Principles of Livestock Improvement


01-2351 Animal Production Systems
Fall 1996

J.P. Gibson

Introduction - Terms and Concepts

Adapted from original notes by A. Robinson

The written evidence from ancient Greece onwards suggests that there was essentially no understanding of the processes of reproduction and genetics throughout most of the 8000 year history of domestication of livestock species and the differentiation into breeds. Even in the late 18th century, it was still generally believed that differences between strains of livestock from different areas was more a reflection of the local environment than an inherent property of the animals. Modern breeds of sheep, cattle, pigs and poultry emerged in Western Europe from a plethora of pre-existing regional stocks in the late 18th century and through the 19th century. This phase of livestock breeding was based on the observation that planned breeding could lead to fixation of desired characteristics and creation and maintenance of a defined breed type. Modern understanding of the processes of genetic change began with the publication of The Origin of Species by Charles Darwin in 1859. Application to livestock improvement began in the early 20th century following the rediscovery of Mendel's work on inheritance controlled by single genes (now known as Mendelian genetics) and the development of quantitative genetic theory that followed. As a broad generalisation, the modern era of rapid genetic improvement, based on an understanding and application of genetic principles to breeding program design, began about 50 years ago. Genetic improvement has certainly contributed a large proportion of modern improvements in efficiency of intensive pig, poultry, dairy cattle, beef cattle and sheep production. Less genetic improvement seems to have taken place in extensive production systems, such as for sheep and beef cattle. Understanding principles of animal breeding and knowing how to access and maintain superior genetic quality has become a key component of competitiveness in modern livestock production.

This is a brief introduction to the principles of genetic improvement. As with most disciplines, animal breeding and genetics has evolved a set of terms and concepts to describe some of the unique aspects of this field of study. Some of the essential principles and jargon of animal breeding are defined below. Key terms are shown in italics for emphasis and major concepts are shown in bold.


Animal breeding is based on variation. In the absence of variation, all animals would be exactly the same and there would be no possibility of selecting better animals to improve a breed or herd. There are two basic types of variat ion: genetic variation and phenotypic variation.

Genetic variation refers to the amount of variation that is controlled by genes. Since genes that are passed on from parents to offspring and the amount of genetic variation determines the potential amount of genetic improvement that can be made in a given breed or strain. Different forms of the same gene are called alleles. Some traits are controlled by alleles of a single gene. Such traits are usually categorical or qualitative, which means that they fall into clearly distinguishable categories. Examples are the polled gene in cattle , sheep and goats (animals are horned or polled, i.e. not horned), or coat colour such as black vs red in Angus cattle. Traits controlled by a single gene can easily be fixed in the population so that no further genetic variation exists; e.g. Purebred Black Angus cattle are all black and show no variation for colour. Most economically important traits in livestock are quantitative. Such traits do not fall into discrete categories, but are measured on a continuous scale (eg, growth rate of individuals in a particular breed of cattle might take any value between 0.5 to 2.5 kg/day). These traits are generally controlled by very many genes and it is virtually impossible to eliminate genetic variation from a given population.

Phenotypic variation refers to the actual variation we observe among animals for each trait of interest.

Related to these two types of variation are the terms genotype and phenotype. The phenotype of an animal is what we can measure or touch; for example, growth rate or backfat depth or number of piglets born in a litter. The genotype of an animal refers to the genes that make up the animal. The genotype contributes to the phenotype, but many other factors also contribute to the phenotype, such as feeding, management, housing, disease exposure and other environmental factors. Thus, observing the phenotype of an animal does not necessarily tell us much about its genotype.

Genetic variation is often attributed to different kinds of gene action. Additive gene action describes the summing up of effects of alleles of a gene and of effects of genes at different chromosome locations to make up a trait. For example, growth rate in cattle is a trait influenced by many genes controlling things such as appetite, tissue deposition, skeletal development, energy expenditure, body composition and so on. The genes for all of these aspects add together to produce the growth rate we can measure. Dominance gene action refers to one allele over-riding or dominating another at the same locus. An example is black colour in Angus cattle, where individuals with either two copies of the black allele, or one copy of the black and one copy of the red allele are phenotypically black and only those individuals carrying two copies of the red allele are phenotypically red. In this case the black allele dominates the red allele. Dominance gene action is usually difficult to take advantage of in breeding programs and is often ignored except for a few single gene traits like coat colour. A practical example is the use of the dominant white colour in swine to eliminate dark hair roots that are a problem for hide value. Epistatic gene action refers to the interaction of different genes so that they tend to enhance each other or cancel each other out, rather than adding together. For example, crossbreeding different coloured breeds of pigs often results in a pig with different coloured spots suggesting that the colour pattern genes interact with the colour genes. Additive gene action is the most important for genetic improvement since it can be influenced by selection programs. Also, additive gene action contributes most of the genetic variation behind most of the economically important traits in swine so it is the best place for us to focus our efforts.


