animalscience

E interaction on genetic gain in breeding programs¹ H. A. Mulder² and P. Bijma

Animal ffects of genotype x environmentBreeding and Genetics Group, Wageningen University, 6700 AH Wageningen, The Netherlands

² Correspondence: P.O. Box 338 (phone: +31-(0)317-485798; fax: +31-(0)317-483929; e-mail: herman.mulder@wur.nl ).

Genotype x environment interaction (G x E) is increasingly important, because breeding programs tend to be more internationally oriented. The aim of this theoretical study was to investigate the effects of G x E on genetic gain in sib-testing and progeny-testing schemes. Loss of genetic gain due to G x E was predicted for different values of heritability, number of progeny per dam, number of progeny per sire, proportion of selected sires, and population size in the selection environment. Two environments were considered: a selection environment (SLE) and a production environment (PDE). The breeding goal was only for performance in PDE. A pseudo-BLUP selection index was used to predict genetic gain. Recording of half-sibs or progeny in PDE limited the loss in genetic gain in PDE due to G x E between SLE and PDE. Progeny-testing schemes had less loss in genetic gain than sib-testing schemes. Higher heritability increased the loss in genetic gain, whereas increasing the number of progeny per sire in PDE decreased the loss in genetic gain. The number of progeny per sire required to minimize loss in genetic gain due to G x E was greater for sib-testing schemes than for progeny-testing schemes. More progeny per dam slightly increased the loss in genetic gain. Genetic gains for sex-limited and carcass traits were less affected by G x E than traits measured on both sexes. Loss in genetic gain was due to decreased accuracy of selection in most situations, but it was due to decreased selection intensity in situations with small population size and a low proportion of selected sires. It was concluded that recording performance of relatives in PDE minimizes loss in genetic gain due to G x E, and that progeny-testing schemes rather than sib-testing schemes are preferable in situations with low to moderate heritability (h² 0.3), relatively short generation interval of progeny-tested sires (L_prog/L_sib 1.7), and moderate to severe G x E interaction (r_g 0.8).

Key Words: Breeding Program • Genetic Gain • Genotype x Environment Interaction • Progeny Testing • Sib Testing

همبستگی و اثر متقابل بین ژنوتیپ و محیط

تهیه و تنظیم:حمیده شیخ زین الدین

دانشجوی کارشناسی ارشد ژنتیک واصلاح  دانشگاه تهران

مقدمه

ژنتیك كمی یكی از شاخه‌های علم ژنتیك است كه در واقع به بررسی خصوصیات صفات كمی می‌پردازد.

این صفات اكثراً تحت تأثیر ژنهای زیادی قرار می‌گیرند كه به آنها صفات پلی‌ژنتیك یا چندژنی گفته می‌شود.

در ژنتیك كمی برای تجزیه و تحلیل صفات كمی از فرمول زیر استفاده می‌شود؛                                              P = G + E

P= در این فرمول كه اولین بار توسط فیشر ارائه شد، P عبارتست از فتوتیپ صفتی كه در فرد یا حیوان یا گیاه برای اندازه‌گیری مدنظر است.

G= عبارتست از مجموع اثرات ژنهای متعدد و اثرات متقابل بین این ژنهاست.

E= عبارت است از مجموع اثرات محیطی یا باقیمانده یا هرچیزی كه غیرژنتیكی باشد كه خود به دوبخش موقتی و پایدار تقسیم می‌شود.

و اریانس و تنوع بین افراد یا گیاهان در صفات كمی ناشی از واریانس در E , G البته امكان دارد كه اثر متقابل بین ژنوتیپ و محیط خود در ایجاد واریانس فنوتیپی مؤثر باشد.

وسعت توزیع یك صفت توسط انحراف معیار بیان می‌شود كه مربع این مقدار كمی تحت عنوان واریانس نامبرده می‌شود.

