SWINE GENETICS NSIF National Swine Improvement Federation Purdue University Cooperative Extension Service West Lafayette, Indiana Fact Sheet Number 13 NSIF-FS13 Across-Herd Genetic Evaluation of Swine Authors: C. M. Wood, Virginia Polytechnic Institute; T. S. Stewart, Purdue University; J. W. Mabry, University of Georgia. Reviewers: Larry Young, USDA MARC, Clay Center, Nebraska; Bruce Leman, Roanoake, Illinois; J. R. Jones, North Carolina State University; Darrel Anderson, West Lafayette, Indiana; Ron Bates, University of Missouri. Introduction What is across-herd genetic evaluation? Across-herd genetic evaluation is the comparison of sires, dams, and/or pigs in different herds based on the analysis of performance information (such as backfat) collected on pigs of the same breed in different herds and at many different times. It may include on-farm records, test station data, national breed test information, and progeny tests. Such evaluations can be used to accurately compare animals at different farms. Across-herd genetic evaluations are used routinely by the dairy and beef industries in the United States to identify the very best genetic material in each breed. Canadian pork producers use an across-herd program to select breeding stock. In the U. S., the STAGES program began using an across-herd evaluation for Yorkshire data in 1990, and the Hampshire, Yorkshire, Spot, and Duroc breeds use a similar program to evaluate centrally tested boars across the country. Why use across-herd genetic evaluation? A major goal of seedstock breeders is to increase the rate of genetic progress to better meet the needs of commercial operations producing high-quality pork for consumers. Accurate, timely information is vital in making selection decisions to meet that need. Across-herd genetic evaluations offer several advantages over other evaluation methods. 1. All available performance information about an animal and its relatives (parents, sibs, offspring, etc.) is used to obtain the most accurate estimate possible about the genetic merit of an animal. These estimates of genetic merit are reported as Expected Progeny Differences (EPDs), which predict how off-spring of an animal will perform when compared to average animals within a breed (NSIF - FS8). Because EPDs are expressed as deviations, they may be positive or negative, and the breed average is zero. This differs somewhat from within-herd evaluations, in which the herd average is calculated and half the animals in that herd are above the herd average and half are below average. Based on an across-herd evaluation, all animals within a herd could be better than the average of the breed, but the converse also is true. In practical terms, neither extreme is very likely; the vast majority of herds will have some animals above the breed average, and some below. An additional benefit of using EPDs is that the unit used for reporting EPDs is the same as that used for the trait, such as pigs for number born alive or pounds for average daily gain. 2. Because information comes from many herds, fair comparison of animals in different locations is possible with across-herd evaluations. In contrast, comparing raw data on animals evaluated within herds (or test stations) to others in different locations is tempting, but such comparisons may result in poor selection decisions because performance differences between pigs in different locations may be environmental and/or genetic. 3. Use of EPDs from across-herd evaluations to select breeding animals will speed up genetic change within a breed, because the best of many animals will be chosen as parents of the next generation. A large data base consisting of many animals alleviates some of the negative influence that low heritabilities have on genetic progress in traits such as litter size. 4. Across-herd evaluations offer the opportunity to effectively test for traits like carcass merit that are difficult to evaluate on a within-herd basis. For example, because carcass traits require slaughter of animals, fewer records are collected, and across-herd evaluations can make the best use of data that are available. Genetic Principles of Across-Herd Evaluations Across-herd genetic evaluations employ the same genetic principles as within-herd evaluations, extended to include between-herd differences. The goal is to increase the rate of genetic progress in traits of economic importance to the industry. What follows is information on aspects specific to across-herd evaluations. Detailed information about applications of genetic principles may be found in NSIF - FS9. Genetic base. The genetic base consists of the initial animals in the population to be evaluated. Across-herd evaluation programs usually define a population as animals of the same breed, because individuals share many of the same genes, making predictions (EPDs) more consistent. The genetic base is frequently defined as all animals in all herds during a specific time period, such as the first five years of a testing program. Specific definitions may vary from breed to breed. By broadening the population to the entire breed, more animals are available from which to choose the next generation. This results in a greater selection intensity, and hence enhanced genetic progress. Environmental influences which vary from herd to herd over time can be accounted for during the evaluation process by comparing performance to the base period. This allows a com- parison of animals based predominantly on genetic merit. Such procedures also allow estimation of genetic trends, or changes in the average breed genotype over time, compared