows for simultaneous solution
pared with - 3 3 3 kg below the base year for of sire equations for n traits, all n traits having
transformed data. Average difference among unequal and missing information. Multiple trait
bulls entering service in 1960 increased from NEAISC includes evaluations for milk, fat,
243 to 292 kg of milk. Average change in protein and stayability and was published for
evaluations was 30 kg of milk with a standard the first time in January 1984. The maternal
deviation of change of 54 kg of milk. Bulls grandsire model, model (2), was used, and the
changing by an average of 54 kg of milk is BLUP equations were

X'R I y
(3)
R -x X Z ' R -x Z + G -x -- \z,R-ly/,
where R + G = the within herd-year-season phenotypic variance,

R = MR*M = environmental (co)variance matrix,


G = HG*H = genetic (co)variance matrix,

R* = 1.00 .87 .94 i / environmental


987 1.00 .90 correlations,
.94 .90 1.00
0 0 0 1.00

G* = genetic correlations,
82 1.00 .77 0
182 .77 1.00 u

0 0 0 1.00
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540 EVERETT AND KEOWN

where a, b, c and d = x/o~ ( 1 Z h : / 4 )

d)
M =

t a b
0
0
c
for milk, fat, protein and stgyability and

H =
a* b*
0
0
c* dl where a*, b*, c* and d* = X/o~ h214 for
milk, fat, protein and sta~ability, o{~
is the within herd-year-season pheno-
typic variance of stayability and the
logged production traits.

Covariances with stayability are assumed 1973, stud B made essentially no genetic
zero so that stayability will monitor the response progress. Stud B changed its genetic program
of the population to selection for production and made rapid progress from 1973 to 1982.
rather than being a correlated trait to produc- Stud A relaxed selection intensity and experi-
tion. enced a period of little genetic gain between
First lactation records on AI daughters 1975 and 1979.
were preadjusted to 305-d, 2x, mature equi-
valent (ME) basis (Miller, 1968) and corrected Conclusions
for days nonpregnant (Schaeffer et al., 1973). Theory and application of mixed model
The BLUP equations are developed as in sire evaluation has advanced significantly
equation (3) with herd-year-seasons absorbed. since first proposed by Henderson (1966,
Sires are grouped by the method of Quaas and 1974). Introduction of the relationship matrix
Pollak (1981). Multiple trait NEAISC has the (Henderson, 1975a,b,c, 1976a,b) was a major
advantages of: step in development of theory and application.
The problem of grouping sires has received
1) utilizing R -1 to account for herd-year- recent attention, and satisfactory methods for
season effects better, application are available (Quaas and Pollak,
2) utilizing known genetic relationships in 1981; Pollak and Quaas, 1983). Genetic pro-
G-1 to more accurately evaluate sires gress resulting from sire selection has been
for all traits and disappointing. Field results indicate genetic
3) obtaining a direct estimate of the CR progress for production to be less than 50% of
from inverse elements of the 4 x 4 diago- the theoretical optimum (Robertson and
nals of the sire equations. Rendel, 1950). Improvements in sire evaluation
provide the opportunity for increased genetic
Genetic Progress progress at little additional expense to the
Genetic progress in retrospect has been producer or consumer.
estimated by many investigators to be .25
to .50 of the theoretical optimum per year
(Everett and Henderson, 1972; Everett et
al., 1976b; Hintz et al., 1978). Progress in STUD A
the AI dairy population on test in the North- ~',
, ~ $TUOS
eastern USA that is due to AI sires is shown in
figure 5. Genetic gain due to better sires of 31 I ~j ."" STUD
STU[ g
kg of milk/yr is equivalent to .4%/yr. Genetic |
merit is estimated as the average of the sire plus ~"
one-half the maternal grandsire of daughters ~_,,
calving in each year.
..,/........'"'".....
Differences between AI organizations is
illustrated in figure 5 with trends shown for "57 "SO "e~ "7O "75 "80 "82
OF FRESHENING
studs A and B. Difference between studs f o r Figure 5. Genetic merit of first lactation AI Hol-
milk was 113 kg in 1963, which increased to stein cows calving (freshening) in the Northeastern
431 kg in 1973. During the period 1963 to United States.
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M I X E D M O D E L SIRE E V A L U A T I O N 541