در یك جمعیت میزان تغییرات فنوتیپی را می‌توان به صورت زیربیان نمود:

                                  VP=VG + VE + 2 Cov (G,E)

و اثرهای متقابل بین ژنوتیپ و محیط؛

كواریانس بین ژنوتیپ و محیط ممكن است مثبت، منفی یا صفر باشد. از نقطه نظر اصلاح دام، اكثر اثرهای متقابل قابل مشاهده آنهایی هستند كه در ژنوتیپ حیوانات دخالت دارند. در بیشتر گونه‌ها، اثر متقابل ژنوتیپ و محیط (Genotype by environment interaction) نقش حیاتی در تعیین تیپ بیولوژیكی كامل مناسب برای محیط خاص ایفا می‌كند. زمانی اثر متقابل ژنوتیپ و محیط (G×E) وجود دارد كه تفاوت عملكرد دو یا چند ژنوتیپ از محیطی به محیط دیگر تغییر كند. مثال كلاسیك اثر متقابل ژنوتیپ و محیط فیزیكی، سازگاری ژنتیكی حیوانات به مناطق معتدل در مقابل سازگاری به مناطق گرمسیری است.

سازگاری ژنتیكی به منطقه یعنی این كه حیوانات طی نسل‌های متمادی تكوین یافته و حامل ژنهایی هستند كه به آنها اجازه می‌دهد تا در آن منطقه زنده مانده و خوب رشد كنند.  

— تصورات بر این است كه اگر ژنوتیپ برتر در یك جمعیت شرایط محیطی بهتر مثل تغذیه یا شرایط بهداشتی بهتر دریافت كند درین صورت كواریانس ژنوتیپ و محیط مثبت خواهد بود.

A large sample of animals is measured for the trait and genotyped for markers. The genotypes can be represented by a variable (x), which takes the values 0 or 1 or 2 corresponding to one of the homozygotes, the heterozygote or the other homozygote. The statistical analysis of the reference population estimates effects for each marker (w), and hence a prediction equation can be generated that combines all the marker genotypes with their effects to predict the breeding value of each animal. This prediction equation can then be applied to a group of animals that have genotypes but not phenotypes, and the estimated breeding values calculated from this can be used to select the best animals for breeding.

www.nature.com/.../v10/n6/box/nrg2575_BX2.html‎www.

www.ces.purdue.edu/extmedia/NSIF/NSIF-FS3-W.html‎

William R. Lamberson, University of Missouri
Erik R. Cleveland, University of Hawaii

Reviewed by

Larry Young, MARC.

Charles Christians. University of Minnesota

Max Waldo, Nebraska Duroc breeder

Bruce Leman, Illinois Hampshire and Yorkshire breeder

Introduction

Efficient production is essential for a pork producer to survive in uncertain economic times. Continuous genetic improvement will allow the seedstock producer to reduce production costs and to compete for sales In the breeding stock market by providing a genetically superior animal. New tools are becoming available to producers for evaluation of the genetic merit of hogs. Knowledge of genetic principles will allow producers to take full advantage of computer programs used in estimation of genetic merit. This publication presents the key concepts of breeding value, heritability and genetic correlation.

Breeding Value and Transmitting Ability

Genetic improvement of a seedstock herd is dependent upon the producer's ability to select breeding stock with superior breeding values. The breeding value of an animal is defined as the animal's value as a parent considering the effect of its genes on all relevant traits whether or not they can be directly measured. The breeding value for a particular trait encompasses the effect of all genes affecting that trait. For example, a producer choosing a boar to be used as a terminal sire should be concerned with the boar's breeding value for traits such as growth rate, backfat thickness, and feed efficiency. Many genes affect each of these traits. The total effect of all genes influencing these traits contribute to the breeding value of the boar. Genes occur in pairs and a sample one-half of a selected animal's genes is transmitted to its offspring. Since a sample one-half of an animal's genes is transmitted to the offspring, on the average, one-half of the breeding value is transmitted to the offspring. One-half of the animal's breeding value is referred to as the animal's transmitting ability. The expected merit of progeny from a particular mating is equal to the average of the parents' breeding values or the sum of their transmitting abilities.

