The New STAGES

Jim Venner
Director of Research and Education
National Swine Registry
West Lafayette, IN


Introduction

The pork industry has incurred tremendous change in recent years, not only in the manner of production, but also in the type of commodity produced. This rapid amount and rate of change has put added pressure on the seedstock industry to provide the genetic tools to produce an acceptable end product. Because genetic improvements made towards more efficient pork production are made first at the seedstock level, the producers of breeding animals have been very innovative in utilizing the most current technology.

Before 1985, genetic evaluation of swine in the United States was conducted on a very limited basis. Because of the biology of swine and the continuous methods of production, genetic evaluation had to include the ability to account for multiple records and large numbers of relatives in order to achieve high accuracy, features that were for the most part, unavailable up to this time.

The development of a Swine Testing and Genetic Evaluation System (STAGES) was initiated as a joint venture between Purdue University, U.S.D.A. Agricultural Research Service, U.S.D.A. Extension Service, National Association of Swine Records, individual purebred associations, and the National Pork Producers Council in 1985. The following year, the first within-herd genetic evaluations were conducted, with across-herd evaluations available in 1990. The STAGES program, supervised by Purdue University, has since been in use for the Yorkshire and Landrace breeds, while PAGE 1, a similar genetic evaluation program conducted by the University of Georgia, has generated EPD's for the Duroc and Hampshire breeds of swine.

In 1998, the National Swine Registry, the registry for these four breeds, released a new version of STAGES, a combination of the original STAGES and PAGE 1. This genetic evaluation program utilizes breed specific adjustments and variance components to generate Expected Progeny Differences (EPD's) and bio-economic indexes for the swine industry.

Industry demands for genetic evaluation places certain requirements on any program that is to be successful. EPD's must be accurate, easy to understand and use, accessible and dynamic. The National Swine Registry has strived to address each of these concerns with the new STAGES.

Database

The across-herd genetic analysis for each breed runs in-house and nightly. NSR members recently submitted the one millionth performance into the STAGES program, with each record representing either a maternal litter record or an individual growth record. Table 1 shows the breakdown by breed performance records, and the time required to run the evaluation each night. It was necessary to keep total computer time under 12 hours in order to run nightly, and currently total run time is slightly over 9 hours.

Table 1. Number of performance records in NSR database and run timea
Reproductive records
Growth records
Total records
Total run time
Yorkshire
228,476
318,546
547,022
4h. 44m. 43s.
Duroc
58,863
121,329
180,192
1h. 59m. 24s.
Hampshire
74,980
91,853
166,833
1h. 26m. 43s.
Landrace
47,359
59,357
106,716
54m. 32s.
Total
409,678
591,085
1,000,763
9h. 5m. 22s.
aData as of October 5, 1998

Change in Genetic Base Year

Genetic base is the original population of animals at the initiation of selection and selection. The average EPD of this population will be zero, and this genetic base will be a point of reference for future generations. With the previous program, the genetic base year for each breed was 1992 or 1993. A rolling or moving base year is currently in place, utilizing a four year prior base for maternal traits and a three year base for terminal traits. This base changes nightly, truly reflecting a dynamic population. The base year today, December 4, 1998, for maternal traits would be December 4, 1994 plus and minus 6 months, or include all animals born from June 4, 1994 to June 3, 1995. Terminal traits would then have a three year prior window of June 4, 1995 to June 3, 1996. The individuals born within these windows would have average EPD's of zero and average indexes of 100. The duration of the prior years account for a complete generation interval, allowing young animals to become parents with sufficient progeny for accurate evaluation.

Index Changes

STAGES has always calculated bio-economic indexes based on EPD's of traits relative to their economic merit, when used in commercial crossbreeding programs. These indexes were developed so that each index point had a value of $.10 per index point per offspring produced. For Terminal Sire Index (TSI), a unit represents approximately $1 for every 10 pigs marketed, and for Sow Productivity Index (SPI) and Maternal Line Index (MLI), a unit is $1 per litter produced by every daughter of the sire or dam. In the past, the terminal sire index weighted the EPD's for days to 230 lbs., backfat thickness and feed conversion, while the maternal line index included EPD's for number born alive, number weaned adjusted for number after transfer, 21-day litter weight and post-weaning performance.

