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 ,'/'-'/
m -136 \ /
N -182 / 2) Sires may change groups if additional sires
-227
51 53 55 57 59 61 63
YEAR USED
Figure 2. Comparison of average evaluation of bulls
entering service in .a year and weighted mean of all
bulls used that year.
good indicator of the genetic merit of semen
used. The disparity between semen usage and
sire's average genetic merit is shown in figure 2.
In 1954, 1955 and 1966, there was heavier use
of poorer bulls. Data for figure 2 are from
BLUP estimates made in retrospect, which may
indicate that dairymen did not have sufficiently
accurate information on which to base their
selection decisions.
Confidence Range
The accuracy of NEAISC sire evaluations are
expressed in terms of confidence range (CR), an
A A.
estimate of the standard error of gl +. Sjk.
Because it is impossible to invert the large
number of absorbed equations, the CR on each
bull was estimated by o2X~e/Skk, where Skk is
the diagonal element of the absorbed equations
corresponding to the kth AI sire.
The stability of NEAISC evaluations with
added daughters was studied in retrospect and
a result, exact solutions are never obtained.
are added to the system because groups are
65 67 69 71
predefined to be a constant size and sires
are allocated to groups in sequence by
birth date. A nonoAI proven bull entering
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
maternal grandsire.
4) Changes in evaluations of sires of contem-
poraries with added information can cause
a change in the evaluation of a sire with
no additional daughters.
In table 2, the typical change in an NEAISC
evaluation with additional daughters given the
number of daughters in a previous evaluation i.s
illustrated. Sires with larger numbers of daugh-
ters change little with added information
compared with sires with fewer daughter s . It
was concluded that CR was a conservative
estimate of expected changes in sire evalua-
tions with additional daughters.
Incomplete and complete lactations are used
in the NEAISC. As shown in table 3, a close
relationship exists between sire evaluations
using incomplete records and subsequent
evaluations with completed records. An average
absolute change of .41 CR and a correlation of
.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:
-2/3 a/V
The inclusion of A-1 in the N E A I S C reduced
the need for grouping sires and increased the
accuracy o f evaluations b e t w e e n bulls in
different AI studs and in different generations.
A c c u r a c y o f y o u n g sire evaluations especially
was i m p r o v e d b y the proper utilization of
pedigree i n f o r m a t i o n supplied by A -1 . However,
grouping of bulls was still necessary because o f
a lack o f pedigree i n f o r m a t i o n on s o m e AI
bulls. F o r example, the sire or maternal grandsire
of an AI bull m a y be identified but will be
classified as u n k n o w n if t h e y are n o t one of the
AI bulls evaluated or are not the sire and(or)
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
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
sires and maternal grandsires. These bulls
required r e t e n t i o n of groups in the m o d e l so
that their evaluations w o u l d n o t be regressed to
the base p o p u l a t i o n of bulls generated by
A-1.
Utilization of A -1 in the N E A I S C changed
the concept and c o m p o s i t i o n of group solutions,
as shown in table 9 for Holsteins. With sires
assumed unrelated, sires' solutions theoretically
sum to zero within a group. Sires no longer
averaged zero within a group w h e n A -1 was
utilized. In fact, if the c o m p l e t e relationship
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 exact composition of group solutions with
A -1 in the model is given by Quaas and Pollak
(1981) and Pollak and Quaas (1983).
The equations for the NEAISC A -1 with
herd-year-seasons absorbed form a sparsely
filled, diagonally dominant matrix. Ties between
bulls as measured by the number of nonzero
elements are summarized in table 10. Of the
2,320 Holstein sires evaluated, 869 had direct
comparisons with 1 to 50 other bulls, 539 bulls
had direct comparisons with 51 to 100 other
bulls, and 14 bulls had greater than 700 direct
comparisons. One bull had direct ties with 981
other bulls. Of primary concern is the number
of comparisons for the typical young sire. For
the Holstein breed, the 10 youngest sires
averaged 56 ties with other bulls, which is
sufficient for a valid ranking of the young sires.
Ties described in table 10 are composed of
relationships due to A -1 and direct comparisons
of sires within herd-year-seasons.
The sparseness and composition of the
equations solved are described in table 11. For
the NEAISC A -1 described in (1), 3,272 sires in
30 groups resulted in 3.8% filled subclasses.
Calculation of A -1 resulted in 305 base sires
defined as sires or maternal grandsires with no
progeny that had at least two sons or grandsons
with progeny.
Maternal Grandsire Model
A common question from dairymen on sire
evaluation concerned bulls' evaluations dropping
with the addition of second-crop daughters. A
second-crop daughter is a daughter conceived
after her sire has a progeny test evaluation and
has been returned to heavy A1 service. Although
changes with added daughters were within the
expected CR, as shown in table 4, there was
concern that certain popular bulls had a greater
tendency to decrease. Research on Holsteins
showed a tendency for positive assortative
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-
dom mates, Quaas et al. (1979) and Everett et
al. (1979) developed the maternal grandsire
model (NEAISC - 1978).
Yijk~mn = # + hysi + gj + Sjk + 89
89 + eijk~mn,
where
Yijk~mn =the nth first lactation daughter
record of the ruth maternal grand-
sire in the ~th group by the kth sire
in the jth sire group initiated in the
ith herd-year-season,
# =the overall mean,
hys i =the fixed effect of the ith herd-
year-season,
gj =the fixed effect of the jth AI sire
group,
Sjk =the random effect of the kth sire in
the jth AI sire group,
gs =the fixed effect of the ~th AI sire
group,
S~m =the random effect of the mth AI
maternal grandsire in the s AI
sire group and
eijk~mn =the random error.
