Grade = 80% exam + 20% case
Case = 15% report + 5% presentation
Exam 4 open questions
Basic principles genetic improvement
Chapter 1: introduction
What is the best animal?
How do you breed animals so that their descendants will be better than today’s animals?
- This course
What is the best animal
Best = relative & subjective
Describe animal through traits
- Trait => any observable or measurable characteristic of an animal
- Observable trait = appearance
- Measurable trait = performance
- Trait = coat colour & weaning weight
P+G+E
- Phenotype => observed categories or measured levels for traits
- Phenotypes = red, 343kg
- Genotype => genetic background for its phenotype
- Environmental effects => effects that external factors have on animal’s performance
Importance of traits depends on: physical environment, management system & economic
factors
- Genotype determines degree to which animals are suited for their function in society
- Breeding objective => sensible goals for breeding programs
Selective breeding: past, present & future (L0)
Domestication selection
Pre domestication: natural selection
- Genetic adaptation of organism to environment
- Survival of the fittest: fitness determined by nature
Domestication => tame an animal, especially by generations of breeding
- Genetic adaptation of animals to new environment
- New env: captivity, food provided, protection
Artificial selection => human determines fitness
- Selective breeding
- Selection for confirmation
, - Exploiting genetic variation
Selective breeding theory
Mendelians vs biometricians
Fisher
- Infinitesimal model => traits are result of infinite #genes each with small effect
Selection index theory
Chapter 3
Optimal weighing of info from relatives & traits
I = b’ X
H = v’ A
Pb = Gv <-> b = P-1 Gv
Mixed model
Chapter 5
Addition to selection index theory
Adjusts for systematic environmental differences
Infinitesimal model
Most of the times: no clue about what genes affect trait
- Animal breeders practice genetics without genes
Genomics revolution
Make polymorphisms visible in lab
More cheap to genotype animal for SNPs
Still hard to detect which gene affects which trait
- Trait affected by many genes
Genomic selection
- Genomic selection can increase selection response still without knowing genes
What has been achieved?
Milk production NL
- Trend: +75kg milk/year
, - Selective breeding does not result in large & fast changes
- Effects of selective breeding are cumulative! makes breeding unique
Selection limits?
- There are limits, but we don’t know what they are
Correlated responses
- By selecting, other parts can also be unconsciously modified
- Fertility decreases when milk yield increases in cows
Balanced breeding
- Multiple trait selection (chapter 3)
- Economic values (chapter 4)
Selection in broilers
- Fast growth, less feed required
- Improved efficiency of food production
- Discussion on responsible breeding
Negative consequences of selective breeding can be avoided by balanced breeding
multiple trait selection
- Mistakes will still be made: we don’t know everything
- Mistakes due to wrong breeding goal
Recent developments
Global challenge regarding food security
- Increased demand for food
- Economics, environment & animal welfare
Additional phenotypes: traits to include in breeding goal
- Methane emission reduction
- Longevity
General problem genetic improvement
- Translate phenotypic observations into breeding values
- Select parents for next generation improvement maximised, while maintaining
genetic diversity
- Extension of breeding goal with new traits (environmental impact) novel tech
- Improve prediction of breeding values, inbreeding & phenotypes based on genomic
info
- Understanding relation between genotype & phenotype genome editing
Novel phenotyping technologies
- Sensors (camera, sound, GPS)
- Omics (protein content, antibodies)
- Organoids in vitro (feed efficiency, stress)
Genomic info & prediction
- Whole genome sequencing (lethal recessives, recombination)
- Gene expression
- DNA methylation
Genome editing
- Precise insertion, deletion, or replacement of DNA with molecular scissors
- CRISPR-CAS
, Chapter 2: response to selection (L1)
Part I
What are expected responses to selection of various plans?