Heritability

Unfortunately, it is impossible to know the true breeding value of an animal. To make selection decisions we must estimate the breeding value of an animal based on information available on that animal or its relatives for traits of interest. The animal's own phenotype or its performance is one indicator of its breeding value. The usefulness of performance data on the individual as a predictor of breeding value is dependent on the heritability of the trait of interest. The heritability of a trait can be defined as the proportion of differences in performance between animals that are due to differences in breeding value. This concept is illustrated diagrammatically in Figure 1. Heritability can, in theory, range from 0 to 1.0. A heritability of zero indicates that all differences between animals are due to nongenetic causes. A heritability of one indicates that all differences between animals are due to genetic causes. Estimates of the heritabilities of some relevant traits are presented in Table 1. For traits that are highly heritable, e.g., backfat thickness, the performance of an animal is a good indicator of its breeding value. For traits with lower heritabilities, e.g., litter size, the phenotype is a poorer indicator of breeding value.

Figure 1. A diagrammatic representation of the proportion of phenotypic differences, which are expected to be due to differences in breeding value for a trait with a heritability of 0.25.

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Table 1. Heritability estimates of some traits of interest to swine seedstock producers.

Trait                  Heritability
-------------------------------------
Litter size              .10
Litter birth weight      .30
21-day litter weight     .15
Number weaned            .05
Survival to weaning      .05
Average daily gain       .40
Feed conversion          .30
Days to 230 lb.          .35
Backfat thickness        .40
Loin eye area            .50
Carcass length           .55
--------------------------------------

The concept of heritability can also be examined from the standpoint of selection response. The heritability represents the proportion of parental superiority in performance (termed selection differential) that is expected to be realized as superiority of the selected animal's progeny. This concept is diagrammed in Figure 2.

Figure 2. A diagrammatic relationship of the performance of parents and the expected performance of their progeny relative to the population mean for traits with differing heritabilities.

The cause of the likeness between parent and offspring is because genes are passed from the parent to the offspring. Sibs tend to be alike because they share genes in common which are received from their parents. There is a greater likeness between relatives for a highly heritable trait than for a lowly heritable trait. For example, a group of sibs is more likely to be similar for backfat thickness than for number born in their first litter. Genes, as compared to management, have a greater effect on performance for a highly heritable than for a lowly heritable trait.

Differences among animals can have both genetic and environmental causes. The heritability of a trait is the ratio of variation due to genetic causes to the variation due to genetic plus plus environmental causes. Producers differ in their ability to control the production environment. Poor control of the production environment can disguise genetic differences among animals. For that reason heritabilities can differ between herds. To help increase heritabilities and improve the accuracy of breeding value estimates producers should: 1) treat animals the same, 2) take complete and accurate records and 3) adjust records for nongenetic sources of variation such as number reared in a litter or age at weighing.

Genetic Correlation

Extremes in performance for certain traits tend to be associated. An animal that is shorter than average at a given age is also likely to be lighter than average. These associations are known as phenotypic correlations. The association between traits can be caused by environmental factors that affect both traits similarly. For example, availability of food or exposure to disease organisms probably affect both of these traits similarly. Association resulting from environmental factors is referred to as environmental correlation. Association between two traits can also be caused by genes that affect both traits simultaneously. This effect results in a genetic correlation. Genetic correlations are of greater importance to the animal breeder. The genetic correlation can be thought of as the correlation between the breeding values of two traits. Genetic correlations can range from - 1.0 to + 1.0. They indicate the strength of the genetic relationship between two traits. An example of a gene that causes association between two traits is the halothane sensitivity gene, which results in improved meatiness but a decline in carcass quality. A negative genetic correlation indicates that animals with breeding values that are negative for one trait are likely to have breeding values that are positive for the other and vice versa. A positive correlation indicates that breeding values tend to have the same sign.