Heritability is the ratio of genetic variation to phenotypic variation. This tells us what proportion of the differences in performance we observe between animals is due to gene action (which can be passed on from generation to generation). The remaining proportion is due to environmental and outside influences (which is not passed on from generation to generation). For example, growth and body composition traits in pigs have a heritability of about 0.30 to 0.50 (or 30 to 50%, when expressed as percentages). This means that about half the variation we observe among animals in backfat depth is controlled by genes and half by environmental effects, such as nutrition. Reproductive traits, such as fertility or number of pigs born in a litter, have a low heritability of about 0.10; i.e. about 10% of the variation we see between animals in fertility or litter size is under genetic control.


Inbreeding is generally something to be avoided in animal breeding. Inbreeding refers to mating of related animals. What this does is increase the chance or probability that more of the alleles at each gene in the offspring or progeny will be identical. The level of inbreeding is measured by the inbreeding coefficient which is a measure of the probability that alleles carried by that individual will be identical. Increased inbreeding causes reductions in fertility, litter size and general viability, and leads to increased incidence of genetic abnormalities. It also leads to loss of genetic variation, and without variation no genetic progress can be made. Overall, therefore, uncontrolled inbreeding should be avoided. However, one of the reasons that pure breeds of livestock are similar in appearance is dues to a low level of inbreeding, referred to as line breeding, during the history of creating each breed. In practice, inbreeding generally refers to mating of closely related animals and line breeding is used to describe matings of animals in the same genetic line or selected group which are not highly related. Line-breeding, if used with care, can help establishing particular characteristics.


Crossbreeding refers to the crossing of two different breeds or lines of animals. It is used in livestock production to take advantage of heterosis (sometimes called hybrid vigour) and complementarity.

Hybrid vigour or heterosis occurs when the genetic merit (and hence performance) of the cross is greater than the average of the parents. Crossbreeding widely used in both plant and animal agriculture, to take advantage of hybrid vigour. In pig production, for example, commercial sows are often crossbreds of Yorkshire (also known as Large White) and Landrace pigs because they exhibit heterosis for all aspects of reproduction. The crossbred sows therefore produce more litters with more piglets per litter than either of the parent breeds.

Crossbreeding also takes advantage of breed complementarity. In commercial pig production, complementarity is captured by using some breeds (eg Large White, Landrace) as specialised female parents, often termed dam lines, and other breeds (eg Hampshire and Duroc) as specialised male parents, often termed terminal sire lines. The dam lines are selected for a combination of good female reproductive performance and growth performance, while the terminal sire lines are selected for growth performance (since their progeny never reproduce in commercial herds, they do not need high reproductive performance).

Estimated Breeding Values

Animal breeders use statistical techniques to calculate estimated breeding values or EBV. An EBV is an estimate of the genetic value of an animal as a potential parent of the next generation (i.e. its value as far as breeding is concerned, or its "breeding value"). EBV are computed using a technique known as Best Linear Unbiased Prediction or BLUP. A statistical model is used to describe each trait of interest (eg growth rate), which accounts for and separates out factors that influence performance such as management, season, age, genotype and residual effects. By accounting for all these factors that influence an animals performance, we can derive a better estimate of an animals genetic value than just observing its performance. In order to improve the estimation procedure the pedigree of all the animals is included in the model, since half of the genes in each animal come from each of the two parents. When the pedigree of all the animals is included, the statistical model is usually referred to as an animal model. An EBV balances information on the performance of an animal compared to others in the same herd or management group with the performance of its relatives in the same and other herds and management groups.

Progeny inherit half their genes from the male parent and half from the female parent. Thus, the expected genetic merit of the progeny of a particular male and female half the EBV of the male parent plus half the EBV of the female parent. The expected genetic merit of a progeny for a given trait is also its expected performance in an average environment (it's actual performance will be better or worse than this depending on the actual genes it receives from each parent and the actual environment it experiences). In some species EPD (expected progeny differences) are calculated rather than EBV. An EPD is simply equal to half an EBV. Thus the expected performance of a progeny in an average environment is simply the sum of the EPD of the male parent plus the EPD of the female parent.


Selection is the process of choosing animals to be the parents of the next generation. To obtain maximum rates of genetic improvement, selection should be based upon defined selection criteria so the process is focused on a particular goal. An EBV (or EPD) is a tool for selecting animals since it estimates the genetic value of the animal and provides the farm manager with an estimate of how well the offspring of that animal should perform.