to the original (base) animals. When genetic progress is occurring, later generations will be genetically improved, but estimated breeding values on older animals will be biased unless all animals are adjusted relative to the genetic base. Contemporary groups. The importance of the proper definition of contemporary groups by the breeder cannot be overemphasized, because contemporary groups form the basis of all evaluation programs. NSIF Factsheet 5 (Per- formance Records for Selection Programs) has a good discussion of the concept of contemporary groups. It is important to avoid single-sire groups, but producers also need to balance size of each group with uniformity within the groups. A good rule of thumb is to include offspring of at least three sires in each group, prefer- ably 40 to 50 per sire. In general, the more progeny per sire the better, as long as they can be managed uni- formly. ________________________________________________________________________ Figure 1. Connecting Herds with Genetic Links. ---------------- | TEST STATION | | | | B1 B2 B3 B4 | -.--.-----.--.-- . . . . ----------.-. . .----------- | HERD 1 .. | . |. HERD 2 | | . | .| . | | S1 S2 S3 | ..S4 S5 | ------.------ ----------- . . ----------- .| HERD 3 | -------------- . . | | HERD 4 | | ..B5 | | | | | | S9 S10 S11 | | S6 S7 S8 | -------------- ----------- Herd 1 is directly linked to Herd 3 and the test station through sons of S2 (B5) and S3 (B1 and B2), respectively. Herd 2 is directly linked to the test station through sons of S4 (B3 and B4). Indirectly, Herd 1 is linked to Herd 2 through the boars in the test station; Herd 3 is linked to the test station through Herd 1, and to Herd 2 through the test station linked to Herd 1. Herd 4, however, is not linked at all because of the lack of genetic ties. In this scenario, across-herd evaluation allows comparison of Sires 1-8 and Boars 1-5, but not Sires 9-11. ________________________________________________________________________ Connectedness. One major advantage of across-herd evaluations is that they tie together information from many sources by using genetic (pedigree) relationships among animals being evaluated. As shown in Figure 1, once a genetic link is established between groups of animals, all animals in those groups can be compared, whether they are related or not. However, just as a rope is made stronger by braiding strands together, the more genetic links (connectedness) between groups, the more accurate the EPDs will be. As a result, it is impor- tant that enough links be present to make an across-herd evaluation worth the effort. For those herds participating in earlier phases of STAGES, within-herd evaluations made over time use genetic links to connect contemporary groups within a herd, and many herds within a breed are already linked by exchange of breeding stock as well as through artificial insemination (AI) and embryo transfer. Test stations can contribute genetic links by evaluating animals from different herds at the same location, and by sending littermates or half-sibs from one herd to several stations (see NSIF Factsheet 11). The fastest way to strengthen genetic ties, however, is through AI, which can also make superior sires available to more produc- ers, and help maintain a broad genetic base. Accuracy. Because EPDs for the same trait on the same animal can change over time, depending on the amount of information available, and how well progeny actually perform, accuracies are assigned to help producers choose among animals that have similar EPDs. The accuracy is a risk management factor: the closer it is to 1.0, the more likely that the 4 average performance of offspring will be close to the parent's EPD, and the less likely an animal's EPD will change drastically with the addition of that new information. Thus, the more performance tested progeny (or other relatives) an animal has, the higher the accuracy tends to be. Conversely, a producer interested in a young boar with an excellent EPD, but a lower accuracy, should be aware that his offspring could be much better or worse than predicted and could cause his EPD to go much higher or lower upon reevalua- tion. Table 1 contains ranges of possible changes in EPDs, depending on accuracy, for four traits evaluated by the STAGES program for Yorkshires. The publication NSIF - FS8 has more details on how accuracy values are determined. _______________________________________________________________________________ Table 1. Possible changes (+/-) associated with accuracies for maternal and growth traits evaluated by the STAGES Program for the Yorkshire breed. ------------------------------------------- Possible Change --------------------------------- Accuracy NBA LW21 DAYS BACKFAT ------------------------------------------- .10 0.52 9.51 5.80 0.06 .20 0.46 8.45 5.16 0.05 .30 0.40 7.40 4.51 0.04 .40 0.34 6.34 3.87 0.04 .50 0.29 5.28 3.22 0.03 .60 0.23 4.23 2.58 0.03 .70 0.17 3.17 1.93 0.02 .80 0.11 2.11 1.29 0.01 .90 0.06 1.06 0.64 0.01 ------------------------------------------- To use the table, find the accuracy reported for an animal (column 1). Subtract the appropriate value for the trait being evaluated (columns 2-5) from the reported EPD to get the lower end of the possible change, and add the same amount to get the upper end of the possible change. A new EPD on the animal should fall within that range under normal circumstances. Example: Two sires have the same EPD of +.25 pigs born alive (NBA). Sire A has an accuracy of .30 and Sire B has an accuracy of .80. Thus the possible change for Sire A is .25 + .40 while the possible change