Fact Sheet #12

Purdue University

Cooperative Extension Service

West Lafayette, IN 47907

Genetic Evaluation Programs

Donna L. Lofgren, Purdue University
Thomas E. Socha, Nebraska SPF
Allan P. Schinckel, Purdue University


Lauren Christian, Iowa State University

Larry Young, US Meat Animal Research Center

Everett Forkner, Missouri seedstock producer

Max Waldo, Nebraska seedstock producer


One way to improve performance in a herd is through selection of genetically superior animals. Selection should be based on an estimate of the genetic merit of the animals. The accuracy of these estimates is important, because accuracy predicts the potential rate of genetic progress: higher accuracy means more genetic progress is possible.

Genetic evaluation programs can be used to predict the genetic merit of the animals for specific traits. These programs combine records on the individual with information on relatives in an in-depth analysis, resulting in very accurate genetic evaluation. The programs express the genetic merit of an individual for a trait as either an Estimated Breeding Value (EBV) or as an Expected Progeny Difference (EPD), which is 1/2 of the EBV.

The genetic merit estimates are calculated for postweaning and/or reproduction traits. The genetic merit estimates are then combined into indexes. Breeders can choose the traits which are economically important for them and can rank the animals based on the appropriate EBV or index. Selection of the superior animals from this ranking allows breeders to make genetic progress in those economically important traits.

This publication discusses three genetic evaluation programs which are available to swine breeders: SWINE-EBV, Nebraska SPF, and STAGES.


SWINE-EBV is a series of computer programs that analyzes performance data. It uses on-farm microcomputers, which allows rapid data verification and analysis. In most cases, performance data from a herd can be analyzed in less than twenty minutes. SWINE-EBV analyzes both reproduction and postweaning traits and then combines the genetic evaluations for these traits into three alternative indexes: maternal, general, and terminal-sire. SWINE-EBV also identifies the top sires within each breed on that farm through comprehensive sire evaluation procedures.

What the Producer Does

To participate in SWINE-EBV, a seedstock producer collects basic information and inputs it into his on-farm microcomputer for analysis. For a postweaning analysis, days to 230 lb, and backfat thickness are measured on boars, gilts, or barrows. For a reproduction analysis, number born alive and 2l-day litter weight are obtained for all purebred or crossbred sows with either purebred or crossbred litters. SWINE-EBV calculates EBVs for crossbreds as well as purebreds, and utilizes their performance data to evaluate their purebred parents.

What the Program Does

Once the actual performance information is submitted, the SWINE-EBV programs adjust the data for known nongenetic effects (e.g., sex, age, parity, and weight), calculate contemporary group averages, and identify data from relatives. Then, each individual's performance data is combined with data from relatives to calculate the EBVs. SWINE-EBV provides EBVs for number born alive, 21-day litter weight, growth rate, and backfat thickness. These EBVs are based on available individual, sib, ancestral, and progeny information.

SWINE-EBV generates indexes that correctly rank animals relative to their intended uses in commercial crossbreeding systems. The indexes weight the traits relative to their economic importance and take into consideration the genetic relationships among the traits. Feed efficiency is included in the economic objective; it is not calculated directly, but is included in the indexes indirectly because of its genetic relationships with growth rate and backfat thickness. Because the indexes are stated in economic terms (dollar value per index point), they can be used to identify the most valuable animals in terms of their influence on pork production efficiency. The resulting reports give a complete summary of the performance of each animal, its EBVs, and its index values.

SWINE-EBV programs are available from computer software developers.

Nebraska SPF Performance Testing Program

Nebraska SPF is an on-farm, whole herd testing program. Since its inception in 1959, a complete and sophisticated system has been developed for use in seedstock herds. Over 90,000 pigs are evaluated each year in the Nebraska SPF system. The program analyzes both postweaning and reproduction traits. Results of the analyses are returned to the farm the day after records are collected by Nebraska SPF fieldmen.

What the Producer Does

For a postweaning analysis, pigs are weighed off test with a three-week spread in ages. Fieldmen visit all herds and weigh and backfat probe all pigs raised on the farms. For a reproduction analysis, number born alive and survival to 21 days are recorded. These are the primary traits used in the sow productivity index (SPI) developed by Nebraska SPF. Litter birth weight and litter 21-day weight also are incorporated in the index if this information is collected by the producer, but the weightings on these add very little to the index.

What the Program Does

Growth rate is reported as age to 220 lb, and backfat is adjusted to 220 lb. Adjustments used for survival and 21-day weights are different from those used in any other SPI calculations. Deviation of survival is based upon a given sow compared to a three year average of all sows of the same breed with the same number of pigs after transfer. Deviation for 21- day weight is based upon the individual litter compared to all litters from the same breed of sow with the same number of pigs on the sow at 21 days. These two adjusted values give a better measure of what a sow actually does when nursing a specific number of pigs. Full-sib and half-sib information is used in addition to the individual's own data for calculating the EBVs for all traits. Calculations also give an estimated SPI for each young pig based upon the SPI of its sire and dam. Listings of bears and gilts mailed to producers are ranked by index.

