Summary: Genetics, math and statistics

Variance components

Variance and variance analysis have been discussed earlier in this blog, so for now let's just remind ourselves that variance expresses the variation of the data: how far apart are the extreme values in the current dataset. Variance is also expressed in the same units than the data, so the unit affects the amount of variance (for example 1,5kg vs 1500g). 

Variance components are just the different factors that create variation between measurements. 

Variance components in animal breeding can be viewed from two perspectives: genetic vs environmental contribution (which together are the phenotypic variance), or dam/sire vs residual variance. Additive, maternal and dominance effects together form the genetic contribution. Common and general environment form the environmental contribution . Therefore

P = Var(A) + Var(M) + Var(D) + Var(e) + Var(eg).

All these contributions are built from variance from the dam, the sire and the residual. The chart below shows how the different components (pillars) are built. Note that sire variance (Var(s)) affects only additive genetic variance, of which it constitutes 25 %. Therefore Var(s) = 0,25 Var(A), and Var(A) = 4*Var(s). Dam variance is also 25 % of the additive genetic effect and dominance effect, but 100 % of common environmental and maternal effects.

Only some of the components above are inherited from parent to offspring. The rest are often ignored, so the formula can be simplified into

Var(P) = Var(A) + Var(M) + Var(e).

One interesting aspect about variation is that when the reliability of the breeding value, r_TI, increases, the variance of estimated breeding values increases as well. This is because the higher the reliability, the better we see the differences between the animals, and the more variation we get. However, when the reliability increases, the variance of the true breeding values decreases between animals with the same estimated breeding value. This is of course because the increased reliability brings our estimation closer to the true breeding value. One has to consider variance in its context.

Heritability h² is often written as additive genetic variance divided by phenotypic variance, i.e Var(A) / Var(P). Considering the previous formulas, heritability can be deduced from sire variance:  h² = 4 * (Var(s) / Var(P)).

Equations

Change of gene frequency under selection is

where q1 is the frequency of the selected gene after one generation, q is the square root of the original frequency (q2), s is the coefficient of selection and q2 is the original frequency as per the Hardy-Weinberg equation (q² + 2pq + p² = 1). 



Number of generations required

The number of generations required to achieve a certain breeding objective is calculated thusly:

where t is the number of generations, qt is the gene frequency after t generations and q₀ is the original gene frequency. q_t = q₀ / (1 + tq₀).



Coefficients

Coefficient of selection, s

Coefficient of selection is the proportionate reduction of gametic contribution of a genotype compared to the standard genotype. It shows how much less animals of a certain genotype, usually the less facorable, affect the next generation when selection takes place. For example how much less gametes do unpolled animals contribute compared to polled, when polled ones are selected for breeding.

The contribution of the favorable genotype is 1, the coefficient is s so the contribution of the less favorable genotype is 1-s.

If s = 0,1, then the contribution of the favorable genotype is 1 and the contribution (and the fitness) of the less favorable is 1-0,1 = 0.9. In practice, for each 100 zygotes by the favorable genotype, 90 zygotes are born by the less favorable.

Basics on animal genetic resources

Farm animal genetic resources, or simply AGR, refers to the genetic material we currently have in live animals and frozen in sperm banks, and which is of economical, cultural and scientific importance. Genetic diversity, both within and between breeds, is vital. Diversity

• helps the animals to adapt to their environment
• is the basis for animal breeding
• allows adaptation to changes and new breeding targets
• prevents inbreeding depression
• keeps the frequency of harmful allelels low.

Domestication has already reduced genetic diversity in farm animal species (and artifical insemination has reduced it even further). Domestication is the process by which captive animals adapt to man and the environment provided, and it is achieved through genetic changes. Genetic factors affecting domestication are inbreeding, genetic drift and selection.  

Impact of domestication on milk yield of dairy cows.

Inbreeding is necessary when selecting a desired trait, but it reduces heterozygosity and thus diversity, although it does not affect allele frequencies. Genetic drift causes alleles to become fixed or deleted randomly, and its direction cannot be estimated. Selection, both natural and artificial, has altered the fitness of certain traits. For example, in domestication species the distance to flee and fearfulness have been decreased, even though they are vital for a wild animal. These are both behavioral changes. Physiological changes involve changes in hormone levels, reproduction cycle and production traits (e.g. the increased milk yield of cows and the all-year farrowing of sows). Morphological changes have also occurred, as animals have grown larger and developed colors unseen in the wild (especially white). For an example of scientific study on domestication, see Giuffra et. al (2000) or Kantanen et al. (1999).

Studying domestication

Domestication can be studied in several methods. Paternal transmission of Y-chromosome shows traits have developed from sire to offspring. It's counterpart is the study of mtDNA (mitochondrial DNA), which is always inherited from the dam to all her offspring. mtDNA haplotypes are sequenced and aligned, and dendrograms or cladograms are drawn based on the multiple-sequence-alignment (MSA) results. The haplotypes can be further divided into groups, which helps to draw a network. For more information visit the blog The Genealogical World of Phylogenetic Networks and their post on interpreting rooted networks.

The most common method by far is still studying microsatellite markers. Usually 20-30 microsatellites are studied, but FAO has published recommendations for each animal species (FAO). Polymorphic loci with 4 or more alleles are recommended to eliminate false positives by identical-by-state -alleles. Unlike mtDNA and Y-chromosome, microsatellites are inherited from both parents to all offspring. Genotyping and aligning SNP-markers is similar to microsatellies, but requires the use of thousands or hundreds of thousands of SNP-markers. Microchip arrays are readily available for several species for SNP-analysis.

Practical application of genetic domestication studies.
(c) ILRI 2006

Studying ancestral DNA is tedious, but can yield valuable information on extinct species. Ancestral DNA can be thousands or tens of thousands of years old. It is collected either from animal remains such as fossils, teeth, wools, hides or bone pieces, or from the ground ("dirty DNA"). Ancestral DNA also helps to chart the spread of different animal and plant species and to determine temporal changes in their genetics. The problem with ancestral DNA is that the concentration of desired DNA is often low, while the concentration of microbial DNA is high. Contamination risk is very high indeed. Sterile environment must be maintained whenever possible when working with ancestral DNA. Another problem is that the ancestral DNA has been fragmented, and many chemical bonds have been broken. C > T and G > A mutations in PCR are common due to deamination. The results must be confirmed in several independent laboratories. In addition, all results derived from ancestral DNA must fit in to earlier context.

