Assessment of Interbull GMACE Evaluations for North American
Holstein Genomic Young Bulls Based on APR in Australia
Brian Van Doormaal, Gerrit Kistemaker & Pete Sullivan
Canadian Dairy Network
June 2014
Background
Effective August 2014, Interbull will offer GMACE evaluation services on an official/routine basis for
Holsteins, which provides a genomic evaluation for “publishable” young bulls on the national scale for
the 30+ countries that participate in MACE. In preparation for this first official release, Interbull has
conducted a series of GMACE test runs as well as GMACE implementation runs in December 2013
and April 2014. Participating countries have included Australia, Canada, Denmark/Finland/Sweden
(joint evaluation), France, Germany, Italy, Netherlands, Poland, Switzerland, United Kingdom and
United States (prior to February 2014 test run). For results distributed in association with a GMACE test
run, data files include all young bulls with a genomic evaluation (official or unofficial) in any of the
participating countries but national evaluations receiving these results are not permitted to release
individual bull evaluations. For the implementation (and official) runs, the distribution files provided by
Interbull to each country only include genomic young sires that have been deemed as publishable.
Since the April 2014 run, the publishable status may be assigned by the owning A.I. organization in
accordance with the status in the assigned controlling country or, in the absence of an assigned
controlling country, the GMACE evaluation will be publishable for bulls that are coded as having an
official genomic evaluation in at least one country participating in GMACE. Interbull imposes a policy
that once a bull has received a publishable GMACE evaluation and is included in the distribution files,
then that bull must continue to receive a publishable GMACE evaluation until they become progeny
proven and therefore receives a MACE evaluation. At least in part, this publication policy resulted in
the decision taken by all North American A.I. organizations to assign “USA” as the controlling country
for essentially all of their bulls along with a publication status of “No”, thereby excluding all such bulls
from the GMACE files resulting from the April 2014 implementation run. Prior to making a decision to
assign a publication status of “Yes”, various A.I. member organizations of CDN requested an analysis
of how their genomic young sires would rank in other countries, especially Australia for which across
country genetic correlations with Canada/North America are lower than average.
Data
Given the focus of analysis was deemed to be the Australian scale, CDN gathered the following data:




From the national genetic evaluation centre in Australia, namely ADHIS, CDN received the
formula for calculating APR (Australian Profit Ranking) as well as a data file with national
evaluations for individual traits and the official APR value for over 13,500 progeny proven sires
(both domestic and foreign).
February 2014 GMACE test run results for all included genomic young bulls, expressed on the
Australian scale. This included over 91,000 young bulls in total, but this was reduced to
approximately 75,300 that had a GMACE evaluation for production, type and key functional
traits required to estimate/calculate an APR value.
From the CDN database, the April 2014 genomic evaluations on the Canadian scale were
retrieved for each young bull, which may be an official GPA LPI, an unofficial GPA LPI or an IGI
LPI (based on GMACE results from Interbull).
For young bulls genotyped by a North American A.I. organization, the NAAB Controller code
was retrieved from the CDN database for bulls with an official GPA LPI otherwise the A.I.
requester was retrieved (for candidate bulls genotyped but not selected by A.I.).
1
Analysis to Estimate APR Values
The first step in the analysis was to use the GMACE evaluations on the Australian scale to calculate an
APR value. This process proved to be much more difficult than initially expected. The formula for APR
is as follows:
APR = (7.096 x Protein) + (1.434 x Fat) + (-0.084 x Milk) + (6.988 x (Survival-100)) +
(1.627 x (Milking Speed-100) + (4.276 x (Temperament-100)) + (0.666 x (Cell Count-100)) +
(-2.708 x (Liveweight-100) + (4.380 x (Daughter Fertility-100))
While the formula itself is relatively straightforward, three main roadblocks were realized for this
analysis. Firstly, the GMACE service offered by Interbull does not currently include Temperament so
evaluations for this trait do not exist. Secondly, the same is true for Liveweight which is also a trait
unique to Australia. Lastly, although Daughter Fertility is in the APR formula, the GMACE service
includes female fertility traits that yield three values on the Australian scale, which equate to Calving to
First Service, First Service to Conception in cows and Days Open. No formula for building Daughter
Fertility on the Australian scale was provided by ADHIS to CDN so the use of the GMACE evaluations
for these three female fertility traits was limited.