Culling is the opposite of selection. Animals that are not selected are culled or removed from the herd and not allowed to breed. The term culling is most often applied to breeding females. Females are culled from the breeding herd because of poor reproductive performance, injury, poor genetic qualities and old age.

Replacement Rate

The replacement rate is a term used in livestock production systems with continuous turnover of breeding females. It is a balance of culling and selection; selection of young females to replace breeding females which are culled. Replacement rate is usually measured as a percentage. It is calculated as:

When there is a good rate of genetic improvement in the population, a replacement rate of 30 to 40% is a good target level. This would apply for pigs and dairy cattle. Lower rates may be more appropriate for sheep and beef cattle. With a 40% replacement rate, 4 out of 10 females in the breeding herd are culled each year and replaced with young females that have a higher EBV (because with continuous genetic improvement, each new generation of young animals is expected to have higher EBV than previous, ie older, generations).

Genetic Progress

Genetic progress results from the various forms of selection discussed above. It is usually measured as change in the average of the EBVs for a herd or whole population over time. Genetic progress is influenced by several factors:

These factors interact, sometimes negatively. For example, to increase selection intensity, fewer animals should be selected. But, selecting fewer animals can increase the generation interval. In practice an optimum balance has to be found which will maximise genetic progress within the various constraints of a breeding and production system.

Genetic progress varies widely between breeds and species. To some extent this variation is due to differences in biology between species. For example, sows produce 8 to 12 progeny in each litter compared to only one progeny for cows; thus far fewer sows are required to maintain a population than cows, so that sows can be selected more intensely than cows, and contribute more to genetic improvement. But much of the variation in rates of genetic improvement reflects different breeding goals, different incentives for genetic change, different industry structures (or lack of them) and differing degrees of use of genetic and reproductive technologies. Rather than describe all the various breeding structures that are encountered in livestock, what follows is a fairly typical structure that applies to pig breeding.

Typical Breeding Program:

The Pig Breeding Pyramid

At the top of the pyramid is the purebred or nucleus breeding herd or herds. These are the pure lines that are selected for particular characteristics. For example, in a nucleus you may want to have lines selected for growth rate and backfat in order to produce pigs which are both efficient and lean at market weight. Another line would be selected for litter size. Yet another line might be selected for carcass characteristics. By combining these lines, a commercial production pig can be produced which grows rapidly and efficiently to produce a lean, high quality carcass, with many piglets produced from each litter to maximise efficiency in the commercial sow herd. Practice is never quite this straight forward, but the principle works. In Ontario, the breeding nucleus is made up of many purebred breeders and several larger breeding companies. Nucleus stocks in Ontario tend to be made up of pure breeds, but some larger breeding company nucleus stocks are synthetic populations that resulted from a mixing of several breeds over many generations.

The middle tier in the pyramid is made up of the multiplier herds and contains many more animals than the nucleus tier. In Ontario, and elsewhere, these herds are usually associated with one particular purebred breeder or breeding company. These herds breed and multiply the different lines of pigs from the nucleus herd and cross these lines to produce crossbred or F1 cross (two-way cross) animals that are sold to commercial producers.

The third tier in the pyramid is made up of the commercial swine producers, and contains the vast majority of pigs in the population. These herds make the final cross between the terminal line sires and the maternal line gilts and sows. Common terminal line sires are Hampshire x Duroc (traditional), Hampshire or Duroc (as a three-way cross) or lately Yorkshire x Duroc (so called "white Duroc"). Maternal lines are almost always Yorkshire x Landrace. Major breeding companies often create hybrid lines which are crossed to produce a maternal line gilt or a terminal line sire. Purebred breeders focus on selecting the breeds for their own characteristics and crossing those to produce maternal or terminal lines.

Crossbreds are used as commercial market hogs to take advantage of as much heterosis and breed complementarity as possible. A point worth noting here is that four-way crosses can exhibit as much heterosis as two-way crosses. Even when the same breed appears on both sides of the cross, a full amount of heterosis can result if two different lines of the common breed are used. Thus, a Yorkshire x Duroc terminal sire crossed with a Yorkshire x Landrace gilt can give a full amount of heterosis, provided that the two Yorkshire lines are unrelated (which they usually are if one is selected for meat and the other for maternal traits).