In order to better serve the users of STAGES, the 230-lb. standard has been raised to 250 lbs., more closely following the existing pork industry. Growth is now reported as days to 250 lbs., backfat is adjusted to a 250 lb. live weight and an EPD is now calculated for loin muscle at 250 lbs. The EPD for loin muscle is not reported; however it is used along with the EPD for backfat to develop an EPD for pounds of lean adjusted to 250 pounds liveweight or a 185-pound carcass.

The equation used for this EPD is:

LBLEAN EPD = (-20.3 x Backfat EPD) + (3.41 x Loin Muscle EPD)

where backfat EPD is in inches, and loin muscle area EPD is in square inches.

The economic value assigned for backfat has also changed within our industry. Previously the value used was $10.86 per inch, or a $1.09 change in value per .1 inch change in backfat depth, while in 1996, NSIF estimated the economic value of backfat as $15.00 per inch, or $1.50 per .1 inch. This value was utilized in the development of a curvilinear economic relationship between carcass value and measurements associated with leanness. This relationship was developed recognizing the fact that extremely lean carcasses, those greater than 52 to 53% lean, have an increased incidence of pork quality problems. Representatives of four major pork processors, when polled as to their current and future carcass merit buying systems, identified the ideal backfat range as .65 to .80 inches, while discounting carcasses with 1.1 in. or greater at an increasing rate. When these carcass merit systems were scaled to a common value ratio, the maximum carcass value index (1.00) was attained at 94 LBLEAN.

Figure 1 shows the relationship between carcass value and LBLEAN. The slope of the dollar value at a specific value for pounds of lean is the marginal value of the next incremental pound of lean. Table 2 shows the incremental values per LBLEAN EPD or per .1 inch change of backfat EPD. The marginal values become smaller as the pigs become leaner, and go to zero at 94 lb. of lean.

The new STAGES indexes utilize this curvilinear relationship between carcass value and the EPD for pounds of lean. The Terminal Sire Index uses a base LBLEAN value of 86 pound, so the economic value for backfat at 0 EPD for backfat will be $11.44 per inch, similar to the $10.86 used previously. A base value of 91 lb. LBLEAN will be used for the Maternal Line Index (value of $5.43), which will reduce the economic value of backfat to about 50% of the old MLI. As the pigs become leaner, the EPD's for LBLEAN will increase as the component EPD's for backfat and loin muscle area change. As the EPD's for LBLEAN increase, the additional economic value of each one pound incremental in LBLEAN will become smaller. Because the maternal line index uses a higher base value (91 vs 86 pounds), the very leanest animals will be given decreased economic value and emphasis in MLI.

The new STAGES indexes are similar to the old indexes, in that they remain bio-economic indexes specifying a dollar value on a per pig or per litter basis. However the changes made should result in a better balance of leanness and growth, because the extremely lean animals will get decreased credit for leanness, favoring an animal with balanced numbers.

Figure 1. Relationship of carcass value to pounds of fat-free lean adjusted to 250-lb. live weight.





Table 2. Incremental increase in carcass value per one pound increase in fat-free lean EPD or one-tenth increase in backfat thickness EPD
Lbs. fat-free lean
/LB lean
/.1 in BF EPD
83
.684
1.388
84
.648
1.317
85
.610
1.239
86
.563
1.144
87
.514
1.043
88
.459
.933
89
.400
.812
90
.336
.682
91
.267
.543
92
.193
.393
93
.115
.234
94
.032
.065

Contemporary Groups

One of the keys to genetic evaluation is proper contemporary group design. Animals are evaluated on their relative merit within a contemporary group. A properly designed contemporary group includes animals that are: 1) the same breed or breed composition, 2) the same gender, 3) of similar age, 4) have had similar care consisting of the same housing, nutrition and health status. Tables 3 and 4 identify the optimum and minimum characteristics of a properly designed contemporary group for STAGES. Submitted performance information is monitored for inappropriate contemporary groups at input, and necessary changes in the structure of the group are made.

Table 3. Contemporary groups for maternal traitsa
Optimum
Minimum
Age Difference
< 7 days
< 45 days
Sires of sows
3 or more
2 or more
Litters
6 or more
2 or more
Weigh Age
17 - 25 days
10 - 35 days
a Adapted from Bates, 1998.


Table 4. Contemporary groups for growth traitsa
Optimum
Minimum
Age Difference
< 7 days
< 45 days
Sex
All same sex
> 2 animals / sex
Litters
6 or more
2 or more
Sires
3 or more
2 or more
Target Weight
230 - 270 pounds
210 - 290 pounds
a Adapted from Bates, 1998.