The sign of the genetic correlation does not indicate the favorability of the relationship between traits, only the statistical relationship. For example, the genetic correlation between feed conversion and average daily gain is negative (Table 2). Because fast gains tend to be associated with low feed required per unit of gain, this illustrates a negative statistical relationship but favorable economic relationship.

Table 2. Genetic correlations among performance traits among sow productivity traits.

Item                        Feed conversion           Backfat probe
--------------------------------------------------------------------
Days to 230 lb.                  60                      -.25
Average daily gain             -.60                       .25
Feed conversion                                           .30
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                        Litter         Number            Litter
Item                  birth weight     weaned        21-day weight
---------------------------------------------------------------------
Number born              .65            .71              .48
Litter birth weight                     .67              .69
Number weaned                                            .93
---------------------------------------------------------------------

The consequence of having a genetic correlation between traits is a correlated response to selection. A favorable correlation results in selection for one trait improving another. An unfavorable correlation between traits increases the difficulty of making simultaneous improvement in the traits.

The relationships of average daily gain with feed conversion and backfat (Table 2) can illustrate this concept. Direct selection for only increased average daily gain would be expected to result in selection of replacements with favorable breeding values for feed conversion because of the positive genetic correlation between the traits. Selection for growth rate is thus expected to improve feed utilization because faster growing animals tend to be more efficient. If selection is solely for average daily gain, a tendency for selected animals to have unfavorable breeding values for backfat would be expected. In this situation care must be taken to choose animals with favorable breeding values for both traits.

A plot of breeding values for backfat and average daily gain are presented in Figure 3. The two animals with the highest breeding values for average daily gain (1 and 2) have unfavorable breeding values for backfat. Animals better than average for both traits (6, 8, and 9) fall in the lower left portion of the diagram. Selection decisions among the animals described depend upon the relative importance of the traits. With knowledge of the concept of the genetic correlation, selection decisions can be aided by computerized multiple trait breeding value estimation programs.

Figure 3. A plot of breeding values for backfat thickness and average daily gain with a genetic correlation between traits of .25.

Summary

The need for production efficiency in the today's uncertain economic times makes accurate evaluation of breeding values essential. It is desirable to simultaneously evaluate traits such as growth rate, body composition, efficiency, and reproductive traits in potential replacement animals. Reproductive traits and feed efficiency are difficult to measure directly, so information from relatives and from other correlated traits are used when estimating breeding values. Aids in breeding value estimation are available to today's producer in the form of centrally operated computer programs such as S.T.A.G.E.S. and the Nebraska S.P.F. performance testing program, and in microcomputer programs available for on farm use.

Application of output of these programs requires a basic knowledge of genetic principles and an understanding of the concepts of breeding value, transmitting ability, heritability, and genetic correlation.

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.

Agdex#:	440/42
Publication Date:	01/88
Order#:	88-014
Last Reviewed:	08/03
History:	Original Factsheet
Written by:	Cathy Aker - Swine Specialist/Orangeville; B. W. Kennedy - Animal & Poultry Science/University of Guelph

Table of Contents

1. Performance Testing of Swine
2. The Canadian Swine Genetic Evaluation Program
3. Estimated Breeding Values
4. Sire and Dam Report
5. Herd Activity Monitor
6. Using EBV's

The performance of any animal is determined primarily by two factors - genetics and environment (management). Often environment can affect an animal's performance as much or more so than the animal's genetic make-up. The key to genetic improvement of livestock is to distinguish between genetic and environmental factors influencing performance and select only those animals which are genetically superior. Performance that is the result of good management will not be passed on to the next generation, whereas performance due to genetic superiority will be repeated.

Performance Testing of Swine

Supervised performance testing of swine began in 1967 with the development of the Record of Performance (ROP) Swine Testing Program. Its purpose was to help pork producers to identify and select superior replacement breeding stock.