To address each of these issues, an analysis was conducted using the official Australian evaluations
for various traits and APR provided in the file for progeny proven sires. Based on a group of 856
progeny proven sires in Australian, a multiple regression analysis was applied to predict the genetic
evaluation for Liveweight based on genetic evaluations for specific type traits also analyzed within the
GMACE service by Interbull. This approach proved to be very successful in terms of deriving a formula
for calculating Liveweight since a prediction formula based Stature, Chest Width and Body Depth
yielded an accuracy of prediction (R-Square) of 99.3%. Pin Width was also tested for inclusion but was
found to be insignificant. Since GMACE evaluations were not available for Temperament and
reconstruction of Daughter Fertility was not feasible based on the three specific female fertility traits, a
second multiple regression analysis was conducted to derive a formula to predict APR based solely on
the other included traits, namely Milk, Fat, Protein, Survival, Milking Speed, Cell Count and Liveweight.
Compared to using the exact APR formula, a prediction formula that excluded only Temperament
yielded an accuracy of prediction (R-Square) of 99.3%. When both Temperament and Daughter
Fertility were excluded from the prediction formula, accuracy decreased slightly to 96.9%.
Using the prediction equation that excluded Temperament and Daughter Fertility, APR values were
estimated for all genomic young bulls based on their GMACE evaluations on the Australian scale.
These APR values were then used to conduct the subsequent analysis to assess how well young bulls
owned by North American A.I. organizations, especially members of CDN, would rank in Australia if
their GMACE evaluations were assigned a Publication Status of “Yes”.
Relative Positioning of North American Owned Genomic Young Bulls
Of the total 75,300 Holstein genomic young bulls with a GMACE evaluation on the Australian scale,
those ranking among the Top 10,000 based on their estimated APR were retained for further analysis.
Of these bulls roughly 5,900 have a genomic evaluation and GPA LPI in Canada based on their own
genotype and about 1,100 foreign genotyped young bulls were coded as Publishable in the April 2014
GMACE evaluation by Interbull and therefore have an IGI LPI in Canada. The remaining 3,000 young
bulls were those that do not have a genotype in North America but were also not assigned a
Publishable Status of “Yes” for GMACE, suggesting they are mainly foreign candidate young bulls that
were genotyped but not selected by an A.I. organization. Figure 1 shows the relationship between the
official GPA LPI in Canada and the APR estimated from GMACE evaluations on the Australian scale for
a group of approximately 400 bulls known at CDN to be owned/controlled by a North American A.I.
organization and a minimum estimated APR of 225. This plot clearly demonstrates that significant
amount for re-ranking that occurs when going from LPI in Canada to APR in Australia. In the case of
genomic evaluations, this re-ranking results from three main factors; (a) differing formula for LPI and
APR, (b) genotype by environment re-ranking proven by MACE to exist between these countries, and
(c) differing methods and results associated with the estimation of genomic evaluations in each country.
Based on a group of 740 progeny proven Holstein sires that have an official domestic APR in Australia
2
and were matched with their official LPI in Canada, the correlation between these national indexes is
approximately 78% once evaluations are based on daughter performance data in both countries.
