English agriculturist Robert Bakewell (Bakewell, Robert) was a very successful breeder of commercial livestock in the 18th century. His work was based on the traditional method of visual appraisal of the animals that he selected. Although he did not write about his methods, it is recorded that he traveled extensively by horseback and collected sheep and cattle that he considered useful. It is thought that he made wide outcrosses of diverse breeds, and then practiced inbreeding with the intent of fixing desirable characteristics in the crossbred animals. He was also the first to systematically let his animals for stud. For these reasons he is generally recognized as the first scientific breeder.

Selective breeding utilizes the natural variations (variation) in traits (character) that exist among members of any population. Breeding progress requires understanding the two sources of variation: genetics and environment. For some traits there is an interaction of genetics and the environment. Differences in the animals' environment, such as amount of feed, care, and even the weather, may have an impact on their growth, reproduction, and productivity. Such variations in performance because of the environment are not transmitted to the next generation. For most traits measured in domestic animals, the environment has a larger impact on variation than do genetic differences. For example, only about 30 percent of the variation in milk production in dairy cattle can be attributed to genetic effects; the remainder of the variation is due to environmental effects. Thus, environmental factors must be considered and controlled in selecting breeding stock.

Although no complete knowledge of the genetic makeup of any breed of livestock exists yet, genetic variations can be used for improving stock. Researchers partition total genetic variation into additive, dominance, and epistatic types of gene action, which are defined in the following paragraphs. Additive variation is easiest to use in breeding because it is common and the effect of each allele at a locus just adds to the effect of other alleles at that same locus. Genetic gains made using additive genetic effects are permanent and cumulate from one generation to the next.

Although dominance variation is not more complex in theory, it is more difficult to control in practice because of how one allele masks the effect of another. For example, let a indicate a locus, with a₁ and a₂ representing two possible alleles at that location. Then a₁a₁, a₁a₂ (which is identical to a₂a₁), and a₂a₂ are the three possible genotypes (genotype). If a₁ dominates a₂, the genotypes a₁a₂ and a₁a₁ cannot be outwardly distinguished. Thus, the inability to observe differences between a₁a₂ and a₁a₁ presents a major difficulty in using dominance variance in selective breeding.

Additive and dominance variations are caused by genes at one locus. Epistatic variation is caused by the joint effects of genes at two or more loci. There has been little deliberate use of this type of genetic variation in breeding because of the complex nature of identifying and controlling the relevant genes.

Additional complications arise from simultaneously trying to improve multiple traits and the difficulty of determining what part of the variation for each trait is under genetic control. In addition, some traits are genetically correlated, and this correlation may be positive or negative; that is, the traits may be complementary or antagonistic. Breeding methods depend on heritability and genetic correlations for desirable traits.

Heritability is the proportion of the additive genetic variation to the total variation. Heritability is important because without genetic variation there can be no genetic change in the population. Alternatively, if heritability is high, genetic change can be quite rapid, and simple means of selection are all that is needed. Using an increasing scale from 0 to 1, a heritability of 0.75 means that 75 percent of the total variance in a trait is controlled by additive gene action. With heritabilities this high, just the record of a single individual's traits can easily be used to create an effective breeding program.

Genetic correlation occurs when a single gene affects two traits. There may be many such genes that affect two or more traits. Genetic correlations can be positive or negative, which is indicated by assigning a number in the range from +1 to −1, with 0 indicating no genetic correlation. A correlation of +1 means that the traits always occur together, while a correlation of −1 means that having either trait always excludes having the other trait. Thus, the greater the displacement of the value from 0, the greater the correlation (positive or negative) between traits. The practical breeding consequence is that selection for one trait will pull along any positively correlated traits, even though there is no deliberate selection for them. For example, selecting for increased milk production also increases protein production. Another example is the selection for increased weight gain in broiler chickens, which also increases the fat content of the birds.