Ontario seedstock producers have been selecting their nucleus herds using EBVs for backfat depth, age and number born in a litter. EBV are produced by recording programs (run provincially) that collect data from nucleus herds and pass it on to the Canadian Centre for Swine Improvement (CCSI), who calculate EBV from all the data collected across Canada. The EBV are returned to each breeder for use in making selection decisions. Rates of genetic improvement for growth rate and backfat are typically about .7% and .2% of the mean each year. This may seem quite small, but genetic changes are cumulative and build up over time. Also, many traits contribute to economic performance and the rate of change in any one trait is expected to be quite small when many traits are being selected. Moreover, individual breeders are achieving much faster rates of progress than the average. With quite intense competition for the sale of breeding stock, it is those breeders making the most progress today who are likely to be supplying the breeding stock of the future. Multinational breeding companies also operate in the Ontario market. They also select their nucleus stocks for a variety of traits, generally based on EBVs also.

The Value of Genetic Improvement

In most livestock species, genetic improvement contributes a substantial proportion of overall improvement in the industry. The economic value of genetic improvement is illustrated for pig production in Canada.

Today's commercial production systems run on small margins per pig and rely on volume for profit. Genetic improvement can increase these small margins per pig and increase the return to the producer with relatively little cost. For example, a recent study of the value of genetic improvement by Dr. Brian Kennedy showed that the value of one day less on feed is $0.45 and the value of 1mm less backfat is $1.83. The current annual rate of genetic improvement in Ontario seedstock pigs is about 1.14 days less to market and 0.31 mm less backfat. Combining these two rates of improvement with the value of a unit change in each trait gives an annual increase in return to the producer of

1.14 x 0.45 + 0.31 x 1.83 = 1.08 $ per pig.

In Canada, there are about 15 million hogs slaughtered annually so this rate of genetic improvement is worth $1.08 x 15,000,000 pigs = $16,200,000 per year increased return to the Canadian pig industry. Note that this is the value of one years worth of genetic improvement in one year of production. But, once made that genetic improvement remains in the population and the economic benefits occur every year. Thus over ten years of production, one year's worth of genetic improvement will be worth 10 x $16.2m = $162m. Allowing for new genetic improvement taking place each year, gives a total value over ten years of both genetic improvement and production of $874m. Although these values were initially calculated as increased profits to the producer, competition in the pig industry will ensure that most of this increased value will be translated into reduced prices to the consumer.

Emerging Technologies

As hinted at above, modern livestock breeding is becoming increasing soph0isticated and complex. In several species, genetic improvement programs are already built upon widespread use of reproductive technologies such as artificial insemination (with fresh or frozen semen), embryo transfer, embryo splitting to produce groups of identical animals, oocyte recovery and in-vitro fertilisation (IVF). All these reproductive technologies are being improved and extended to other species.

EBV are calculated using complex data handling and statistical analysis programs. Indeed a whole branch of research has focused on deriving efficient computing algorithms to allow the complex equations to be solved for very large data sets on modern computers. For example, calculating the EPD for Canadian dairy cattle involves solving some 10 million simultaneous linear equations, a feat that would have been totally impossible ten years ago, but now only requires a couple of hours computing time! Research today is focusing on harnessing the computing power of modern computers and communications systems to deal with more complex situations for a wider range of traits of interest. In some species it is already possible to record data for some traits on the farm and instantly return an approximate EBV (or EPD). The day is probably not too far away when it will be possible to automatically capture information on the farm, communicate it to a central data base, calculate new EBV using all available information and have those EBV available electronically for access by all interested parties automatically, all within a matter of a few minutes.

Rapid developments in molecular genetics and biology promise new tools for animal breeders in the near future. Several molecular genetic tests for deleterious genes are already available in different species. One example is the test for the gene causing Porcine Stress Syndrome (PSS), developed by researchers at the University of Toronto and the University of Guelph. This test is used extensively by pig breeders worldwide to detect pigs that carry the defective gene and cull them from their populations. Pigs carrying two copies of the gene are extremely susceptible to stress (often to the point of dying when stressed) and produce poor quality meat. Elimination is therefore having substantial effects on both pig welfare, product quality and profitability. This test, and others like it are based on the polymerase chain reaction (PCR), in which millions of copies of the DNA of interest are rapidly made from minute starting quantities of DNA. A single drop of blood, or a few hair follicles provide sufficient DNA for several tests.

To date, molecular tests are commercially available for a limited number of single gene defects. But research is progressing rapidly into use of similar techniques to identify genes controlling quantitative traits (such as growth rate, milk production, reproduction, etc.), with the objective of using these tests in routine breeding programs. How useful such information will turn out to be remains uncertain at present, but at least 25 large research projects are under way in various species internationally, and at least three breeding companies have full scale commercial trials under way.