Retroviruses have been used as a study method on sheep. Retroviruses are viruses, which insert their RNA to the sheep's system, and with reverse-transcriptase produce DNA from the RNA. The viral DNA is then integrated as a part of the sheep's own genome. The viral DNAs which have infected germline cells are hereditary, and thus provide a tool for studying the evolution of sheep. The original virus infections happened 5-7 million years ago, and have continued to branch even during the last 10 000 years. Studies of retrovirus-DNA has shown that originally all sheep in Europe were used for meat production. A meat-and-wool producing breed was introduced later,  and replaced the old breed nearly completely. Still existing breeds originating from the first migration are Soay sheep, Gutesheep and Finnsheep.  

Determining the level of endangerment and the value of a breed

There are thousands of animal breeds in the world. FAO's DAD-IS -information system classifies breeds into four categories:

• local breeds, which exists in one country or area only
• transboundary breeds, which exists in several countries
• regional transboundary breeds, which exists in several countries but only in one continent
• international transboundary breeds, which exists in many continents.

Each breed is also classified based on the level of endangerment. There are five levels, which are determined by the population size and number of breeding males and females. Other classification systems also consider the direction of population size (growing or decreasing), the purity of the species and the number of populations (e.g. herds). FAO's five levels are

1. Extinct
2. Critical (with or without a conservation program)
3. Endangered
4. Not at risk
5. No information on the population size.

Currently DAD-IS lists (among others) 3093 cattle breeds, 2558 chicken breeds/lines and 1283 pig breeds. Altogether there are 14544 breeds listed for 38 animal species. Of the listed local cattle breeds, 181 are extinct (209 in 2006) and only 399 are not at risk. For pigs there are 110 extinct breeds (140 in 2006) and 206 not at risk. The numbers from the year 2006 are larger, probably due to renewal of the concept of breed or improved methods of separating breeds and collecting information. Below are a few examples of the tables created from DAD-IS system, showing the status of cattle, pig and sheep breeds in different regions.

The level of endangerment is the likelihood of the breed going extinct in the current circumstances within a certain time period. It can be used to estimate how much there is time to save a breed. The level depends on demographic factors (population size and its changes) and genetic variation. Genetic variation is calculated from effective population size N_e, which again is deduced from the change of inbreeding (Ne = 1/2 ΔF). Growth factor can be calculated from r = anti-log (( logN2–logN1) / t ), where N1 and N2 are the population size at two different measurements (generation 1 and 1+n), and t is time in years. The growth factor depends on animal births and deaths, cullings, changes in market prices and agricultural politics and on epidemics.

Method of estimation impacts the value of  ΔF. Pedigree-based studies give consistently lower estimated of ΔF than SNP-based evaluation. In one study, pedigree analysis found that 15 % of animals had F > 6.25 %, while in an SNP-study the percentage was 25 %. For pairwise kinship coefficients both methods are equally reliable for close relatives. For more distant relatives the pedigree analysis gives higher estimates than SNP-analysis. (Li et al. 2011)

However, N_e, ΔF and the growth factor are only single meters. To estimate the value of a breed for genetic conservation requires a more holistic approach. In addition to the meters mentioned before, the breed value depends on several factors. The factors, and examples related to them, are listed below.

•  its ability to adapt to a certain environment (Yakutian cattle, goat breeds in arid African countries)
• economically important traits (the excellent cheese-making qualities of the milk of Finncattle)
• unique traits (breed-specific mutations, alleles and gene combinations)
• cultural heritage, historical value (Yakutian cattle)
• unique genetics.

One must remember that the breed must be able to cope even in the future, and to continue being useful for the herders. It is not a viable option to maintain breeds which cannot survive for example after global warming or if their surroundings change due to industrialization. 

Yakutian cattle (c) EPFL / Anu Osva

Managing risk in animal breeding schemes

Animal breeding is not exact science in the sense that normally one cannot exactly predict the outcome, or even select the "ingredients". Each gamete (an egg cell or a sperm) is different, and their combination and further cellular divisions all include an effect of randomness. So each breeding scheme has risks. This post will address some of those risks and how to minimize their impact.

Inbreeding

Breeding always requires some inbreeding. This is because we want to increase the genes from one or few excellent animals, so we use them for males/females of several generations. Consider horse racing and show jumping: it's common to list the famous parents, siblings, half-sibs and grandparents of any horse to prove its value.

The change of inbreeding can be calculated as

ΔF= 1 / 2N_e

where N_e is the effective population size. If the pnumber of parents of different sexes isn't equal, then we estimate

ΔF ≈ (1 / 8N_m) + (1 / 8N_f)

Inbreeding works in two ways: inbreeding increases variance between lines/populations, but decreases variance among a line/population. Remember that inbreeding depression, the negative effect of inbreeding on genetic diversity, can be negated by breeding two animals of completely different lines.

Genomic selection versus progeny testing

Both agenomic selection schemes (GS) and progeny testing schemes (PT) have their own risks. Professors Alban Bucket  and Jarmo Juga from the University of Helsinki have studied the risks in bovines. They state that in GS schemes the rate of inbreeding is slightly higher than in PT schemes, but reciprocally the genetic response is much higher in GS than in PT. The choice becomes a matter of balancing the risks. How high of an inbreeding level do we accept to get strong genetic response? 

Bucket and Juga state that if the amount of sires is not increased, the risk is comparable between GS and PT schemes. The risk in GS can be further minimized by increasing the amount of MOET (multiple ovulation, embryo transfer) and the number of genotyped females.This increases the genetic diversity and allows effective Mendelian variance. However, increasing the amount of AI bulls in a GS scheme increases the risks of inbreeding.

Preserving genetic diversity

As has been stated earlier, selection and inbreeding impact genetic diversity in two ways: the variance between lines increases, while the variance within lines decreases. If a line equals a breed, the impact can be very strong.One example can be found from the study by Uimari and Tapio, who studied how the effective population size has changed over generations in two pig breeds. During 50 generations, selection has decreased the effective population size from 600 to a mere 50. The decrease is simply due to breeding selection.

The impact of selection to the Ne of two pig breeds.
(c) Uimari and Tapio

Maintaining genetic diversity should be duly considered in every breeding scheme. By genotyping a large amount of animals it is possible to ensure diversity by pairing unrelated animals. By genotyping one can also ensure that rare alleles stay in the population, and that there is enough heterozygozity. These two go often hand in hand: rare alleles are found most often in heterozygotes than in homozygotes. By genotyping one can also preserve traits of specific interest and genomically control the level of inbreeding.

FAO, The Food and Agriculture Organization, has created a simple chart about preserving genetic diversity. The chart is part of their publication considering The State of the Worlds ANGR for Food and Agriculture (ANGR = Animal genetic resources). It shows that the actions required are rather simple. Because really - 

all it takes is the courage to look beyond monetary gain and efficiency.