When traits have a negative genetic correlation, it is difficult to select simultaneously for both traits. For example, as milk production is increased in dairy cows (cow) through genetic selection, it is slightly more difficult for the high-producing cows to conceive. This negative correlation is partly due to the partitioning of the cows' nutrients between production and reproduction, with production being prioritized in early lactation. In the case of dairy cattle, milk production is on the order of 20,000 pounds per year and is increasing. This is a large metabolic demand, so nutrient demand is large to meet this need. Thus, selecting for improved fertility may result in a reduction in milk production or its rate of gain.

Types of selection are individual or mass selection, within and between family selection, sibling selection, and progeny testing, with many variations. Within family selection uses the best individual from each family for breeding. Between family selection uses the whole family for selection. Mass selection uses records of only the candidates for selection. Mass selection is most effective when heritability is high and the trait is expressed early in life, in which case all that is required is observation and selection based on phenotypes. When mass selection is not appropriate, other methods of selection, which make use of relatives or progeny, can be used singularly or in combination. Modern technologies allow use of all these types of selection at the same time, which results in greater accuracy.

Genetic gain per year (ΔG) depends on balancing several factors, as expressed in the equation

Methods of ranking animals for breeding purposes have changed as statistical and genetic knowledge has increased. Along with increases in breeding knowledge, advancements in computing have enabled breeders to quickly and easily process routine breeding evaluations, as well as to develop research needed to rank large populations of animals. Evaluating and ranking candidates for selection depends on equating their performance record to a statistical model. A performance record (y) can be expressed as

The first task in estimating g is to statistically eliminate environmental effects, a process that involves setting up a system of equations to simultaneously solve for all of the genetic effects for the sires and cows. Information from relatives is included in g and increases the accuracy of evaluation of the candidates for selection. All relatives that are available can be incorporated in this type of evaluation. This model is called the animal model.

The animal model is used extensively in evaluating beef and dairy cattle, chickens, and pigs. To apply this model for evaluating large populations requires use of high-speed computers and extensive use of advanced mathematical techniques from numerical analysis. In evaluating the dairy cattle in the United States, a system of equations with more than 25 million variables is needed.

Because close relatives share many genes, an examination of the relatives of a candidate for breeding can improve accuracy of selection. The more complete the genealogical record, or pedigree, the more effective the selection process. A pedigree is most useful when the heritability of a trait is relatively low, especially for traits that are expressed later in life or in only one sex.

Progeny testing is used extensively in the beef and dairy cattle industry to aid in evaluating and selecting stock to be bred. Progeny testing is most useful when a high level of accuracy is needed for selecting a sire to be used extensively in artificial insemination. Progeny testing programs consist of choosing the best sires and dams in the population based on an animal model evaluation, as described in the preceding section. A description of progeny testing in dairy breeding provides a good example. The best 1 to 2 percent of the cows from the population are chosen as bull mothers, and the best progeny-tested bulls are chosen to produce another generation of sires. The parents are mated to complement any individual deficiencies. The accuracy of evaluation of bull mothers is typically about 40 percent, and of sires that produce young bulls the accuracy is more than 80 percent. This is not as high as the industry wants for bulls to be used in artificial insemination. To reach greater accuracy, the next generation of sires is mated to enough cows in the population for each sire to produce 60 to 80 progeny. After the daughters of the young sires have a production record, the young sires are evaluated, and about the best 10 percent are used extensively to produce commercial cows. Some of the progeny-tested sires will have thousands of daughters before a superior sire is found to replace them. About 70 percent of dairy cattle are bred by artificial insemination, so these sires control the genetic destiny of dairy cattle. Consistently applying this selection procedure has been very successful.

The genetic gain has been consistent over the years. The actual first-lactation milk production varies more than the sire breeding value because differences in environmental conditions affect first-lactation production, but these environmental effects have been adjusted out of the breeding value calculations. There is no indication that the rate of gain in the sire breeding values is about to reduce. This level of achievement can only be realized if artificial insemination organizations and producers work together.