Breed Specific Adjustments

Swine producers need to accurately measure performance in order to estimate genetic merit. Historically, adjustment factors have been used to standardize performance records and allow isolation of the genetic component of observed variation. The National Swine Improvement Federation provides litter adjustment factors common to all breeds; however these factors have been found to differ between breeds, as well as to deviate from NSIF guidelines. Litter size can be affected by contemporary group, parity, age at farrowing, previous lactation length and weaning to conception interval. The development of these adjustment factors included these factors as well as the genetic merit of the female in order to more accurately assess reproductive performance. Tables 5, 6, 7 and 8 show the breed specific adjustment factors used in the development of the maternal EPD's and indexes.

Table 5. Breed specific adjustments for number born alivea
Yorkshire
Landrace
Hampshire
Duroc

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.
1
<210
1.46
1
<240
1.10
1
<240
1.04
1
<240
0.98
1
210-239
1.24
1
240-329
0.73
1
240-299
0.84
1
240-329
0.73
1
240-269
0.96
1
330-359
0.45
1
300-329
0.65
1
>=330
0.55
1
270-299
0.81
1
>=360
0.81
1
>=330
0.49
2
<365
0.78
1
>=300
0.57
2
<395
1.04
2
<395
0.79
2
365-424
0.37
2
<365
0.99
2
395-424
0.71
2
395-424
0.47
2
425-534
0.08
2
365-424
0.60
2
425-484
0.53
2
425-484
0.25
2
>=535
0.17
2
425-534
0.18
2
>=485
0.23
2
485-564
0.00
3,4
0.00
2
>=535
0.00
3,4,5
0.00
2
>=565
0.18
5
0.09
3,4,5
0.00
6
0.09
3,4
0.08
6
0.28
6
0.34
7
0.42
5
0.20
>6
0.67
7
0.50
>7
0.97
6,7
0.55
>7
0.86
>7
1.06
a Adapted from Mabry et al., 1997.


Table 6. Breed specific adjustments for number weaneda
Yorkshire
Landrace
Hampshire
Duroc

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.

Parity
Age @

Breeding

Adj.
1
0.00
1
0.15
1
0.00
1
<210
0.00
2
<365
0.31
2
0.00
2
0.00
2
210-269
0.00
2
>=365
0.58
3,4,5
0.15
3,4
0.10
3,4
270-359
0.15
3,4,5
0.77
6
0.28
5
0.20
5
>=360
0.40
6
0.99
7
0.33
6,7
0.28
6
0.50
7
1.06
>7
0.39
>7
0.40
>6
0.55
>7
1.11
NAT
NAT
NAT
NAT
1,2
9.2
1,2
9.2
1,2
8.7
1,2
7.6
3
8.2
3
8.2
3
7.8
3
7.3
4
7.3
4
7.3
4
6.8
4
6.4
5
6.3
5
6.4
5
5.8
5
5.5
6
5.4
6
5.5
6
4.9
6
4.6
7
4.5
7
4.6
7
4.0
7
3.7
8
3.6
8
3.7
8
3.1
8
2.9
9
2.7
9
2.7
9
2.3
9
2.1
10
1.9
10
1.9
10
1.5
10
1.4
11
1.1
11
1.2
11
0.8
11
0.8
12
0.5
12
0.5
12
0.4
12
0.4
13
0.0
13
0.0
13
0.0
13
0.0
a Adapted from Mabry et al., 1997.


Table 7. Breed specific adjustment for weaning age (multiplicative)a
Yorkshire
Landrace
Hampshire
Duroc
Age
Factor
Age
Factor
Age
Factor
Age
Factor
10
1.33
10
1.35
10
1.31
10
1.33
11
1.30
11
1.32
11
1.28
11
1.30
12
1.26
12
1.29
12
1.25
12
1.27
13
1.23
13
1.26
13
1.22
13
1.23
14
1.20
14
1.24
14
1.18
14
1.19
15
1.18
15
1.20
15
1.18
15
1.16
16
1.15
16
1.15
16
1.14
16
1.15
17
1.12
17
1.13
17
1.11
17
1.11
18
1.09
18
1.09
18
1.06
18
1.09
19
1.06
19
1.07
19
1.04
19
1.05
20
1.03
20
1.03
20
1.02
20
1.02
21
1.00
21
1.00
21
1.00
21
1.00
22
0.97
22
0.96
22
0.97
22
0.97
23
0.94
23
0.93
23
0.93
23
0.93
24
0.91
24
0.90
24
0.90
24
0.90
25
0.88
25
0.87
25
0.89
25
0.86
26
0.85
26
0.84
26
0.84
26
0.82
27
0.82
27
0.83
27
0.82
27
0.79
28
0.79
28
0.79
28
0.79
28
0.77
29
0.76
29
0.75
29
0.76
29
0.74
30
0.73
30
0.72
30
0.73
30
0.71
31
0.70
31
0.69
31
0.71
31
0.68
32
0.67
32
0.65
32
0.68
32
0.65
33
0.64
33
0.62
33
0.65
33
0.62
34
0.61
34
0.59
34
0.62
34
0.59
35
0.58
35
0.56
35
0.59
35
0.55
a Adapted from Mabry et al., 1997