In order to assess how well the North American owned bulls would rank based on APR in Australia, an
analysis of the top ranked progeny proven bulls in Australia was conducted including those with an
official domestic proof as well as foreign sires with a MACE evaluation in Australia (Table 1). In April
2014, a total of 4 progeny proven bulls received an APR exceeding 300 with two extreme outliers at
348 (domestic) and 337 (foreign), respectively. A group of 10 bulls received an APR of at least 290 and
this count increased to 14 and 22 bulls (6 being foreign) surpassing the levels of 280 and 270 APR,
respectively. A total of 138 bulls have an APR of at least 225 in Australia, of which 102 have an official
domestic progeny proof there and 36 are foreign proven sires with a MACE evaluation in Australia
(Table 1).
The main purpose of including Table 1 in this report is to serve as a reference point for assessing how
well genomic young sires in North America would rank if their GMACE evaluations were to become
officially distributed by Interbull for publication in each country participating in MACE, which includes
Australia. Assigning an actual “APR Rank” for each bull is impossible without knowing the full subset of
bulls that would receive a publishable GMACE evaluation. In this analysis, this situation is further
complicated by the fact that there would be several genomic young bulls from other countries outside of
North America that could rank high for APR in Australia but the publication status of those bulls is not
known to CDN.
Based on the APR values estimated in this study, Table 2 provides a count of young bulls by level of
APR and NAAB Controller code. Having such a Controller code suggests these bulls (or at least the
marketing rights) have been purchased by that A.I. organization. Among these bulls, the highest
estimated APR is 291 and a total of 6 and 18 reach 280 and 270 APR or higher, respectively. In total,
nearly 400 North American owned genomic young sires have an estimated APR of 225 or higher based
on their GMACE evaluations on the Australian scale. This number suggests that the North American
group of genomic young bulls will rank highly and compete well in Australia, especially relative to the
proven sires already ranked in that country.
3
Table 1: Origin of Holstein Proven Sires with Minimum APR of 225 in April 2014 (Local and Foreign Proven)
Progeny Proven in Australia
APR
Foreign Proven Sire
Total
Cum
Total
2
1
3
1
1
1
1
1
1
1
1
1
2
1
1
2
2
1
3
2
2
3
3
2
3
1
1
2
3
2
3
4
2
1
1
1
1
5
2
2
4
5
4
1
4
3
2
1
2
2
2
3
2
5
3
6
4
5
2
9
3
1
2
3
4
5
6
7
8
10
11
12
14
16
17
20
22
24
27
30
32
35
36
37
39
42
44
47
51
53
54
55
56
57
62
64
66
70
75
79
80
84
87
89
90
92
94
96
99
101
106
109
115
119
124
126
135
138
36
138
AUS BEL CAN CZE DEU FRA GBR NLD NZL USA Total BEL CAN DEU DNK FRA GBR ITA NLD NZL SWE USA Total
348
337
312
305
299
296
295
292
290
287
284
282
276
275
274
273
269
268
266
265
264
262
261
260
257
256
255
254
253
252
251
250
249
248
247
246
245
244
243
242
241
240
239
238
237
236
235
234
233
232
231
230
229
228
227
226
225
1
1
2
2
3
1
3
1
3
4
2
1
6
2
Total
85
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
1
2
1
2
3
1
1
1
1
2
1
2
3
1
1
1
1
1
1
1
2
1
1
2
1
1
1
3
2
2
2
1
2
3
1
1
1
2
1
1
1
1
2
2
3
1
3
3
1
1
1
1
1
1
1
1
1
2
2
1
3
4
3
1
2
3
1
1
1
4
2
1
1
1
1
1
1
1
1
1
3
5
3
1
4
3
1
1
1
1
1
1
1
1
1
1
2
0
0
1
1
6
0
6
102
1
1
1
1
1
1
1
2
1
1
2
1
1
0
2
2
3
1
2
1
5
2
1
1
1
1
2
2
3
1
4
1
3
4
3
1
6
2
2
1
15
0
5
1
1
2
3
Missed Opportunity
Table 2 also provides a count by estimated APR of candidate young bulls that were genotyped by a
North American A.I. organization but subsequently not selected for purchase (based on data at CDN).
