Summary animal breeding and genetics

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Summary - animal breeding and genetics

  • 1 Introduction

  • Definition of animal breeding :
    Animal breeding involves the selective breeding of domestic animals with the intention to improve desirable (and heritable) qualities in the next generation.
  • Selective breeding
    - Only use males and female for breeding that have passed a certain quality criterion.
    - With a predefined goal in mind
    - to genetically improve the population in a certain direction (= artificial selection)
  • 5 points important to realise in animal breeding:
    1. It is essential that the trait under selection is heritable
    2. Animals have different genetic backgrounds so selection is possible
    3. Direction of selection is defined by humans and they decide which animals are allowed to mate and produce members of the next generation
    4. Animal breeding workds at population level, not automatically at individual level.
    5. Succes of animal breeding can be measured as the cumulative result of multiple generations of selection. Breeding decisions are made with the future in mind.
  • Natural selection
    - The environment determines survival en reproductive succes of animals
    - animals that are better adapted to their environment have a higher chance to survive and produce more offspring than less adapted animals
  • A trait is 'a distinguishing phenotypic characteristic, typically belonging to an individual'. In practise it means you can record or measure it on an individual.
  • Animal breeding
    - involves the selective breeding of domestic animals with the intention to improve desirable (and heritable) qualities in the next generation
  • A phenotype is what you observe or measure on the animal for a certain trait. It can depend on the genetic background of the animal (as long as it is heritable) and external circumstances
  • Important points of animal breeding
    1. It is essential that the trail (running speed or milk production) under selection is heritable 
    2. The animals must have different genetic backgrounds so that selection is possible 
    3. The direction of selection is defined by humans and they decide which animals are allowed to mate and produce members of the next generation
    4. Animal breeding works at population level, not automatically at individual level
    5. Succes of animal breeding can be measured as the cumulative results of multiple generations of selection (future in mind)
  • Selective breeding = artificial selection
    What also plays a role: natural selection
    Animals adapt to the environment
  • Trait
    - A distinguishing phenotype characteristic, typically beloning to an individual
    - so anything you can record or measure on an animal
    - A trait is heritable if the performance for that trait, at least in part, depends on the genetic make-up (DNA) of an animal
  • Natural selection is the process whereby animals that are better adapted to their environment have a higher chance to survive and produce more offspring than less adapted animals. The next generation thus, on average, will be more adapted than the current.
  • Phenotype
    - What you observe or measure on the animal for a certain trait
    - It can depend on the genetic background of the animal and external circumstances (nutrition etc.)
  • Selective breeding often competes with natural selection
  • Domestication
    - Process of conversion of wild animals to domestic use
  • Selective breeding will only be succesul in case the trait under selection is heritable.
  • Prerequisites of domestication
    1. Animals should be able to adapt to the type of feed they are offered by humans. This may be different from what they were used to in the wild
    2. Animals must be able to survive and reproduce in the relatively closed quarters of captivity. Animals that need very large territory are not suitable to be domesticated
    3. Animals need to naturally calm
    4. Animals need to be willing to recognize humans as their superior, which means they must have a flexible social hierarchy
  • Domestication is the process of conversion of wild animals to domestic use
  • Progeny testing
    - The method of evaluating performance of the first group of progeny and use that information to select the best fater of the future progeny
  • There is a list of prerequisites for succesful domestication
    1. The animals should be able to adapt to the type of feed they are offered by humans. This may be different (in diversity) from what they were used to in the wild.
    2. Animal must be able to survive and reproduce in the relatively small closed quarters of captivity. Animals that need a very large territory are not suitable to be domesticated.
    3. Animals need to be naturally calm. Very skittish or flighty animals will be hard to prevent escaping.
    4.Animals need to be willing to recognise humans as their superior, which means they must have flexible social hierarchy.
  • Breed
    - A group of animals of a certain species that through generations of selective breeding has become the uniform in performance, appearance and selection history 
  • Robert Bakewell (1750s) introduced keeping accurate records of performance of animals so that objective selection became possible. He introduced Progeny testing; the method of evaluating performace of the first (small) group of progeny and use that information to select the best father of future progeny
  • Species
    - The largest group of animals that are capable of interbreeding and producing fertile offspring
  • A breed is a group of animals of a certain species that through generations of selective breeding has become uniform in performance, appearance and selection history.
  • Alleles
    - dominant -> Only one copy determines the expression of a gene
    - Recessive -> 2 copies are required for expression
    - additive -> a copy of both alleles result in an expression that intermediate to that of having 2 copies of either of the alleles
  • a species is the largest group of animals that are capable of interbreeding and producing fertile offspring.
  • Estimated breeding value (EBV)
    - Made it possible to rank the animals according to their estimated genetic potential, which resulted in more accurate selection and thus a faster genetic improvement across generations
  • Gregor Mendel published in 1865 the results of his studies of genetic inheritance in garden peas. He showed that genetic material is inherited from both parents, independently of each other. Each (diploid) individual thus carries 2 copies of the same gene and they pass 1 to their offspring.
  • Genetic marker
    - a kind of 'flag' on the genome
    - Its location and composition are know
    - These can be used to compare animals based on looks of the various flags
  • Alleles an be dominant, recessive or additive (a copy of both alleles results in an expression that is intermediate to that of having 2 copies of either of the alleles)
  • Measure phenotype
    - You do not have to wait until the phenotype can be measured on the animals anymore 
    - you have the associated DNA information
    - You can select animals already at a very early age and you do not have to wait until they become an adult
  • The statistician R.A. Fisher (1930s) showed that the diversity of expression of a trait could depend on the involvement of a large number of so-called Mendelian factors (genes).
  • Large scale animal breeding
    - a big infrastructure is needed combined with high quality data collection, large computing capacity and highly educated people to run the breeding program
  • Fisher, together with Sewall Wright (1940s) and JBS Haldane were the founders of theoretical population genetics.