Literature Cited
breeding values. Biometrics 32:69.
Everett, R. W. and C. R. Henderson. 1972. The Henderson, C. R. 1976b. Multiple trait sire
Northeast AI sire comparison. Why? Animal evaluation using the relationship matrix. J.
Science Mimeograph Series No. 19. Dept. of Dairy Sci. 59:769.
Anim. Sci., Cornell Univ., Ithaca, NY. Henderson, C. R. and R. L. Quaas. 1976.
Everett, R. W., J. F. Keown and E. E. Clapp. Multiple trait evaluation using relatives'
1976a. Relationships among type, produc- records. J. Anita. Sci. 43:1188.
tion, and longevity in Holstein cattle. J. Hintz, R. L., R. W. Everett and L. D. Van Vleck.
Dairy Sci. 59:1505. 1978. Estimation of genetic treods from
Everett, R. W., J. F. Keown and E. E. Clapp. cow and sire evaluations. J. I/airy Sci.
1976b. Production and stayability trends in 61:607.
dairy cattle. J. Dairy Sol. 59:1532. Hirsh, D. E. and I. R. Hedges. 1949. Dairy
Everett, R. W., J. F. Keown and J. F. Taylor. breeding cooperatives. Their development,
1982. The problem of heterogeneous within practices and policies. Farm Credit Adminis-
herd error variances when identifying elite tration, - USDA, Washington, DC. Circ.
cows. J. Dairy Sci. 65(Suppl. 1): 100. C-133.
Everett, R. W., R. L. Quaas and A. E. McClintock. Miller, P. D. 1968. Simultaneous estimation of
1979. Daughters' maternal grandsires in sire sire effects, age correction factors, genetic
evaluation. J.DairySci. 62:1304. trend, environmental trend, herd effects and
Henderson, C. R. 1966. Sire evaluation method cow effects. Ph.D. Dissertation. Cornell
which accounts for unknown genetic and Univ., Ithaca, NY.
environmental trends, herd differences, Pollak, E. J. and R. L. Quaas. 1983. Definition of
seasons, age effects, and differential culling, group effects in sire evaluation models. J.
Proc. National Tech. Syrup. on Estimating DairySci. 66:1563.
Breeding Values of Dairy Sires and Cows. Putnam, D. H. and H. C. Gilmore. 1968. The
Washington, IX3. evaluation of an alternate am/pm monthly
Henderson, C. R. 1974. General flexibility of testing program and its application for use
linear model techniques for sire evaluation. in the DHIA program. J. Dairy Sci. 51:985.
J. Dairy Sci. 57:963. Quaas, R. L., R. W. Everett and A. E. McClintock.
Henderson, C. R. 1975a. Rapid method for 1979. Maternal grandsire model for dairy
computing the inverse of a relationship sire evaluation. J. Dairy Sci. 62:1648.
matrix. J. Dairy Sci. 58:1727. Quaas, R. L. and E. J. Pollak. 1981. Modified
Henderson, C. R. 1975b. Use of relationship equations for sire models with groups. J.
among sires to increase accuracy of sire Dairy Sci. 64:1868.
evaluation. J. Dairy Sci. 58:1731. Robertson, A. and J. M. Rendel. 1950. The use
Henderson, C. R. 1975c. Inverse of a matrix of of progeny testing with artificial insemina-
relationships due to sires and maternal tion. J. Genet. 50:21.
grandsires. J. Dairy Sci. 58:1917. Schaeffer, L. R., R. W. Everett and C. R. Hender-
Henderson, C. R. 1976a. A simple method for son. 1973. Lactation records adjusted for
computing the inverse of a numerator days open in sire evaluation. J. Dairy Sci.
relationship matrix used in prediction of 56:602.

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