Basics of animal breeding

Animal breeding is not just about pedigree dogs, champion cats or winning horses. Breeding aims at improving the genetic level of a certain trait in a population. First, laws, politics and regulations set the framework for animal husbandry. Second, a breeding programme is needed to establish common goals for what the breeders aim at. The programme can be about improving the genetics of the population, or about preserving the genes. What traits should be improved, and how to stress each trait in relation to the others? Third, a system is needed to store the measurable metrics of the traits which the breeders are interested in.

Breeding is based on two techniques: selection and pairing. They're not synonymous. Selection is about choosing which animals to use for breeding. Can one mate animals of different breeds? Which are the best breeds and animals in this situation and in this production environment? For example, one cow might excel in a tie-stall, but be run over in a free-stall barn. Certain cow breeds tolerate cold environments better than others, etc. Pairing happens only after the selection, when the selected animals are used for breeding.  To make these decisions, breeders need information about the animal itself, it's parents, sibs and possibly it's offspring. The gathered data is then used to answer one question: will the offspring be genetically better than their parents?

Breeding is full of equations. The foremost is simply P = G + E. But because genetics are never that simple, the equation is actually

P = µ + G_A + G_D + G_I + E_k + E_s

where P = Phenotype, everything about the animal which can be seen or measured
µ = the mean value of the trait in the population (for example, milk yield)
G = genes, where A denotes additive genetic traits, D dominance and I epistasis
E = environment, which may affect either positively, negatively or not at all to a given trait (for example, illnesses and quality of feed). E_k stands for random errors, and E_s for systematic errors.

As the equation suggests, what we see in an animal is created and modified by it's genes, the mean of the population and the environment. Genetically identical animals (clones) can be very different if they are raised in different environments. Then again a genetically superior animal can produce well even if the environment is less than desirable.

Comparing animals

If we're about to select animals and then pair them, we should be able to compare animals. The selection is based on measurable information, which can be gathered and combined. For a single trait each animal can be assigned a  calculated breeding value, which changes each time more information is gathered from the animal. The more information is available, the higher the accuracy of the breeding value. The formulae for calculating the breeding value (BV) and the accuracy may vary in each country.

Since the environment cannot be calculated into the value, it must be evaluated separately for systematic or random errors. That's why the formula above has two E's (Ek and Es). Systematic errors affect the BV results systematically, i.e. always the same way. Age, gender and permanent environmental conditions are systematic errors. Young animals are smaller than adults, males cannot produce milk, females produce less offspring than males etc. Systematic errors can be predicted and must be corrected when calculating the BV to make the results for all animals comparable. Random errors are errors which cannot be corrected. They just happen, like misspelling the results or a measurement error. Factors affecting the BV are listed below.

Strengthen BV or accuracy	Weaken BV or accuracy
Accuracy of data Corrected systematic errors Data from several offspring Data from parents Data from sibs and half sibs Genomic information Wide range of reference data from other animals in the population	Only a few results Random errors No data from offspring or relatives  No genomic information available Low heritability of a trait No or only little data about the animal population