Calculating breeding values

Basics of animal breeding have been covered earlier in this blog. We've discussed the very basics of animal breeding as well as the  Mathematics of animal breeding . Optimization of animal breeding schemes has also been briefly considered. Today we take a closer look at calculating the breeding value using statistical concepts and information from various sources.

Estimated Breeding Value

When calculating EBV (estimated breeding value) for an animal, we usually want to combine information from various sources. We have results from the animal itself, but also from its relatives. However, EBV is always for one trait only.

The formula for an EBV is

 = b₁x₁ + b₂x₂ + ... b_nx_n

where  is the EBV, b1 is the regression coefficient for trait 1 and x1 is the result for trait 1. Seems simple, doesn't it? Now all we need to do is calculate the b values. The key to the b values is to remember where dealing with several bits of information at once, and every "bit" is actually an equation

 Â = (y1 - μ) = a₁ + e₁

where  is the EBV, y1 is the animal's own result in trait 1, μ is the population mean result in trait 1, a1 is the additive genetic effects contributing to the trait and e denotes the environmental factors contributing to the trait. Simply put: an EBV consists of genetics and environmental factors.

So, the b's must fulfill equations for traits 1 ... n at the same time. Instead of a group of equations we use matrices to calculate the b's. Only then can we continue to calculating the actual selection index. The matrix notation for calculating b's is

b = P^-1G

Here P and G are matrices. P includes the variances and covariances between phenotypic results. The marking P^-1 simply means that the transpose of the matrix P is used in the calculation. G is another matrix, which links the information sources to true breeding values. In the G matrix Ai denotes the true breeding value of animal i. Info1 and Info2 below are different information sources, for example animals 1 and 2.

You might remember that we never know the actual breeding value A, so we always work with the estimated BV, denoted as Â. However, with enough information and correct calculations it is assumed that A = Â. The trick in matrix G is to consider the genetic relationships between the information sources, here animals 1 and 2. If Info 1 is the animal itself, so that the source for info 1 = i, then Cov(Info 1, Ai) = Var(Ai). More generally,

Cov(Info x, Ay) = a(x,y) * Var(A)

and

Var(A) = h2 * s.d. (P)

where a(x,y) is the coefficient of genetic relationship between animals x and y. If x and y are full siblings, their coefficient of genetic relationship is 0,5, and Cov(Info x, Ay) = 0,5 Var(A). If they're half-sibs, it's Cov(Info x, Ay) = 0,25 Var(A) and so on. s.d. (P) is the standard deviation of the trait P, or the trait for which we are calculating the breeding value for. Standard deviation of P is the square root of the variance of P.

Selection index and economic breeding value

So now we can calculate the EBV for one trait. What if we want to combine several traits into one number? Then we need a selection index. It works like EBV, but combines information from several sources and several traits into one.

A selection index can either be optimal or common. The difference is in the coefficients: optimal coefficients minimize the variance between true breeding values and estimated breeding values. In a common selection index the coefficient b is said to be "any b₀", but in the optimal index b = P^-1Cv. The optimal index considers covariances, and breeding accuracies impact the b coefficients.

Here we can see a new matrix, C. C is used if the measured traits are not the same as the traits to be improved. For example, we might measure weight and thickness of back fat, but we want to improve weights and percentage of lean meat. Now we need the matrix C, which relates to the other matrices as shown in the picture below.

If we want to include money to the calculations, we get a total breeding value. Money is used in breeding values to give economical weights to each trait. This weight is entirely decided by animal breeders, and based on what they think is most important. Economical weight isn't linked to genetics or phenotype in any way. It is simply a way to put the traits into some order of importance.Often economical values is derived from actual profits or costs regarding the trait in question. The weight is currency per 1 unit of increase/decrease in the trait, for example euros per +- 1 kg of meat or dollars per +- 1 weaned piglet. The economical value can be used to ompare the costs and profits between different breeding schemes.

(c) Wikipedia Commons

For example:
We have two schemes for pig breeding. One scheme gives us - 0,5 piglets per sow, but 10 kg more meat since the surviving piglets are heavier. The other scheme gives + 0,7 piglets but -6 kg meat.  Let us assume that 1 kg of meat is +10 euros and 1 piglet is 15 euros.

Now the first scheme yields (-0,5 * 15) + (10*10) = 92,5 euros, and the second scheme (0,7 * 15) + (-6 * 10) = -49,5 euros. With these exaggerated numbers it is easy to see which scheme would be more profitable for the producer.

Economic weight can also be used when restricting a selection index. We may want to improve one trait, but leave another trait untouched. In that case the economic value of the trait, which is not allowed to change, is set to 0,

Total breeding value

Using indices and economic breeding values we can calculate a total breeding value for an animal. The formulas are

H = v'g

I = b'x where b = P^-1Gv

 H = total breeding value, estimated using the index I
v = economical weights of traits
g = breeding values of traits
I = selection index
b = regression coefficients for traits
x = vector of observations [result1    result2    resultn]
P = covariances and variances between observations
G = covariances and variances between traits to be improved and measured traits.

Additional information and sources

Mrode, R. A. Linear Models for the Prediction of Animal Breeding Values, 2nd edition. CABI Publishing, USA. ISBN-13: 978-085199-000-2

Cameron, N. D. Selection Indices and Prediction of Genetic Merit in Animal Breeding. CAB International, USA. ISBN-13: 978-085199-169-6

GenUp-software for playing with genetics: http://www-personal.une.edu.au/~bkinghor/genup.htm

Fur farming - breeding and welfare

When talking about animal breeding, it is important to understand what it is. Breeding aims at improving the genetics of an animal population with methological breeding systems and programs. Breeding has clear targets, traits to be measured, recorded and followed etc. Breeding is not about increasing the animal population by mating animals to one another, which is what some pet "breeders" do.

Colors of mink pelts (c) Fur Commission

Fur animal breeding has always aimed at producing pelts which fetch the highest price in the market. Three main qualities affect the price: the size, quality and color of the pelt. Size is measured as the length of the pelt. As a breeding target larger pelts require larger animals, so often the largest and the ones that grow fastest are selected as breeding animals. Large in this context means fat. This however has lead to severe problems with fertility: fat females give birth to small litters. Fur animals breeders must therefore balance between size and litter size to produce enough pelts of an adequate size.

Pelt quality consists of several traits. The most important quality factors are

• flaws (such as bite marks)
• the quality of the guard hairs
• the quality of the undercoat

The quality of the pelt is a combination of its mass and the coverage of the guard hairs. The ratio between guard hairs and undercoat contributes to the mass of the pelt. In a pelt of good mass the undercoat is thick, strong and elastic, and it supports the guard hairs. In a high quality pelt the guard hairs are longer than the undercoat, there are no color flaws and the length of the hairs is even.