Through the ROP Program, breeders have been provided with performance test information on pigs tested either on the home farm or at a central test station. Central testing has provided performance comparisons of young boars from a number of different herds. All boars are tested under similar environmental and management conditions, therefore, differences in performance can be attributed to genetics rather than herd management. The central test station also gives an indication of the genetic merit of a herd relative to other herds in the province using the test station. The number of boars that can be tested each year, however, is limited to approximately 1500. The home test component allows performance testing of larger numbers of young boars and gilts. Home test evaluations have been of limited value because comparisons of breeding stock are valid only for the herd in which the pig was raised. The comparisons are only valid within a herd because evaluations for each pig are expressed relative to the average performance of all pigs in that herd only, and herds can differ greatly in genetic merit and management (environmental) conditions.

Performance test information, generated either on the farm or at the test station was based strictly on the pigs own performance and did not take into account information on tested relatives. Information on related animals is useful in determining the genetic merit of a pig, together with the pigs own performance data. Because related animals are similar in their genetic make-up, their test results can also be used to predict an animal's genetic worth.

The Canadian Swine Genetic Evaluation Program

To overcome these limitations, the Canadian Swine Genetic Evaluation Program was developed in 1985. It provides pork producers with Estimated Breeding Values (EBV's) for backfat thickness and days to 90 kg on performance tested pigs. EBV's are estimates of the genetic (breeding) values of an animal for a particular trait.

Estimated Breeding Values

Estimated Breeding Values are simply an extension of the ROP Program. Data are collected in the same way; however, the analysis of the data is quite different. EBV's take into account the following factors:

1. the heritability of the trait, or that part of a trait that is expected to be inherited;
   
2. the amount of information available on each boar or sow i.e. number of relatives as well as number of progeny, number of litters, and number of herds;
   
3. the genetic merit of the herd in which the pig was raised; and
   
4. the genetic trend (change) in the breed over time for all ROP-tested pigs in the region (Ontario).

EBV's take into account performance information (backfat and days to 90 kg) on the individual as well as all related animals (sire, dam, littermates, etc.) and progeny as their test information becomes available. The more information that is available on related animals, the greater the accuracy of the EBV. This is referred to as 'repeatability'. Theoretically repeatability values can range from 0 to 100% but in practice published values on sires and dams will range between 45 to 99%. The higher the repeatability value, the more accurate is its EBV. For example, sires with many progeny will have repeatability values approaching 99%. As performance information becomes available on progeny, the importance of the animal's own record as well as records on its other relatives diminish since the performance that the selected animal has passed on to its progeny becomes the most important factor.

EBV's also account for the effect of management on an animal's performance. This is achieved through the use of genetic links between herds. Genetic links are created through the use of artificial insemination, the central test station and the sale of breeding stock from one herd to another. Through these methods, animals of a related genetic background are raised in different herds, thus herds become "linked". Because EBV's account separately for the effects of environment and genetics, the management effect can be removed, allowing valid comparisons of breeding stock in different herds. This means that an individual can be compared genetically to all other ROP tested pigs of the same breed.

The Canadian Swine Genetic Evolution Program provides producers with two valuable reports:

(1) Sire and Dam Report
(2) Herd Activity Monitor

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Sire and Dam Report

A separate sire and dam report is produced for each breed (Yorkshire, Landrace, Hampshire, Duroc, Lacombe) and region (Maritimes, Quebec, Ontario, Western). To be listed in the report a boar or sow must meet the following criteria:

(1) the animal must have a complete identification, including herd letters, pig number and year letter (according to Canadian National Livestock Records); and
(2) must have at least 1 progeny and a repeatability on EBV index of at least 45%.

The report lists animals identification, EBV's for backfat thickness and days to 90 kg, as well as an index combining EBV's for backfat and days and its repeatability. The report also lists for each breeding animal the number of progeny tested, the number of litters and the number of herds (including the test station) in which progeny were tested. The last herd in which the sire or dam had progeny is also given. EBV's are expressed relative to the average of all pigs of the same breed born and tested in ROP herds within the last two years. Because the goal is to reduce backfat and days to 90 kg, sires and dams with negative EBV's are breed improvers. Their use will result in a decrease in backfat and/or days. The EBV index is useful for breeders who wish to select for growth rate and backfat thickness at the same time. The traits are weighted so that a change of 1 mm in backfat has approximately the same value as a change of 4 days in growth rate. The average index for each breed is 100, but the average,in genetically superior herds will be greater than 100 and the average in genetically poorer herds, will be less than 100.