for Sire B is .25 + .09. _______________________________________________________________________________ Interpreting Across-Herd Evaluations Across-herd evaluation is simply a tool that will help in making selection decisions. Therefore it is critical that a producer know how to get the best use of this tool. Know the genetic base. Currently, EPDs are based on breed averages. Thus animals in different breeds cannot be compared based on EPDs. The genetic base may also change over time, so EPDs published at different times cannot be compared. And EPDs generated by different programs (for example, STAGES and the central test sta- tions) cannot be compared because different animals are included in each evaluation. In fact, the best way to make comparisons is to compare the magnitude of differences in EPDs among animals on the same list. This is particularly important for seedstock producers who need to compare their own animals to those in other herds. Balance multiple traits. If more than one trait is of interest, the importance of each trait will have to be weighted, because in most cases animals will have better EPDs for some traits than others; rarely will an animal be outstanding in all traits. Some programs similar to STAGES offer indexes which combine EPDs of several traits based on the relative accuracy of the estimates and an assigned relative economic importance. Individual producers must decide, however, whether the indexes fit their particular situations. Other programs report only EPDs for each trait, leaving it up to each producer to decide which trait(s) should carry the most weight. Such decisions include the same factors (accuracy and economic value) used in the indexes, but indivi- duals must make the weighting decisions. Know how traits are reported. Negative EPDs can be favorable for traits like days to market, whereas traits like average daily gain should be positive. In this case, both evaluate growth potential, and breed average is zero. Application of Across-Herd Evaluations In addition to knowing how to interpret EPDs from across-herd evaluations, it is important to realize that EPDs may play different roles in different herds. For example, purebred breeders and commercial operators will probably use EPDs differently. Implementation of across- herd evaluations may also impact on the structure of the seedstock industry. Seedstock producers. For the most timely selection decisions, across- herd genetic evaluations should be used in conjunction with within-herd evaluations. The across-herd evaluations will enhance within-herd performance testing programs, which may include STAGES within-herd analyses, SPIs, NSIF selection indexes, or other methods which rank animals on genetic merit relative to the average of their contemporary groups (see NSIF- FS8, Estimating Genetic Merit). Within-herd evaluations normally have faster turnaround times, but are less accurate, than across-herd ana- lyses. Thus a producer may wish to use within-herd information to make preliminary selection decisions, such as which gilts to retain at market weight. The producers may use across-herd evaluations to fine tune the decisions, such as whether to keep bred gilts or sell them. Another possibility would be to use across-herd evaluations to compare potential breeding stock within one herd to pigs in other herds, or in central test stations (see NSIF - FS11, Utilizing Central Boar Test Sta- tions to Enhance Genetic Progress). Across-herd comparisons allow breeders to identify herds and lines that are genetically superior for the traits in which they are interested. A breeder can locate the best sires and dams in the breed, then use within-herd analyses to evaluate sons and daughters that are currently available. A breeder can decide whether to find replacements from within the herd, or to purchase animals from a dif- ferent source. In other cases, producers may be interested in evaluating traits not included in the across- herd evaluations; within-herd evaluation is the only possibility. Across-herd EPDs provide seedstock producers with a better idea of strengths of their own animals on which they should build, relative to other herds within a breed. In addition, EPDs provide the most accurate infor- mation possible for making culling decisions, deciding on how boars should be used in the breeding program, and determining the value of animals offered for sale. EPDs alert seedstock producers to areas needing improvements. Commercial producers. Across-herd evaluations can be used to improve commercial operations, albeit in a dif- ferent manner. Although crossbreeding is economically critical for commercial operations, it does not result in on-going genetic change. Continual genetic progress in commercial herds is directly dependent on progress made in the operations from which breeding animals are purchased. Commercial producers should choose seedstock sources naming similar goals and management, then purchase animals with the best EPDs possible, given budget constraints. However, decisions must be made within breeds, because EPDs on animals in one breed cannot be compared to EPDs on animals in another breed. EPDs should not be the basis for deciding which breeds to use in a crossbreeding program. Breed choices should be made based on breed averages, maternal effects, and heterosis. Because they are based on the average, half of the animals in each breed will have favorable EPDs and the other half will be below average. However, the number of published EPDs can help determine the availability of breeding stock for a particular breed: the more animals