The third important quality factor is the color of the pelt. The desirability of different colors varies yearly and depends on fashion trends. Color can be determined by several qualities, such as hue and darkness.

Breeding traits

The breeding objectives can be divided to three classes, all of which may or may not be used for all fur animal species. The targets are evaluated in a two-step process, first in grading and then as pelt quality factors.

Grading is a process where the quality and color of the fur of live animals is manually estimated. Four qualities are estimated: the size, color, purity and quality of the pelt. Grading is done at the fur farm, and may be done several times a year. The size of the pelt is either estimated or measured. Pelt size is measured from the tip of the nose to the beginning of the tail. The purity of the color is also evaluated. For blue foxes the pelt can have four hues ranging from blue to red. The darkness of the color is graded and the mass of the pelt is estimated.

Mink pelts at an auction (c) Searching for Style

The same traits are measured again after skinning in a process called evaluation of the pelt quality. The differences are that pelt quality evaluation is done post-mortem and usually automatically, while grading is done when the fur isn't yet fully developed and is a manual task. The number of classes to which pelts are classified also varies between grading and pelt quality evaluation. For example in grading the pelt quality gets a score from 1-5, while the pelt quality classes depend on the company selling the pelts.  There are six traits evaluated as pelt quality: grading qualities (the size, color, purity and quality of the pelt) plus mass and coverage of guard hair.


Fertility is probably the most important breeding target. There are two main fertility traits:

• Litter size = number of puppies alive at 3 weeks of age / number of dams with at least one 3wk old pup
• Litter result = number of puppies alive at 3 weeks of age / number of mated females

The litter size and result are counted after the pups are three weeks old, because the highest pup mortality is during the first weeks of life. Studies show that young blue fox dams produce larger litters, but the pups have higher mortality than the pups of older females. 2 year old blue fox vixens have the best litter results.

Heritabilities (h²) and genetic correlations in blue foxes

Heritabilities are a way of measuring how much genes impact a certain trait, i.e. how well can the trait be developed by animal breeding. Traits with high heritability are easier to develop than traits with very low heritability. Heritability ranges from 0 to 1, where 0 means that genes have nothing to do with the trait, and 1 means that the trait is affected by genes only and there's no environmental impact at all.

A Finnish doctor of animal science, Jussi Peura, has calculated heritabilities to several breeding traits for the blue foxes. He found that pelt traits have the highest heritabilities and fertility traits have the lowest. For example, color darkness has a heritability of 0.55 and pelt size 0.30. On the other hand, litter size at 1st parity (1st litter) had a heritability of 0,1, which is fairy low.

Litter of silver foxes (c) Bioacoustica

Peura also studies genetic correlations, i.e. how much traits depend on other traits. For example, in humans height often correlates with weight: the taller, the heavier. For blue foxes there were clear positive genetic correlations between size in grading and size in pelt quality (0,74), color in grading and pelt quality (0,84) and quality in pelt quality and mass in grading (0,75). When a correlation is positive, both traits increase simultaneously.

Negative correlations mean that increasing one trait decreases the other. Blue foxes had a significant negative correlation between size and litter size (-0,28). There were mild negative correlations also between size and color purity in grading (-0,25) and color in pelt quality and size in grading (-0,17).

What all these mean is that grading gives a reliable estimation of the actual size and quality of the pelt. However, the purity estimation in grading is a poor estimation of the actual purity. The correlations also clearly show that increasing the size of the animals result in poor litter results.

Welfare of fur animals

The issues and solutions presented in this text are based on WelFur, which is again based on WelfareQuality -protocol. Welfare issues here are classified under the four basic principles of WelfareQuality: good feeding, good housing, good health and appropriate behavior.

Animal welfare is a complicated concept with several different definitions and theories. Here animal welfare means the subjective experience the animal has about its own psychological and physiological state as the animal tries to adapt to its surroundings. Welfare cannot then be measured directly. Animal cannot have a welfare of "9.5" or "good" - we can merely measure its behavior and surroundings, and deduce the level of welfare from the findings.

Good feeding

Body condition score for blue foxes

As has been previously discussed, obesity is a severe problem for blue foxes. They naturally would eat a lot during fall, and show this behavior also in fur farms. In farms feed is easily available and high in energy, so the animals gain weight very fast, and the size of their pelt increases. Obesity causes their front paws to bend, which again makes mobility very difficult. Healthy paws are rare in any blue fox farm.

Fat animals cannot breed well, so the animals kept alive for breeding are nearly starved during the winter. While it would be natural for them to lose weight, in farms the difference between the Fall weight and Spring weight is much greater than in the wild. Normally a blue fox would weigh 3-5 kg - the average weight of farmed blue fox males is a staggering 19 kg, and 10 kg for the females.

In any farm where animals are kept in group cages there is no peace during feeding. The animals fight over the food, which causes stress, and fearful animals may be underfed while the more dominating animals are overfed.

Another problem common to all fur farms is the availability of fresh, clean water. During winter the water pipes may freeze, and during summer the water may heat and become unsanitary. Problems with availability of water are usually technical in nature: unlike with feeding, there is no reason to purposefully limit the animals' intake of water.

Good housing

Good housing is a wide concept, which consists of a comfortable place to lie, warmth and the easiness of mobility.

Foxes on a shelf (c) Dyrevern Alliansen

Small fur animals, like minks and ferrets, must have a nest box available all year round. Foxes have a nest only during whelping. The nest is the only part of the cage with solid floor and walls: otherwise the animals sleep, play and walk on a metal net ( = mesh). The nest box has been proven to increase fearfulness towards humans, because it gives a place for the animals to hide to. That, and the animals' tendency to defecate on solid surfaces, are the main reasons for keeping the nest box available only for a short while. 

Foxes must also have a shelf in their cage, unless they can lie on top of the nest.The shelf is actually very important for the foxes, who prefer high places from where they can scan their surroundings.

The main reason for using mesh flooring is that urine and feces pass through it. Fur animals have a tendency to defecate on a solid surface, which would then need to be cleaned daily to prevent the animals from soiling their fur. While a mesh floor sounds unpleasant, foxes actually prefer mesh over earth floor or solid floor such as wood at least as a resting place. This may be because the mesh allows their fur to stay "puffy" so the animal stays warm. There are no similar studies done on other fur animal species.

Good health

In order to have and to maintain good health, the animals must have good housing and good feeding. Good health means that the animals have no sicknesses, but also no internal or external injuries or disabilities. In fur farms mortality due to diseases is somewhat low, 3-4 % in foxes between April - October. Treatment of illnesses may be rare. Many animals are kept until skinning even if they are sick, or left to die.


