theory to know Flashcards
animal breeding definition
selecting animals to be parents of the next generation. improve the genetic level of a population of animals. Maintain genetic diversity
genetic improvement
can be done by artificial selection of the best animals, next generation better, improvement across generation is cumulative.
inbreeding
- mating of relatives
- loss of genetic variation
- inbreeding depression
crossbreeding
hybrid vigour of heterosis, crossbred is doing better than average of parents
what you have to take into accoung before you start breeding
- circumstances = production system
- direction in which you want to go
- breeding goal
describe production system
- Geographical location (climate)
- Purpose of animal (production, sport, working, saving)
- Animal species and breed
breeding goal
- Combination of specific traits
- Their desired direction of change over generations
- Relative emphasis on each trait
define breeding goal
- Economic or non-economic
- Directed to the future (legislation, expected developments in costs, changes in consumer preferences)
breeding values
- Measure of genetic merit of animal
- Indication of performance of offspring
collection of information
- Phenotypes to estimate breeding values
o Repeatability (how similar are subsequent measures
on the same animal but at different times)
o Reproducibility (how similar are measures on the same animal between different persons/locations)
- Pedigree ( info of relatives, avoid mating close relatives)
- Genotypesdissemination
spread information
evaluation of a breeding program
- Selection response (revenue) realized response versus predicted response
- Costs
- Inbreeding and genetic diversity
revenue
income in a company
phenotype may be influenced by…
- Genes of an individual G
- Current environment E
- Juvenile environment
- Treatment by mother
- …
epistasis
interactions between genes at different loci
infinitesimal model
most traits are determined by an infinite number of genes, each sith infinitely small effect
full sibs mendelian sampling different or same?
different mendelian sampling terms
identical twins
same Mendelian sampling terms
common environment
individuals, in this case, resemble each other because they have more genes in common and because of same environmental effects
forces changing genetic diversity
- Genetic drift (alleles lost by coincidence)
- Inbreeding selection
- Mutation
- migration
additive genetic relationships
reflects what proportion of alleles two individuals share on average because of a common ancestor
- Full sibs= ½
- Half sibs = ¼
- Parents = ½
- Grandparents= ¼
inbreeding due to drift in small population size can or cannot be avoided?
it cannot be avoided
inbreeding due to non-random mating can or cannot be avoided?
can be avoided (offspring gets a copy of the same allele from both parents)
when is an individual inbred?
an individual is inbred if its parents are related
inbreeding coefficient
is the probability that an individual inherits two copies of the same allele, originating from a single common ancestor
inbreeding rate indicates
- Risk of inbreeding depression
- Decrease in genetic diversity
FAO advises an inbreeding rate…
…below 0.5-1%
how should an optimum trait be improved?
Take the derivative of the profit equation; the direction of selection depends on where the optimum trait is relative to the current population mean
T/F?
economic values should be based on historic prices
false
T/F?
the economic value is derived from a profit equation
true
for a certain trait, the phenotypic value of the heterozygote is not exactly in-between the two homozygotes genotypes. What is the name for this phenomenon?
Dominance
repeatability
SNP
single nucleotide polymorphism is a variation at a single position in the DNA sequence among individuals. It can be used in large numbers.
Heritability is… (not actual definition)
…the regression coefficient of the breeding value of an individual on its phenotype.
selecting sows for larger litter size + random boars = larger litter size but decrease in piglet survival. What does this indicate?
the additive genetic correlation between litter size and survival is negative.