The other consideration in crossbreeding is heterosis, or hybrid vigour, which is displayed when the offspring performance exceeds the average performance of the parent breeds. This is a common phenomenon in which increased size, growth rate, and fertility are displayed by crossbred offspring, especially when the breeds are more genetically dissimilar. Such increases generally do not increase in successive generations of crossbred stock, so purebred lines must be retained for crossbreeding and for continual improvement in the parent breeds. In general, there is more heterosis for traits with low heritability. In particular, heterosis is thought to be associated with the collective action of many genes having small effects individually but large effects cumulatively. Because of hybrid vigour, a high proportion of commercial pork and beef come from crossbred animals.

Mating animals that are related causes inbreeding. Inbreeding is often described as “narrowing the genetic base” because the mating of related animals results in offspring that have more genes in common. Inbreeding is used to concentrate desirable traits. Mild inbreeding has been used in some breeds of dogs and has been extensively used in laboratory mice (mouse) and rats. For example, mice have been bred to be highly sensitive to compounds that might be detrimental or useful to humans. These mice are highly inbred so that researchers can obtain the same response with replicated treatments.

Inbreeding is generally detrimental in domestic animals. Increased inbreeding is accompanied by reduced fertility, slower growth rates, greater susceptibility to disease, and higher mortality rates. As a result, producers try to avoid mating related animals. This is not always possible, though, when long-continued selection for the same traits is practiced within a small population, because parents of future generations are the best candidates from the last generation, and some inbreeding tends to accumulate. The rate of inbreeding can be reduced, but, if inbreeding depression becomes evident, some method of introducing more diverse genes will be needed. The most common method is some form of crossbreeding.

Genetic progress in domestic animals has been made using quantitative methods to date. It would be very desirable to know the genes (gene) that control the many traits that have economic significance in domestic animals. This should make selection more accurate. Information from sequencing human genes, as well as those of other species, is being used to find chromosomal segments with high probabilities of coding genes in livestock. Another approach is to scan a chromosome segment and look for associations with economic traits. Several quantitative trait loci have been discovered that are or promise to be useful in livestock breeding. For example, an estrogen receptor in pigs is associated with increased litter size—on average, an increase of 0.6 to 2.0 pigs per litter, depending on the genetic background in which the gene is expressed. Other genes have been found that control the secretion of casein in cow's milk. Genes are also known for growth hormone, and many others could be enumerated. With improvements in sequencing DNA, more genes will be discovered that affect economic traits—genes that will need to be tested in different genetic backgrounds and environments before they can be commercialized.

It is now much less expensive to sequence DNA, which has led to new methods of evaluating animals using large segments of 30,000–50,000 bases. With the use of these large segments of DNA, animals are evaluated without looking for markers for individual traits. This is intuitively an appealing approach because much more of the DNA can be evaluated; perhaps in the future the entire genome can be used to evaluate animals. This method of selection, called genomic selection, is now being applied to dairy cattle, but results are not yet available.

The connection between an organism's genetic makeup and its immune system, as well as applications of that knowledge, form the young science of immunogenetics (genetics, human). In particular, producers must control diseases (animal disease) in their livestock if they are going to be profitable. While vaccines, hygiene, and other therapeutic methods control most diseases, vaccines are expensive and none of these methods is completely effective. However, there is evidence from experiments and field data of some degree of genetic control over the immune system in humans and animals. For example, bovine leukocyte adhesion deficiency (BLAD) is a hereditary disease that was discovered in Holstein (Holstein-Friesian) calves in the 1980s. The presence of the BLAD gene leads to high rates of bacterial infections, pneumonia, diarrhea, and typically death by age four months in cattle, and those that survive their youth have stunted growth and continued susceptibility to infections. It was soon found that these calves carried two copies of a recessive gene that was present in nearly 25 percent of Holstein bulls. Cattle with only one copy of the gene, or carriers, had normal growth patterns and immune systems. Holstein bulls are now routinely tested for the BLAD gene before being used for artificial insemination. With a high percentage of Holsteins being bred artificially, a potentially major problem has been avoided.