Disease epidemics in fur farms are relatively rare. The only exception is plasmasytosis for minks, which occasionally causes significant losses due to sickness and exterminations. The most common diseases vary between animal species. For foxes and minks infections of the womb and gut are the most common illnesses. Eye and skin infections, urinary tract infections and diarrhea are sometimes seen in foxes. Diarrhea can also infect minks, but rarely raccoon dogs, who are capable of eating even partially rotten meat without trouble.

As has been noted before, bent front paws and obesity are extremely common health risks in blue foxes. They are not usually life-threatening or even painful in fur farm conditions, but most likely they do decrease the animal's welfare.

Compared to most farm animals (cows, pigs etc.) fur animals receive no painful treatments. For example, there are no surgical castrations, tooth cutting or cutting of the ears, which are all performed on piglets. Still, care must be taken to ensure that all fur animals are killed humanely and quickly before skinning. The killing and skinning must be done far away from the live animals to prevent fear and panic.

 Appropriate behavior

Expressing normal and appropriate behavior is mostly impossible in fur farms. Pups can be weaned at the "correct" age, but they cannot spread apart like they would do in the wild. Animals are not allowed a space for their own. They also do not need to hunt or forage, which in the wild would occupy most of their time.

Silver foxes would normally live in small groups, where only the dominant female would raise a litter, and the females of lower rank would kill their own pups if they have any. To keep thousands of females in adjacent cages, all with their own litter, may cause stress and increase situations where females kill their pups.

Group vs single housing is an important question for all fur animals, but many study results are contradictory. Group housed minks can fight more and therefore damage the pelts. Their stress levels may also be elevated if the group is not balanced. On the other hand, group housed minks have company, can play with one another, and in a balanced group are also less stressed than individually housed animals.

Fur farming - animal species and annual cycle

Fur animals are farmed to provide raw material for clothes designers and the fashion industry. The ethics of fur farming is an important topic and should always be considered, but it will not be covered here. This post is about the practices of fur farming, fur animal species and caring for fur animals.

Every year nearly 60 000 000 mink pelts and 4 000 000 fox pelts are produced, with Denmark as the leading producer of mink pelts (over 15 million annually) and Finland of fox pelts (nearly 2 million). When these numbers are considered, it is obvious that fur farming is important to the national economy to some countries. Still, major fur producing countries like the Netherlands have banned fur farming due to ethical concerns. Finland's house of parliament voted on the subject in 2012, and vetoed a bill demanding to end fur farming.

Fur animal species

Mink (Neovison vison)
Minks are the smallest of fur animals, weighing 1-4 kgs and ranging from black to brown to white in color. Minks, like all fur animal species, come to heat once in a year in the spring. Female minks are in heat during the beginning of March. Mating induced ovulation, so the mating time does not need to be carefully planned, and usually each female is mated 2-3 times. One male is allowed to mate with 4-5 females.

The gestation period for minks is 40-70 days. Most minks in one farm have their litter within 2 weeks from each other. Naturally minks would deliver 6-7 pups, but in captivity only 4-5 pups survive to adulthood. Minks are killed with gas (CO / CO₂) and skinned in November, apart from breeding animals which are kept over the winter and mated again in Spring.

Minks are raised either alone, or two or four animals in one cage. Studies show that group housing reduces stereotypical behavior, but only if the groups are kept steady and balanced. Usually groups consist of pups from the same litter, with one female and one male, or two of both. In Europe, four pups or 2 adult animals may be kept in a cage of 2550cm² in size. In the wild each mink would live alone in a territory covering several hectares.

(c) greengirlabroad

Blue fox (Vulpes lagopus)
The blue fox originates from the endangered arctic fox. Its weight ranges from 8-12 kg, but the largest males can be near 19 kgs. The largest animals are not muscular but obese: foxes are overfed to make them fat, which increases the size, and thus the price, of the pelt.

Obese animals suffer from major health issues, such as bent legs and difficulty to move. In recent studies in Finland, blue foxes with healthy legs are a rarity. Because fat animals breed poorly, the animals kept for breeding are kept on minimum food during the winter, so they lose weight and are able to breed in the Spring. While it mimics the natural habit of the animals (gathering body fat in the fall for the harsh winter), in farms it is taken into extremes and thus causes major stress for the animals.

Blue fox females, vixens, are in heat for 4-5 days during February and March. Most vixens are artificially inseminated using sperm collected from male foxes in the same farm. The gestation lasts 51-53 days, and each litter has 5-7 pups. This is a very poor result compared to the litter size of wild arctic foxes, which is 8-10 pups.

Blue foxes have a very thick fur to keep them warm. Because on solid surface the fur would flatten, the animals actually prefer net flooring to solid flooring. Still, overgrown claws and wounded paws may occur even if the net is covered with plastic.

(c) Wikimedia commons

Silver fox (Vulpes vulpes)
Silver foxes are descendants of the common red fox. They are smaller and leaner compared to the blue fox, and their fur is less thick. Silver foxes are not fattened and then starved like blue foxes, because due to their heritage they are more finicky eaters.

Silver foxes are in heat for 2-3 days during January-April, and deliver litters of 3 pups after 51-53 days of gestation. In the wild the litters have 4-5 pups. Artificial insemination is rarely used, and one male mates with 4-5 females. Breeding blue and silver females are kept in the farms for approximately 5 years, after which they too are killed and skinned.

In Europe silver foxes are raised in cages of two, or a female with her pups.The cages have a nest during whelping, and a shelf to provide a "solitary" place where the animal can watch its surroundings. Foxes want to see what happens around them, which is why they are often raised in a "shadow house" with free visibility to every direction.

(c) PeTA Asia-Pacific

Raccoon dog (Nyctereutes procuonoides)
Raccoon dogs weigh from 5-15 kgs, and come to heat for 3-4 weeks during February-April. Like with silver foxes, each raccoon dog male mates with 4-5 females. The gestation period is 60 days, after which a litter of approximately 6 pups is born. In the wild litters have 6-12 pups.

Raccoon dogs are monogamic: in the wild they form life-long partnerships, and both parents tend to the pups together. In fur farms this kind of behavior is entirely denied, and each female has to tend to her pups alone. On the other hand the farmed female doesn't need to hunt her food, and therefore doesn't have to leave the pups to go foraging. It is not known whether raccoon dogs should be farmed in pairs to improve their welfare.