T/F?
the genetic model for analysis of litter size from multiple parities per sow should include a permanent environmental effect
true
T/F?
the genetic model for analysis of individual growth of piglets within litter should include a common environmental effect
true
breeding value
measure of genetic merit, which is transmitted to offspring
accuracy of EBV
is the correlation between estimated and true breeding values
BLUP
Bes Linear Unibased Prediction
breeding value is in the DNA
- With DNA-markers we can estimate the breeding value of an animal
- We can estimate breeding value when the animal is born or when it is still and embryo.
genomic selection
is used to pre-select young animals (only male?) that enter the progeny test
- Early prediction
- More accurate than parent average
- Shorten generation interval
genomic selection what is needed
- High-density marker genotypes
- Phenotypes
- Method to estimate breeding values based on SNP-markers
- Genotypes or selection candidates
accuracy of selection
is correlated between true breeding value and the selection criterion
- Increases with more information from relatives
- Accurate breeding values often require half-sib progeny groups
genetic standard deviation
measures how large the heritable differences in the population are
generation interval
is the average time between birth of an individual and the birth of its average offspring
indirect selection
improving trait by selecting for a related trait.
selection for the correlated trait will indirectly improve the response trait.
first selection, then mating
- Define your breeding goal
- Select the best males of females
- Make matings
mating effects on individual and population offspring
mating may have an effect on individual offering
mating has NO effect at population level
intensive use of specific individuals is risky. 2 reasons
- Increase in rate of inbreeding
- They will spread recessive disorders
heterosis
- Crossbred offspring is better than parent average
- Caused by dominance ( and epistasis)
measure genetic improvement
- Increase in mean phenotype
- Not only genetic but also management improvement
predicted and realized gains may be lower due to:
- Lower selection intensity
- Lower accuracy
- generation interval
- genetic standard deviation
- two more
- reproductive failure
- lower heritability, less information
- longer than expected
- is lower than estimated
- genotype by environmental interaction
- selection limits
correlated responses
change of other traits when we select for a certain trait
occurs when genetic correlation is NOT equal to 0
pleiotropy
a single gene affects multiple traits. causes of correlated responses
Linkage disequilibrium
genes affecting different traits are inherited together. Offspring inheriting the positive allele for size will also inherit the negative allele for health, correlated response negative
multi-trait selection
possible? success depends on?
- In many cases it is possible to improve multiple traits simultaneously
- Success of multi-trait selection depends mainly on
o Genetic correaltions
o Weight in the breeding goal
in vitro
performing or taking place in a test tube, culture dish or elsewhere
cryo-conservation in liquid nitrogen
in vivo
performed or taking place in a living organism
keep the population alive
expensive but adaptation to changing environment possible
what to monitor for genetic diversity?
- Demographics
a. Numbers of inbreeding animals, age distribution
b. AIM: timely observe reduction in number - Rate of inbreeding
a. Measure risk of inbreeding depression &defects - Increase in mean additive genetic relatedness
a. Measure true (permanent) loss of diversity
rate of inbreeding
relative increase in inbreeding level from one generation to the next
Forces that reduce genetic diversity
Drift and selection
the population of Marge has been genotyped. for each parents genotypes for 70.000 SNP markers are available. describe in max three sentences how you could use this information to search for lethal recessive disorders. what is your hypothesis?
Hypothesis is that lethal recessive genotypes do not occurs in the population, so that the genotype frequency deviates from HW. this you can test for each SNP with a Chi square test.
In which way could the breeding company increase the accuracy of genomic selection in order to increase genetic gain?
the breeding company should increase the number of genotyped and phenotypes animals to increase the reference population. the alternative would be to use the accurate EBV of males
mention three criteria to assess breeding schemes
genetic gain, rate of inbreeding and costs
(Ax(CxD))
describe two adventages of the three-ay cross-breeding system for rabbits
- explotation of heterosis, direct and maternal on litter size
- specialization of lines: A line can be selected on growth, whereas lines C and D can be selected on reproduction
(Amale x(CxD female))
indicate where selection for genetic improvement takes place in the three-way crossbreeding scheme and write down the breeding goal for each line
genetic improvement is created within the pure lines A, C and D
Line A is mainly selected on production
Lince C and D are mainly selected on reproduction, with some emphasis on production still
in general breeding value estimaticon can be based on progeny testing, half sib testing or own performance. give 1 argument for and against each type of information sources.
- own performance: easy and cheap; not very accurate especially when heritability is low
- sib testing: fast and moderately accurate; need pedigree recording
- progeny testing: accurate; expensive and has a long generation interval.