evaluated, the more likely a producer can find what is needed. Genetic Improvement of Sire and Dam Lines for Enhanced Performance of Terminal Crossbreeding Systems (NSIF - FS14) provides a discussion of combining the advantages of crossbreeding with genetic selection. ------------------------------------------------- Table 2. EPDs (and accuracies) of three Yorkshire sires evaluated in 1991 * ------------------------------------------------- Sire NBA LWT DAYS BF ------------------------------------------------- Ulf .54 4.97 -.53 - .11 (.60) (.62) (.62) (.74) California .21 4.69 -1.39 - .05 (.59) (.60) (.56) (.70) K. D. Boss .51 5.51 .54 - .02 (.62) (.63) (.53) (.58) ------------------------------------------------- * Adapted from the July 1991 American Yorkshire Club STAGES National Sire Evaluation Trait Leaders list. ------------------------------------------------- Once the choice of breed is made, then individual animals within each breed should be chosen based on EPDs. A commercial producer can use the across-herd analyses to locate superior sire and/or dam lines, then use the within-herd analyses to select among the available sons and daughters. For example, Table 2 contains EPDs on number born alive (NBA), litter weight (LWT), growth (DAYS) and backfat (BF) for three Yorkshire boars evaluated in 1991. All three have similar accuracies for each trait, so decisions can be made based on EPD. If a producer is interested in improving one trait, say NBA, then EPDs for NBA would be most important in making decisions. In this case, Ulf and K. O. Boss have similar EPDs for NBA, and are better than California. How- ever, it is always wise to note EPDs on other traits, because improvement in one should not result in a loss in another. For both boars, EPDs for LWT (positive) and BF (negative) are favorable, but DAYS is a different story: favorable (- .53) for Ulf, but unfavorable (+.54) for K.D. Boss. Thus, a producer would have to deter- mine how important growth is when deciding whether to purchase sons or daughters of these two boars. On the other hand, if growth is very important, a producer may want to consider progeny of California. Even though the EPD for NBA is less than those of the other two boars, it is favorable, as are the EPDs for LWT and BF. The indexes provided by STAGES can sometimes be helpful in making such decisions, but producers must under- stand how the indexes are formulated. The Yorkshire breed association has material which provides such infor- mation, and producers need to be familiar with it before using the indexes. Industry structure. Across-herd evaluations will enable breed associations to implement true national breed tests that could incorporate the current central testing organization with on-farm evaluations of additional animals. This would allow herds from across the country to merchandize animals without physically transporting them to central locations, because EPDs are comparable. It should be noted, however, that EPDs will not replace a critical assessment of physical and reproductive soundness, breed type, and conformation. Across-herd EPDs would also allow more accurate comparisons of small groups of pigs, especially in central test situations in which several breeds may be on test concurrently. If a test station has only one pen of a breed, for instance, the only way to index the animals is to use the average of all pigs of all breeds in the station at the same time. Because all breeds are not equal in the growth and carcass traits, however, that one pen may be severely penalized when ranked on index. For larger operations concerned about the risk of disease, across-herd evaluations will permit the evaluation of all breeding stock in each of several nucleus herds, and could allow for the incorporation of data from multiplier herds to increase the accuracy of evaluation. Cooperative arrangements among independent breeders with herds made up of animals of similar genetic backgrounds could work in the same manner. Such agreements would allow the producers to take advantage of having large numbers of performance tested animals to merchan- dise, without relinquishing individual ownership. To fully realize the potential of across-herd evaluations, a viable AI industry is vital, whether it be independent boar studs, AI centers, or a combination thereof. Embryo transfer and exchange of breeding stock among seedstock producers will also contribute to the success of across-herd evaluation programs. In all cases, accurate identification of semen, embryos and animals is essential, as well as complete performance records on resulting offspring. The NSIF Guidelines contains information on standardization of records, the use of which would immensely improve the efficiency of genetic evaluations. Summary Across-herd genetic evaluations could significantly increase the rate of genetic progress in traits of economic importance to the swine industry. Several programs are available to seedstock producers. The pro- grams will improve as more animals are added to the data base. To fully realize the potential of across-herd evaluations, however, seedstock producers, breed associations, AI companies, and others interested in genetic improvement must work together to obtain complete, accurate performance data for use in the programs. NEW 2/92 (3M) ______________________________________________________________________ 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. It is the policy of the Cooperative Extension Service of Purdue University that all persons shall have equal opportunity and access to our programs and facilities. .