(c) CBS Minnesota

Ferret (Mustela putorious)
Ferrets are possibly the least farmed species, even though they can have up to two litters of 6 pups in one summer. In the wild each litter would have 2-17 pups, so the ferret is the only farmed animal whose litter size in captivity is not markedly smalled than in the wild. Ferrets come to heat in April and gestate for 42 days. The second heat occurs two weeks after the first pups are weaned.

While these are the same animals than the ferrets kept as pets, farmed animals receive none of the caring of pets. They are raised in small cages, bred, weaned, killed and skinned like all other fur animals. The instructions and laws regarding pet ferrets do not apply for their farmed counterparts.

The annual cycle of fur farms

Each year in a fur farm can be divided into six phases, regardless of the farmed animal species. Each year follows the same pattern: mating in early Spring, whelping during Spring and early Summer, and raising of the whelps and separating them into their own cages during Fall. Selecting breeding animals and killing and skinning the rest takes place in early Winter, after which the breeding animals are "kept alive" until they can again be mated in Spring.

Poultry production: meat chickens and turkeys

Meat chickens

A layer and a broiler hen, both at 6 weeks of age
(c) Coop cam

Meat chickens (broiler chickens) are brought to European countries from Scotland (Ross-breed). The grandparent birds are brought to the country as eggs, and hatched there. The grandparents will produce the parent generation, which are raised until 18 weeks of age in another poultry house. The 18 week old broiler chickens are then transferred to a breeding facility, where the live until 60 weeks of age producing the progeny. A fourth poultry farmer incubates and hatches the production generation birds. Finally a fifth farmer buys the day old hatchlings, which arrive in crates and are simply poured on the floor. The birds are reared for 32-39 days, at which time they are slaughtered. Before another flock is brought in, the hall is disinfected and left to dry for 2-3 weeks. Flock sizes in Norther Europe are usually 20 000 - 80 000 birds.

Broiler chicken females used for breeding grow very fast. But since fast growth would cause severe injuries and deformations, the females receive only 1/3 of the feed they need. The nearly starving birds are constantly hungry and frustrated. Only because malnutrition their growth slows down, and the birds are able to mate with the roosters and lay fertile eggs.

Broiler chickens meant for meat production (instead of breeding) live only 5-6 weeks before slaughter.  During this time the currently used chicken hybrids grow from 40 g to 2,1 - 2,5 kg. In comparison, a layer-breed chicken of 6 weeks of age would weigh less than 800 grams. The temperature of the poultry hall is decreased from 34 C to 20 C as the birds mature. Injured and dead birds are removed from the flock and destroyed. During the rearing time mortality of 3-4 % is expected and accepted. In a flock of 54 000, ~1890 birds will die of various reasons before slaughtering. In Europe, broiler chickens are not medicated in any way. If the hall is disinfected properly between flocks and the rearing conditions are good, the birds stay free from any diseases or parasites, eliminating any need for treatments or preventive medication.

The rearing is mostly automatized. Ventilation, temperature and humidity control, feeding, watering and light programming are all automated. While it saves work, even relatively short power outages can kill the entire flock to suffocation due to rapidly raising levels of ammonia, H₂S and CO₂ in the air. Because the light/dark program is carefully designed and obeyed, broiler halls have no windows or any inlet for daylight (organic farms are an exception). Meat chickens are still manually inspected twice a day. The farmer ensures all the automated systems work, and that the litter is dry and clean.

Meat chickens are fed crumbled feed from the floor during the first two days. The chicks would survive from nutrients in their yolk sacs, but solid feed helps the development of  the digestive tract and production of gastric juices. Later the chicks eat granulated feed from feeding cups. Feed and water are freely available, and the height of water nips and feed cups are altered as the birds grow. Feeding is usually phased with four different feed mixes suitable for birds of different ages. Each successive phase has less amino acids, calcium and phosphorus than the previous phase, but the energy content stays at 12,4 MJ/kg ME. This is because the bones of the birds develop fast and need Ca, P and proteins to grow strong. The last phase has no coccidiostates to ensure drug-free meat at slaughter.

Australian broiler shed. (c) Animals Australia

The EU directive for meat chicken welfare sets strict requirements for animal density. Densities are measured as kg / square meter at the end of the rearing period. Density of < 33 kg / m² has no additional requirements. If each meat chicken weighs 2,5 kg, a density of 33 would mean 13,2 birds / m². Animal density of 33-39 kg/m2 requires the farmer to have a writter description of the rearing facilities and equipment available at all times. A secondary power source is required, and the indoor air must fulfill cleanness, humidity and temperature requirements.  The highest allowed animal density is 39-42 kg/m2, roughly 17 birds / m2. In addition to the previous requirements, a farmed using the highest density must have impeccable results from animal welfare auditions and daily bookkeeping on bird deaths and removals with reasons attached. The mortality per flock is limited, and exceeding the limit forces the farmer to drop the animal density to 39 until the conditions improve.

Turkey production

Wild Turkeys (c) Turkey Management

The turkey is the largest bird used in animal production. It's meat has more protein and less fat than that of chickens, geese, sheep or cows. The current production turkeys are white hybrids, descendants of the still-living wild turkey (Meleagris gallopavo).  Turkeys are classified by color (bronze, white or black) and by size (heavy, medium heavy and light). Heavy males weigh 15-16 kg, medium males 8-10 kg. Hens weigh only half of the males' size.

Turkeys are raised in flocks like meat chickens. During the long rearing time of 3-4 months (compared to the 5-6 weeks of broiler chickens) the turkeys grow to weigh 6-12 kg. Hens and roosters are reared separately because of the size difference. Otherwise they are reared much like meat chickens. Turkeys are, however, much more demanding. They must be given time to develop strong bones at first, so their feed cannot be too strong. Young turkeys must have 8-10 cm of warm, dry and clean litter.  The first few days they are kept under a heat lamp in 38 C degrees and in bright lightning. The behaviour of turkey chicks is closely monitored. If they are huddled together, the temperature is too low, or they are stressed. If they are scattered away from the lamps, the temperature is too high.

After the first few days all birds know where to find water and food, so the light intensity can be lowered. Light program is changed gradually to allow for a dark time of 8-10 hours. Humidity is kept at 60-75 %, and by the end of the rearing period the temperature has been decreased to 14-17 C . 

Turkeys are fed mostly with complete feeds consisting of wheat, soybeans and peeled oats. Feeding is phased. For example, the recommended phasing for Nicholas-breed turkeys is:

• prestarter (0-2 weeks)
• starter (2-6)
• Grower 1 (6.9)
• Grower 2 (9-12)
• Finisher 1 (12-16)
• Finisher 2 (week 16 onwards)

Commercial breed turkeys. (c) Zimbio

Prestarted feed has the most proteins, espcially lysine and methionine. Energy content grows slightly towards the finisher feeds, but otherwise the contents stay rather similar. The phasing is designed by weeks of age, but weight of the birds is a more accurate measurement since each flock is different. However, it is important to stay with the prestarter and starter feeds long enough for the bird to develop strong bones before the period of fast growth. 4-phased feeding can also be used with the same principle of gradually lowering the amino acid content.