Oddly enough, one such bull reaches the highest estimated APR of 300 and three others rank above
270 APR. In total, there are 111 such bulls that have an estimated APR of at least 225, which is
another group of 28% more high ranking young bulls in Australia that could potentially have been
purchased by a North American A.I. organization. This situation arises due to the significant re-ranking
that can occur between rankings for LPI (or TPI) and ranking for APR in Australia. The ideal way for
4
capitalizing on this missed opportunity is to have a genotype exchange agreement between North
America and Australia that includes all genotyped candidate young sires (not just those selected by
A.I.) in addition to progeny proven sires (for the reference population). Such an exchange agreement
should also require that ADHIS provide data files back North America (for distribution of results to the
genotype submitter and/or genomic evaluation requester) with the Australian genomic evaluations by
trait and the directly calculated APR. Without such an opportunity for North American A.I. organizations
to specifically select genomic young sires from around the world that would best be suited for the
Australian marketplace, domestic bulls offered within Australia will continue to have an advantage.
Table 2: Number of North American Owned/Genotyped Holstein Genomic Young Bulls with APR of at least 225 in
Australia based on February 2014 Test Run GMACE Evaluations
Estimated
APR
300
291
289
285
282
280
278
276
274
273
272
271
270
269
268
267
266
265
264
263
262
261
260
259
258
257
256
255
254
253
252
251
250
249
248
247
246
245
244
243
242
241
240
239
238
237
236
235
234
233
232
231
230
229
228
227
226
225
Total
NAAB A.I. Controller Code
7 200 14 11 29
Total
1 2200 151 76 534 54 147 180 203 513 2139 2224
1
1
1
1
1
1
1
2
1
1
1
1
1
1
1
1
1
1
1
3
1
1
1
1
2
2
2
1
2
1
1
1
3
2
2
3
2
1
1
2
1
3
3
2
5
5
4
5
3
8
6
4
3
7
4
6
6
5
6
4
5
5
4
3
5
7
2
1
1
2
1
1
1
2
1
1
2
1
1
1
1
1
1
1
1
1
1
1
2
1
1
1
2
1
1
2
2
1
2
2
1
1
1
2
1
2
2
1
2
2
1
3
1
1
1
1
3
2
1
1
1
1
1
1
2
1
2
2
1
2
2
1
5
5
5
4
2
3
3
2
1
3
1
1
2
3
1
1
2
1
2
2
1
2
1
1
3
4
1
2
2
2
1
2
1
2
1
1
1
1
1
2
3
2
2
1
1
1
1
3
3
1
2
1
1
2
1
2
2
1
1
2
1
1
1
1
1
2
1
2
2
1
2
1
155 60 40 35 34 28
1
1
16
7
4
4
3
2
5
2
2
2
2
1
0
1
1
1
2
1
3
1
3
1
1
1
2
2
3
2
1
7
4
4
5
2
0
5
2
4
2
6
4
2
6
6
7
7
8
7
9
12
10
8
6
13
8
8
12
11
11
15
19
12
19
13
21
15
16
10
16
19
397
Cum
Not
Cum
Total Selected Total
0
1
2
3
5
6
9
10
13
14
15
16
18
20
23
25
26
33
37
41
46
48
48
53
55
59
61
67
71
73
79
85
92
99
107
114
123
135
145
153
159
172
180
188
200
211
222
237
256
268
287
300
321
336
352
362
378
397
1
1
1
1
1
1
1
1
1
1
1
1
4
1
2
4
1
1
3
3
2
1
2
1
3
4
4
3
6
6
7
10
5
9
6
11
111
1
2
3
5
7
8
12
13
16
18
19
20
22
24
27
29
30
37
42
47
52
55
56
62
64
68
70
76
81
84
91
101
108
116
126
137
147
160
173
181
190
205
213
222
236
248
262
281
304
319
344
363
391
416
437
456
478
508