Table 8. Breed specific adjustments for 21-day litter weighta
Yorkshire
Landrace
Hampshire
Duroc

Parity
Age @
Breeding

Adj.

Parity
Age @
Breeding

Adj.

Parity
Age @
Breeding

Adj.

Parity
Age @
Breeding

Adj.
1
<240
9.96
1
<240
14.00
1
<270
10.20
1
<210
13.20
1
240-299
7.24
1
240-299
10.90
1
270-329
9.10
1
210-269
10.10
1
>300
4.29
1
>=300
7.60
1
>=330
4.80
1
270-359
8.00
2
0.00
2,3
0.00
2
<395
3.70
1
>=360
4.20
3
0.57
4,5
1.20
2
>=395
1.00
2
0.00
4
2.53
6
5.70
3,4
0.00
3
1.10
5
4.69
7
7.00
5
1.10
4
3.10
6
7.16
>7
10.00
6
1.60
5
6.40
7
9.16
7
4.10
6
8.60
>7
11.78
>7
5.00
>6
10.80
NAT
NAT
NAT
NAT
1,2
93.7
1,2
94.3
1,2
80.5
1,2
69.2
3
75.6
3
74.2
3
71.4
3
65.2
4
62.2
4
58.4
4
58.7
4
54.4
5
49.5
5
48.4
5
46.0
5
43.4
6
37.8
6
37.6
6
34.9
6
32.2
7
26.4
7
26.3
7
24.2
7
21.9
8
16.4
8
16.0
8
14.6
8
13.7
9
7.2
9
6.4
9
6.2
9
6.1
10+
0.0
10+
0.0
10+
0.0
10+
0.0
a Adapted from Mabry et al. 1997.


Implementation

In the competitive industry of producing food for our nation, pork producers must utilize all available tools in order to remain a viable enterprise. Performance testing and the subsequent genetic evaluation and development of Expected Progeny Differences allow breeders to take a hands-on role in cutting edge technology. The new STAGES program was implemented in September 1998 and provides the most dynamic genetic evaluations available in the swine industry. A rolling genetic base year, nightly runs, breed specific adjustments and variance components, proper monitoring of contemporary groups and a curvilinear relationship between carcass value and pounds of lean in the indexes combine for accurate assessment of genetic merit of animals. The program allows the strengths and weaknesses of each breed to be accounted for, and gives us an extremely powerful tool to help produce the meat of the future.

Literature Cited

Bates, R.O. 1998. Designating contemporary groups. Presented at Ninth Annual STAGES Roundtable, March 23, 1998. West Lafayette, IN.

Culbertson, M.S., and J.W. Mabry. 1995. Effect of age at first parity and lifetime sow performance.

Mabry, J.W., M.S. Culbertson, J.K. Bertrand and A.H. Nelson. 1997. Effect of age at first mating on SPI. NSIF Proceedings 22:82-94.

NSIF. 1997. Guidelines for uniform swine improvement programs.

Schinckel, A.P., D.L. Lofgren, and M.E. Einstein. 1998. Recent STAGES changes. Proceedings of Purdue Swine Day.

Stewart, T.S., D.L. Lofgren, D.L. Harris, M.E. Einstein and A.P. Schinckel. 1991. Genetic improvement programs in livestock: swine testing and genetic evaluation system (STAGES). J. Anim. Sci. 69:3882-3890.

Stewart, T.S., D.L. Lofgren, D.L. Harris, M.E. Einstein and A.P. Schinckel. 1993. Using STAGES: a guide to interpreting STAGES reports for breeders and their clients. Purdue University and U.S. Meat Animal Research Center.

Venner, J.J. 1998. STAGES: National Genetic Evaluation Trait Leader List, May, 1998.