Since turkeys are the largest of domesticated birds (not including ostriches or emu), their rearing densities are much lower than that of broilers. At the rearing phase, 3-4 hens or 1 rooster / m2 is used. In farms producing turkey eggs the density is 2 hens or 1 rooster / m2.

Breeding and growth of chickens

Egg-laying hens and meat chickens are sometimes infertile. They are hybrids, produced from two selective breeds or lines in a breeding facility. Meat chicken and egg producers do not raise their own animals, but buy them in large batches from the sellers.

In a breeding facility chickens are either inseminated or allowed to mate with a rooster. The sperm  cannot enter the ovaries immediately, because there are always developing eggs blocking the way. The sperm is deposited in the vagina, which has small membrane sacs for storing the sperm. When the oviduct is free after the oviposition (laying of the egg), the sperm can continue towards the ovaries. The funnel-like end of the oviduct, the infundibulum, has membrane sacs similar to the vagina. Here the sperm stay fertile for a long time: 8-10 days in chickens, less than a week in geese and 3 weeks in turkeys. Most fertilizations happen 2-3 days after the insemination. In poultry houses, best results ar achieved by inseminating non-pregrant hens once a week.

(c) Margaret Gunning

Roosters are sexually mature at the age of 16-20 weeks, but aren't selected for breeding until the age of 24-32 weeks when their sperm quality has increased. Most roosters cannot produce high-quality sperm for long. Roosters' testicles are located in the body cavity right behind the lungs. They have no penises, so the ductus deferens leads to the cloaca. Roosters and chickens mate by rubbing their cloacas together, during which the sperm enters the vagina. Breeding henhouses have one rooster for 10 hens, but using artificial insemination, the sperm from one rooster can be used for 48 hens weekly.

Two hormones affect the development of spermatozoa: FSH (follicle stimulating hormone) and LH (luteinizing hormone). FSH increases the development of spermatozoa, and LH increases the secretion of androgens from the testes.

Most production-line hens no longer sit on their eggs. This vital trait has been lost during the animal breeding, so the fertilized eggs must be incubated in an automated incubator. The incubation temperature is 37,6 - 38,6 C. Ventilation must allow constant supply of oxygen and removal of CO₂. The developing fetus "breathes" since day 1. Air humidity must be 60-70 %, and the eggs must be turned to avoid the fetus from touching the egg shells. Before incubation most eggs are treated with gas. The gas kills 96 % of the bacteria covering the egg shell (dirty eggs can have 50 000 - 200 000 bacteria). If needed, the eggs can also be medicated by dipping them into a liquid medicine.

The fetal cells start dividing within three hours after the internal temperature of the egg has risen above 22 C. The development of a chick proceeds as follows:

• Day 1: a yolk sac is formed, providing nutrients for the embryo. The Embryo weighs 0,0002 g.
• Day 2: The fetal membranes are developed. The heart starts to beat and ears are formed.
• Day 3: Nostrils, feet and wings can be seen.
• Day 4: Tongue starts to form. The fetus weighs 0,05 g.
• Day 5: Genitalia starts to form, the gender of the fetus is developed
• Day 6: The beak starts to develop
• Day 8: The feathers start to develop. The fetus weighs 1,15 g.
• Day 10: The beak hardens
• Day 14: The fetus turns around into a hatching position, head towards the blunt end where it can breathe from the air bubble. The weigh is 9,74 g.
• Day 19: The yolk sac starts to retreat to the chick's abdominal cavity during day 19, and is completely assimilated by day 20. 
• Day 21: The chick uses a sharp "tooth" on its beak to break the egg shell, and the bird hatches. The chick weighs over 30 grams.

The hatching times vary in different bird species. For chickens the development of the fetus lasts 21 days, 30-32 for geese, 28 for turkeys, 18 for doves and 42 for ostriches.  If the incubation temperature varies from the optimum (depends on species), the incubation time will also decrease (in colder temperatures) or increase a few days.

Growth of chicks and young chickens

(c) Unknown

Newly hatched chicks need water and warmth immediately. Their yolk sac has enough nutrition for 2-3 days, after which the chick will need to eat to survive. During the first days the chicks need a temperature of 31-32 C, and it can be decreased by 3 degrees weekly until the temperature is 16 C. For hygienic and safety reasons the chicks are raised separately from hens. The animal density is max 12 chicks / m² until they reach 12 weeks of age. Young chicks must be kept in a draftless area with good ventilation and 5-10 cm of litter.

The sex of the chick can be determined during the first three days after hatching. Male chicks are deemed useless and destroyed, usually by crushing . Chicken sexing is done manually, and can be very painful for the bird.

Egg and meat chicken producers byu their animals in batches (flocks). Therefore the breeders must make sure that each bird in a flock grows evenly: 90 % of the birds should weigh +- 10 % of the eaverage weight of the flock. Chicks are weighed 2 or 3 times between 5 and 15 weeks of age to assure even growth. In practice a selected sample will be taken and weighed, since each flock may have tens of thousands of birds. Young birds are also vaccinated. The light/dark program and light intensity are very important for young animals. If they will be raised in a poultry house with roosts, the chicks should be allowed to roost already at a young age.

The chick feeds depend on the breed of the bird. Chicken breeders have exact feeding programmes for the rearing poultry houses to use. Starter feed is usually fed for the first 3 weeks, or until the bird has reached a certain weight. The started feed includes all needed nutrients in pressed crumbs, preventing the chicks from selecting their feed. Grower feed has less energy, and is fed during weeks 1-8. Developer feed has as much energy as the grower feed, but less amino acids. Pre-laying feed accustoms the ~17 week old chickens for the feed they will be eating when they start laying eggs.

Genomic selection

Genomic selection in animal breeding means that genomic information is used together with phenotypic information to calculate estimated breeding values. Genomic information in itself is rather useless. It only shows what genetic markers, QTLs, SNPs or microsatellites one animal has. Only by connecting those markers to wanted traits can we select the animal with the "right" markers. For example, we may know that a marker X1 is connected with high milk yield, and X2 with susceptibility to metabolic illnesses. Then we can choose animals with X1 but not X2. Genetic mapping is the key to connect genetic information with phenotypic observations. However, once the traits have been linked with genetic markers, pure genotype information is enough to value an animal. In practice, genomic estimated breeding value GEBV always combines genotypic data with pedigree information.