  • Reasons to prevent showing animals in public
    - prevent infectious diseases to spread
    - production figures had become more important than looks
  • Thomas Hunt Morgan (1900s) and co-workers connected the chromosome theory of inheritance to the work by Mendel and created a theory where chromosomes of cells were believed to carry the actual hereditary material. Morgon won the Nobel prize for it in 1933.

  • Farm animal breeding
    - increasingly global industry
    - breeding companies need to develop products that fit the various markets
    - Introduction of reproduction techniques like artificial insemination (AI) that made it possible to have very large numbers of offspring per father, made it possible to select only the very best males for breeding, without decreasing the population size
    - Embryo transplantation (ET) and ovum pickup 
  • Jay L. Lush was known as the modern father of animal breeding (1950s)

  • Negative correlated responses
    - examples where selective breeding has not only improved certain performances but simultaneously and unintendedly also deteriorated other performances that were not under selection
    - these effects can be reversed by selecting the opposite direction
  • Lanoy Nelson Hazel (1970s) was inspired by Lush's book and developed the selection index theory, a method used for decades to determine what weights should be put on the different traits under selection. and how to estimate genetic correlations
  • PTA
    - predicted transmitting abilities
    - indicate what part of the breeding value is transmitted to the offspring
  • CR Henderson (1960s) was a student of Hazel. The estimated breeding value made it possible to rank the animals according to their estimated genetic potential (the ebv) which resulted in more accurate selection and thus a faster genetic improvement across generations.

  • A genetic marker can be considered a kind of 'flag' on the genome. Its location and composition ('looks') are known. They can for example be used to compare animals based on the looks of the various flags
  • Main idea behind genomic selection is that the association between the DNA make-up and performance of animals can add to the estimated breeding v alue or even replace it. Because you do not have to wait until the phenotype can be measured, you can select animals already at very early age and do not have to wait until they become adult. You can also use this for traits that are difficult to measure such as disease related traits.

  • From farmers owning males and females, to artificial insemination (AI) companies owning the males (in cattle) and later also breeding females (in pigs). 
  • Selective animal breeding already has almost 300 years of history
  • Introduction of new selection techniques made it possible to select the best animals for breeding more accurately and efficiently. Especially the introduction of reproduction techniques like artificial insemination (AI) made it possible to have very large numbers of offspring per father to select only the best males.
  • Also in females techniques like embryo transplantation (ET) or ovum pickup have made it possible to produce much larger number of offspring of excellent females than with normal reproducion techniques in species where normally only one or few offspring per year were feasible.
  • Selective breeding is the most important reason for the strong increase in body weight at size weeks. 
  • There are also examples where selective breeding has not only improved certain performances but simultaneously and unintendedly also deteriorated other performances that were not under selection: the so-called negative correlated responses. Both types of engative responses to selective breeding are difficult to predict and are usually only noticed afterwards.
  • Import is to realise that certain negative effects can be reversed by selecting in the opposite direction (eyes in chicuawua's)
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Crossbreeding systems
- before animals are crossed they are first selected for relevant traits
- crossbreeding requires maintenance of the pure breeds
Motivation for crossbreeding
  1. Heterosis is one reason to apply crossbreeding of breeds or lines. It can be concluded that estimates for heterosis are higher for traits with a low heritability
  2. benefit from direct and maternal herterosis
  3. exploit the complementarity of breeds or lines: Combinations of the characteristics of two breeds or lines is favourable
  4. crossbreds combine characteristics that cannnot easily be improved simultaneously in a single breed
  5. last reason for crossbreeding is the protection of the genetic improvement in the selection lines of commercial companies 
Heterosis/hybrid vigour
- The extent to which the performance of a crossbred in one or more traits is better than the average performance of the two parental lines 
- based on the phenomenon of domimance
Crossbreeding
- matings between animals of different breeds or lines
- crossing takes place after the selection of parents in different breeds or lines and is structurally embedded in a breeding program
- Not only applied with different breeds but also with different selection lines
Pedigree recording might be of poor quality
  1. In some group mating systems where multiple males/females housed together.
  2. When many offspring is born on the same day tagging is often not done very accurately 
  3. It is not always clear which calve belongs to which cow because there was no supervision 
  4. When mating fail females are mated again. Sometimes to the same male, sometimes to another male
  5. An extensive DNA test can be used to test how related two animals are with incomplete pedigree 
  6. To discourage false matings 
The long term genetic contribution
- measure of the level of relatedness between animals in a population because of a shared common ancestor
Compensatory mating
- finding the best mate for individual females to compensate her shortcomings
- It may have an effect on individual mating results but it has no effect at population leven
Why is the offspring performance for a certain trait as poor as that of the dam even though the sire was expected to improve it?
- Mendelian sampling: Chance factor
- Pleiotropic and epistatic effects 
- What is the accuracy of the information?
- Environmental effects
Mating decisions
- no influence on population leven but may have some effect at the level of individual mating
- mating decisions at the level of individual breeder may have consequences for the rate of inbreeding at population level
- will not result in extra genetic gain
Mate choice depends on
- intended use of the offspring
- the quality of the female
- the price fo the desired mating
- distance to the mate