Nebraska SPF has added new selection criteria for breeder or nucleus herds and for multiplier herds. Replacements selected for the herd must be from within the top designated percentage of a contemporary group based upon their index value. Herds also must meet a designated generation interval to be considered a breeder or nucleus herd. This system also allows the breeder to have a degree of flexibility in selecting herd replacements. With the current criteria, Nebraska SPF breeder herds are making about 80% of maximum potential genetic improvement. Over 80% of all pigs raised in Nebraska SPF herds are sired by boars selected from within their own herds. Breeder herds are decreasing days to 220 lb. by about one day per year and decreasing backfat by about 0.005 inches per year. Litter size is increasing in some, but not all, breeder herds.

Future plans include analyses between herds through the use of reference sires, which will allow the identification of the best sires in each breed within the program. Future programs may also incorporate data from commercial herds tied back to the breeder herds. An Al stud consisting of the top breed sires will be established to allow better use of the genetically superior animals in more herds.

For more information about the Nebraska SPF program, contact the Nebraska SPF Swine Accrediting Agency, 1840 North 48th St., Lincoln, NE 68504.


STAGES, the Swine Testing and Genetic Evaluation System, is a series of computer programs run by all of the purebred breed associations to serve their members. The development of the complete STAGES program was a joint project of Purdue University, USDA Agricultural Research Service, USDA Extension Service, National Association of Swine Records, the purebred associations, and the National Pork Producers Council. The STAGES programs are implemented on the purebred breed associations' computers, where they have been tied into the existing pedigree systems. STAGES extension materials have been written to educate purebred breeders and their commercial customers about the system.

STAGES computes genetic evaluations for several traits within a single herd. Postweaning traits include growth rate (days to 230 lb. or average daily gain) and backfat thickness; reproduction and lactation traits include number born alive and litter weight The genetic evaluations also are combined into comprehensive indexes. Analysis of test station data will be possible for postweaning traits. When enough data have accumulated, there will be a periodic across-herd analysis for all traits. This national sire evaluation will combine information from progeny in all herds for the genetic evaluation of sires, and will identify the best sires in each breed.

What the Producer Does

With the STAGES programs, all animals in the herd should be performance tested by the producer and their records included in the analysis. For reproduction traits, all sows should be included, with number born alive and litter weight recorded. For postweaning traits, days to 230 lb. and backfat should be measured on all pigs: boars, gilts, and barrows. (Records of barrows give information about the genes they share with their sibs, so they should be included even though knowing their genetic merit is of little value.)

These records are submitted for a single contemporary group. A contemporary group contains animals which were tested at the same time and were treated alike, so they had an equal opportunity to perform. Thus they can be fairly compared to each other, increasing the accuracy of the genetic evaluations. For postweaning traits, the group includes pigs of the same breed or breed cross that were tested at the same time. For reproduction traits, the group includes sows of the same breed that farrowed at the same time; however, sows with purebred and crossbred litters are in separate contemporary groups.

What the Program Does

Records are first adjusted for nongenetic effects: backfat is adjusted to 230 lb.; number born alive is adjusted for parity; and litter weight is adjusted for age when weighed, parity, and number nursed. The STAGES programs compare the individual's performance record with records of other animals in the same contemporary group to remove the effect of the environment in which the records were made. Genetic correlations between the traits (between days to 230 lb. and backfat, or between litter size and litter weight) are taken into account. Finally, information from records of all relatives in the herd is included. Since relatives share genes, their records give information about the animals in the current group. Using information on all relatives increases the accuracy of the genetic evaluations.

The genetic evaluation which results from the analysis is expressed as an EPD. It is a measure of how an individual's offspring can be expected to perform compared to offspring of an average individual. Because they are expressed relative to an average animal, EPDs can be positive or negative, with an average of 0. For example, a boar with an EPD of -3.0 for days to 230 lb. will be expected to sire offspring which reach market weight 3 days sooner than offspring of an average boar whose EPD is 0.

Over time, if genetic improvement is made, the average EPD will not be 0, but will reflect that improvement. Thus, the change in EPDs over time will give an estimate of the genetic progress that has been made in the herd. This will allow any change in herd average to be separated into genetic and environmental trends.

The EPDs for individual traits are combined to calculate economic indexes. The indexes are expressed as expected profit per litter relative to an average of 100. Four indexes are calculated, because different breeders may wish to select for different traits. The General Purpose Index puts equal emphasis on postweaning and reproduction traits. It would be appropriate for selection of animals to be used in a rotational crossbreeding program, or for general selection purposes where all traits are of importance. The Maternal Line Index puts twice as much weight on reproduction as on postweaning traits, while the Terminal Sire Index includes postweaning traits only. These two indexes can be used to select dam and sire lines, respectively, for use in a terminal crossbreeding program. Finally, a Sow Productivity Index is calculated, which involves reproduction traits only.

For more information about participating in STAGES, contact the purebred breed associations.

New 7/90

Cooperative Extension work in Agriculture and Home Economics, State of Indiana, Purdue University and U.S. Department of Agriculture cooperating: H.A. Wadsworth, Director, West Lafayette, IN. Issued in furtherance of the acts of May 8 and June 30, 1914. The Cooperative Extension Service of Purdue University is an equal opportunity/equal access institution.