Using genomic information increases accuracy in all traits.

Single nucleotide polymorphisms, SNPs, are used in genomic selection. At one time, current genotyping technology can identify up to 800 000 SNPs from a given DNA sample. Those SNPs are evenly distributed to the DNA strand. SNPs are known to be connected to productive traits. Animals are genotyped, their genes are valued based on the SNPs, and then best animals are selected for breeding. We don't need to know where or what the actual wanted genes are - we just know which SNPs are connected to them, and use those as a basis for selection. It's a bit like orienteering: you see from the map where you are and where you have to go, even if you have no clue in which city or country you're in!


Illumina is a manufacturer of bead chips, chips which are used to identify SNPs from a genome. For example, the  PorcineSNP60 chip has 65000 evenly spaced probes for recognizing SNPs. It can be used for four pig breeds: Duroc, Landrace, Pietran, and Large White. More information about the chip can be found from the product information sheet.

Simulations

There are two ways for evaluating genetic variation in quantitative traits: simulations and experimental genetics. Simulations are cheap and easy to repeat, but the assumptions used in the simulation may not be realistic.Experimental genetics uses real data, but is more cost and labour intensive. Simulations are carried out with different computer programs. They estimate population evolution under different conditions. Each simulation is based on real data about

• allele and genotype frequencies
• linkages between markers and genes
• population and family structure
• effective population size
• reproduction parameters
• selection (if any)
• isolated / open population
• DNA alteration parameters

Simulations work with four basic forces of evolution: mutation, recombination, selection and genetic drift. Mutation adds diversity, recombination creates new combinations of alleles and breaks linkage between chromosomal regions, selection favours some genotypes with selective advantage and genetic drift makes allele frequencies fluctuate over generations. The key for simulations is that the researcher can change the underlying variables, and study the impact of (for example) population size or family structures to genetic evolution. For a free simulation software, you can try QMsim by Sargolzaei and Schenkel (http://www.aps.uoguelph.ca/~msargol/qmsim).

4N_eμ is an important term in simulations. According to professor Alban Bouquet, in a mutation drift equilibrium the SNP (or allele) frequency depends on the variable 4N_eμ.  If 4N_eμ < 1, the distribution is U-shaped. Large % of markers are fixed, and diversity is low. When 4N_eμ  = 1, the distribution is uniform, and when it's > 1, the distribution is curved out: only a few markers are fixed, and there's high diversity. In most mammals 4N_eμ is about 0,001, so most loci are fixed at MDE and many markers need to be simulated.

Comparing the effectiveness of genomic and traditional selection

(c) informedfarmers.com

In animal breeding, there are four selection pathways: sire of bull, sire of cow, dam of cow and dam of bull. Each pathway has their own selection intensity i, accuracy r_TI and generation interval L. For bovines, dams of bulls have the highest selection intensity (around 2 %), because only the best of the best are chosen. A few more sires of bulls are chosen, about 5 %, while as much as 80 % may be chosen for dams of cows. With strict selection and reliable genomic information the genetic gain is largest when dams and sires are selected at one year of age. In such a juvenile scheme (JS), genetic gain increases while rate of inbreeding decreases. Genetic gain increases the most with strictest selection intensities, but rate of  inbreeding is also higher. (Bouquet & Juga 2012)

The study by Bouquet and Juga (2012) showed that with JS, using a multiple-ovulation embryo transfer (MOET) herd of 75 heifers genetic gain is significantly increased.  MOET does not significantly increase inbreeding rates if over 33 AI sires used. Doubling the number of flushed heifers may change response to selection with over 50 AI sires, but only if the number of genotyped females is increased as well. Increasing the number of flushings per heifer from 2 to three increases both genetic and rate of inbreeding, and may not thus be advisable. All in all, MOET and JS combined impact production traits very strongly, but functional traits only little. Compared to traditional pedigree-based selection, the variance of response is slightly increased in JS schemes whereas genetic gain istremendously increased.

(c) eadgene.info

For pigs genome information also increases the accuracy of breeding values. In a study by Tribout, Larzul and Phocas (2012) a simulation generated 39% - 58% more accurate EBVs with genomic breeding schemes. Annual genetic gain increased 63% - 128%. There was variation in the results between different traits. Rate of inbreeding was reduced 49% - 60%.  They conclude that genomic breeding schemes can increase accuracy and genetic gain while decreasing rate of inbreeding without a need to modify current breeding scheme structures. 

Defining breeding targets and trait values

An animal breeding is not just about calculating breeding values and creating statistics. It starts with a difficult task: defining what "best animals" are like, and what to measure. Only that which is measured can also be improved.Good breeding goals are

• well defined
• reliable, easy and cheap to measure and record
• aim to the future (help the animals adapt to the coming changes.

Goals can also be ethical, political or biological, and either global, national or areal. For example, national policy may dictate that local breeds are to be conserved, which prevents cross-breeding. Biological goal could be the need to improve fertility, and ethical goals such as breeding only healthy animals is (or should be) a global target. Also,  breeding can only target traits which have genetic variation. If every animal already has long horns, it's not feasible to aim at short horns.

Once a list of breeding goals has been made, the goals need to be weighed. Every goal cannot be the most important. Factors influencing the weighing process are

• defining efficiency: biological and economical views
• target of selection: maximizing profit or minimizing costs
• production system: developing animals / herds / breeds
• limiting factors: Limiting production inputs, number of animals
• range of planning: what needs to be inmproved first, and what later
• different roles in the food production chain: slaughterhouses have different goals than piggeries or animal welfare professionals

Example: values of fertility and udder health

 Animal breeding for farm animals targets mostly at better income for the farmer. Each trait can be given an economic value based on how it increases profits or decreases costs. Better fertility decreases medical costs, while inreased milk/meat yield increases profits and decreases cost of milk liter/cow.. A profit function has been defined to describe changes in net profit as a function of modifiable parameters (physical, biological and economical). For breeding to be profitable, the changes leading to better revenues must be caused by genetic improvement. But focus on profits has its downside. Animals are culled as soon as their production decreases, even if their best production seasons would still be ahead. Increased production is a heavy stress on metabolism and health, causing a variety of ailments on the animals.

Costs of traits for pigs have been valued to show how much an improvement of one unit of standard deviantion increases the price of pig meat. In one study, the most profitable trait was the size of litterm which increased the price of pig meat  2 cents / kg. The least profitable traits was the size of the first litter. Some breeding programmes like the Northern European NAV has defined clear values for different traits, as can be seen in the picture below.

Values of traits in NAV. (c) http://www.nordicebv.info