Sire and dam reports are published quarterly and are provided to all producers enrolled on the ROP Program. Additional copies can be obtained from: Supervisor, Sheep and Swine Performance Testing, Guelph Agriculture Centre, Box 1030, Guelph, Ontario, MIH 6Nl Phone: (519) 836-3560.

Herd Activity Monitor

The Herd Activity Monitor (HAM) is a confidential report provided to each ROP breeder on a quarterly basis. This report allows the breeder to assess genetic and management progress in the herd. The report lists the number of pigs tested in the last two years as well as the average EBV of pigs tested during this time period (compared to all other ROP herds in the region). The report also gives a measure of environmental or management performance of the herd, both in absolute terms and relative to the average herd. Trends in genetic and management performance over time are also given based on six-month periods. These trends can be used as an indicator of the effectiveness of a breeding program, provided that reasonable numbers of pigs are tested in each six-month period. The trends are also useful for determining the results of a change in management.

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Using EBV'S

The Canadian Swine Genetic Evaluation Program provides breeders and commercial producers with a means of identifying and selecting genetically superior breeding stock. Because EBV's account for the effect of management on an animal's performance, the selection of breeding stock is greatly simplified. Within a breed and region (i.e. Ontario), comparisons can be made between all pigs in ROP-tested herds. Prior to the development and use of EBV'S, accurate comparisons of breeding stock in different herds could not be made. The environment under which the animal was raised was not accounted for. Therefore an animal's performance could not be attributed strictly to genetics or management but some combination of the two factors. Genetic improvement results from the selection and use of genetically superior animals, not animals that have been raised under ideal management conditions. Table 1 compares two methods of selection of breeding stock - one using the traditional ROP Index and other, the EBV Index.

Accurate selection of breeding stock is only the first step. Designing an effective breeding program is essential for the selection process to be of any benefit. EBV's can be used by breeders to predict the outcome of a specific mating. By simply averaging the EBV's of the parents the genetic merit (value) of the progeny can be determined. An example is given in Figure 1.

 

Figure 1. Genetic (Breeding) Value of progeny from mating a boar with an EBV of -6.0 days and a sow with an EBV of -2.0 days.Not all progeny would have a genetic value of -4.0, however over a large number of matings the progeny would, on average take 4 days less to reach 90 kg than progeny of parents with breed average.

Which boar is likely superior? * If both boars are from the same herd? 'A'

Why? Because of lower backfat fewer days to 90 kg and higher overall index in the same herd.

Why? Given only this information it cannot be determined whether Boar A's apparent superiority is due to his genetic make-up or the management of the herd under which he was raised.

Which boar is likely superior? 'B'

Why? Because of better EBV's for backfat and days to 90 kg and a resulting higher EBV Index.

Comments: It can now be concluded that Boar A's apparent superiority in Example 1 was due to good management. Boar B is actually genetically superior, but poor management prevented him from showing his true potential. His genetic potential will be passed on to his progeny, however. Had Boar A been selected over Boar B on the basis of his performance figures as in Example 1, a genetic error would likely have been made.

Breeding programs must be evaluated on a regular basis in order to determine their effectiveness, Breeders can use the Herd Activity Monitor (HAM) to assess their breeding strategies. The HAM lists trends in genetic performance over time, indicating the amount of genetic improvement, or lack of it, in the breeder's herd. Similar trends are given for management performance, allowing the breeder to determine the effectiveness of management practices in the herd.

The Canadian Swine Genetic Evaluation Program will also allow evaluation of current breeding practices and testing programs on a national level. Routine monitoring of genetic trends (genetic change) in performance - tested breeding stock ensures continued genetic improvement for the entire industry.