Genetic control of the immune system is based on the DNA of the individuals. Histocompatibility genes that serve several functions are on one area of a chromosome, called the major histocompatibility complex (MHC), which exists in all higher vertebrates. There are large numbers of genes involved in the MHCs of different species. There are more than 60 different alleles at one locus and other loci are multi-allelic. There are also differences among species in the number of genes known. In addition, selection experiments have demonstrated genetic variation between lines selected for high and low response to different antigens (antigen). Some vaccinations are more efficacious when the animals have been selected for resistance to the antigen for which they are vaccinated.

Substantial progress has been made in the field of immunogenetics, but limited use has been made of this knowledge. One reason for this is that immune systems have evolved to be generally robust. Changing the frequency of some genes that control immune function may inadvertently change the function of other genes and result in adverse effects. Experiments are now under way to determine whether sires' immune responses can be used to predict the health of their daughters under field conditions. The results indicate that there are differences among sires' daughter groups, but the differences are not large enough to control a high proportion of the variability. The tests used were based primarily on leukocytes (leukocyte), which are the first line of defense when an antigen invades an animal. Application of knowledge in the area of immunogenetics must be used with caution.

It might seem that integrating molecular markers and quantitative methods would be a trivial task. However, the effect of some genes depends on the presence of others, and these interactions need to be considered along with the particular breeding scheme. Furthermore, there are nongenetic influences that may turn genes on and off. Thus, some genes act individually, some genes interact, and the environment has a further impact. Finding how these all affect the phenotypic expression of an organism is complicated. However, this challenge presents an opportunity for future research and for producers.

Many advances in reproductive technologies have been made, though many are too expensive for everyday use. Most of the advanced techniques use artificial insemination, which was developed decades ago, though refinements continue.

Cloning, an asexual method of reproduction, produces an individual with the same genetic material (DNA) as another individual. Probably the best-known examples of clones are identical twins, which result when cells in the early development stage separate and develop into different individuals. Though the DNA in cloned individuals is the same, environmental influences may make them differ in phenotype. Thus far, the commercial use of clones has been limited. Cloning can be used to produce clones from a highly productive individual, but the cost would have to be low enough to recover the expense quickly. Animals have been cloned by three processes: embryo splitting, blastomere dispersal, and nuclear transfer. Nuclear transfer is most common and involves enucleating an ovum, or egg, with all the genetic material removed. This material is replaced with a full set of chromosomes from a suitable donor cell, which is microinjected into the enucleated cell. Then the enucleated cell, with the transplanted chromosome, is placed into a recipient female to be carried through gestation.

There is a commercial demand for the ability to predetermine the sex of livestock. For example, a producer may want female calves from the best cows for replacements and male calves for beef production. Dairy producers may want more females for replacing cows or for expansion of their herds. The sex of mammals is determined by the sex chromosomes (sex chromosome), or X and Y chromosomes. Animals with two X chromosomes develop into females; animals with an X and a Y chromosome develop into males. Thus, the detection of X and Y chromosomes on sperm has been the focus of research to predetermine the sex of domestic animals.

In one process, sperm is pretreated with a dye that fluoresces when exposed to short wavelength light. The fluorescence is brighter from a sperm bearing X chromosomes, which contain about 4 percent more DNA than the Y chromosome. A stream of dyed sperm is passed through a flow cytometer, a computer determines the degree of fluorescence, and the sperm is separated into different containers. The success rate can be as high as 40 percent. When “sexed sperm” has been used on a commercial basis, though, it has had limited success. The conception rate using sexed sperm is lower in cows, though it is higher in primiparous cows. In addition, sperm are killed in the typing process, and the rate of sexing the sperm is slower than desired. While economical processing of sperm is just getting started, it is expected to become another useful tool in animal agriculture.