Pedigree combinations used in calculating
A -1 for the NEAISC-1978 are shown in table 8
and are similar to those of the NEAISC-1968.
Model 2 results in a large increase in percentage
filled subclasses because of inclusion of maternal
grandsires in the model (table 11). There is also
an increase in the number of equations to solve
because of 230 additional bulls that have no
daughters and are only maternal grandsires (AI
sires of mates of AI bulls). In recent years, 66%
+ of the AI first lactation records have identified
(2) AI maternal grandsires.
Changes in sire evaluations due to model (2)
are shown in table 12. The changes in sire ranks
and evaluations were large while the rank
correlations between the sires remained near
1.00. Using the same variance ratio, Oe2/O~, the
standard deviation of sire evaluations decreased
in the NEAISC-1978, which indicates positive
assortative mating occurred in the population.
Reduction in differences among sires was the
result of accounting for maternal grandsires
when there was positive assortative mating.
Because of large differences among AI studs in
the genetic merit o f their bulls, it was esti-
mated that approximately 50% of the positive
assortative mating occurred because dairymen
used the services of one bull stud, and the other
50% was the result of dairymen selectively
mating their top cows to the best bulls and
b o t t o m cows to the poorer bulls (Everett et al.,
1979).
Stayability
The concept of stayability, a measure of
longevity, was introduced by Everett et al.
(1976a). Stayability is a binominal trait where
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
differences between bulls for total merit to stay
in the herd, a composite of all traits for longev-
ity. The relationships between stayability and
other traits are given in table 13 for Holsteins.
Under the assumption that 84-mo stayability is
the ultimate measure of longevity, genetic
correlations in table 13 indicate that genes for
longevity can be measured accurately at 48 mo
of age, 3 yr earlier than 84-mo stayability.
Genetic correlations with 36-mo stayability
indicate it is not as accurate an indicator of
84-mo stayability. Table 13 also indicates a
consistent moderate genetic correlation between
production and stayability as well as consistent
negative genetic correlations between type and
other traits. Further evidence of these relation-
ships is given in table 14 where Holstein sire
evaluations are sequenced in quartiles by milk
production. The positive relationships with
stayability and negative relationships with type
are evident.
Nonrandom use of AI bulls within and
between herds is a symptom of an underlying
problem pointed out by a dairyman. The
problem is heterogeneous within herd error
variances and their effects on genetic evaluations
(Everett et al., 1982). In table 15, correlations
among herd parameters and the error standard
deviation from information on 7,398 Holstein
herds are presented. The relationships in table
15 indicate heavy use of AI and many years on
DHI are negatively associated with the within
herd-year error variance of milk. Because a
2 2s is used in evaluating all
constant ratio of Oe/O
herds, the distribution or variance of estimated
genetic merit is in proportion to the error
variance. This indicates a lower probability of
finding elite cows in herds using AI and being
on test for many years because the genetic
variance within a herd is related to the error
variance. Therefore, dairymen using all the
recommended procedures are less likely to have
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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permission.
540 EVERETT AND KEOWN
M =
t a b
0
0
c
H =
a* b*
0
0
c*
Covariances with stayability are assumed
zero so that stayability will monitor the response
of the population to selection for production
rather than being a correlated trait to produc-
tion.
First lactation records on AI daughters
were preadjusted to 305-d, 2x, mature equi-
valent (ME) basis (Miller, 1968) and corrected
for days nonpregnant (Schaeffer et al., 1973).
The BLUP equations are developed as in
equation (3) with herd-year-seasons absorbed.
Sires are grouped by the method of Quaas and
Pollak (1981). Multiple trait NEAISC has the
advantages of:
1) utilizing R -1 to account for herd-year-
season effects better,
2) utilizing known genetic relationships in
G-1 to more accurately evaluate sires
for all traits and
3) obtaining a direct estimate of the CR
from inverse elements of the 4 x 4 diago-
nals of the sire equations.
Genetic Progress
Genetic progress in retrospect has been
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
the AI dairy population on test in the North-
eastern USA that is due to AI sires is shown in
figure 5. Genetic gain due to better sires of 31
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
studs A and B. Difference between studs f o r
milk was 113 kg in 1963, which increased to
431 kg in 1973. During the period 1963 to
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where a, b, c and d = x/o~ ( 1 Z h : / 4 )
d)
for milk, fat, protein and stgyability and
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.
1973, stud B made essentially no genetic
progress. Stud B changed its genetic program
and made rapid progress from 1973 to 1982.
Stud A relaxed selection intensity and experi-
enced a period of little genetic gain between
1975 and 1979.
Conclusions
Theory and application of mixed model
sire evaluation has advanced significantly
since first proposed by Henderson (1966,
1974). Introduction of the relationship matrix
(Henderson, 1975a,b,c, 1976a,b) was a major
step in development of theory and application.
The problem of grouping sires has received
recent attention, and satisfactory methods for
application are available (Quaas and Pollak,
1981; Pollak and Quaas, 1983). Genetic pro-
gress resulting from sire selection has been
disappointing. Field results indicate genetic
progress for production to be less than 50% of
the theoretical optimum (Robertson and
Rendel, 1950). Improvements in sire evaluation
provide the opportunity for increased genetic
progress at little additional expense to the
producer or consumer.
STUD A
~',
, ~ $TUOS
I ~j ."" STUD
STU[ g
|
~"
~_,,
..,/........'"'".....
"57 "SO "e~ "7O "75 "80 "82
OF FRESHENING
Figure 5. Genetic merit of first lactation AI Hol-
stein cows calving (freshening) in the Northeastern
United States.
 M I X E D M O D E L SIRE E V A L U A T I O N
Literature Cited
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