Basic principles of genetic improvement
Understand different types of selection
Understand key components of response to selection
Breeding goal => specific traits with their desired direction of change over generations
Genetic model
Describe genetic quality
Phenotypic value = breeding value + environmental effect (+ µ)
Heritability => proportion of var(P) due to additive genetic effects
Other genetic models
- Repeated observations: repeatability (r)
Ep = permanent env effect
Et = temporary env effect
Repeated measurements model
- Multiple offspring: common env effects (c2)
Transmission model
Breeding value => prediction of genetic merit
- A≠G
- Gives an indication of performance of offspring
- Bull with A = +1000 kg milk daughters produce +500 kg more than average
Selection of parents = key to genetic improvement
Different types of selection
Case = 15% report + 5% presentation
Exam 4 open questions
Basic principles genetic improvement
Chapter 1: introduction
What is the best animal?
How do you breed animals so that their descendants will be better than today’s animals?
- This course
What is the best animal
Best = relative & subjective
Describe animal through traits
- Trait => any observable or measurable characteristic of an animal
- Observable trait = appearance
- Measurable trait = performance
- Trait = coat colour & weaning weight
P+G+E
- Phenotype => observed categories or measured levels for traits
- Phenotypes = red, 343kg
- Genotype => genetic background for its phenotype
- Environmental effects => effects that external factors have on animal’s performance
Importance of traits depends on: physical environment, management system & economic
factors
- Genotype determines degree to which animals are suited for their function in society
- Breeding objective => sensible goals for breeding programs
Selective breeding: past, present & future (L0)
Domestication selection
Pre domestication: natural selection
- Genetic adaptation of organism to environment
- Survival of the fittest: fitness determined by nature
Domestication => tame an animal, especially by generations of breeding
- Genetic adaptation of animals to new environment
- New env: captivity, food provided, protection
Artificial selection => human determines fitness
- Selective breeding
- Selection for confirmation
, - Exploiting genetic variation
Selective breeding theory
Mendelians vs biometricians
Fisher
- Infinitesimal model => traits are result of infinite #genes each with small effect
Selection index theory
Chapter 3
Optimal weighing of info from relatives & traits
I = b’ X
H = v’ A
Pb = Gv <-> b = P-1 Gv
Mixed model
Chapter 5
Addition to selection index theory
Adjusts for systematic environmental differences
Infinitesimal model
Most of the times: no clue about what genes affect trait
- Animal breeders practice genetics without genes
Genomics revolution
Make polymorphisms visible in lab
More cheap to genotype animal for SNPs
Still hard to detect which gene affects which trait
- Trait affected by many genes
Genomic selection
- Genomic selection can increase selection response still without knowing genes
What has been achieved?
Milk production NL
- Trend: +75kg milk/year
, - Selective breeding does not result in large & fast changes
- Effects of selective breeding are cumulative! makes breeding unique
Selection limits?
- There are limits, but we don’t know what they are
Correlated responses
- By selecting, other parts can also be unconsciously modified
- Fertility decreases when milk yield increases in cows
Balanced breeding
- Multiple trait selection (chapter 3)
- Economic values (chapter 4)
Selection in broilers
- Fast growth, less feed required
- Improved efficiency of food production
- Discussion on responsible breeding
Negative consequences of selective breeding can be avoided by balanced breeding
multiple trait selection
- Mistakes will still be made: we don’t know everything
- Mistakes due to wrong breeding goal
Recent developments
Global challenge regarding food security
- Increased demand for food
- Economics, environment & animal welfare
Additional phenotypes: traits to include in breeding goal
- Methane emission reduction
- Longevity
General problem genetic improvement
- Translate phenotypic observations into breeding values
- Select parents for next generation improvement maximised, while maintaining
genetic diversity
- Extension of breeding goal with new traits (environmental impact) novel tech
- Improve prediction of breeding values, inbreeding & phenotypes based on genomic
info
- Understanding relation between genotype & phenotype genome editing
Novel phenotyping technologies
- Sensors (camera, sound, GPS)
- Omics (protein content, antibodies)
- Organoids in vitro (feed efficiency, stress)
Genomic info & prediction
- Whole genome sequencing (lethal recessives, recombination)
- Gene expression
- DNA methylation
Genome editing
- Precise insertion, deletion, or replacement of DNA with molecular scissors
- CRISPR-CAS
, Chapter 2: response to selection (L1)
Part I
What are expected responses to selection of various plans?
Basic principles of genetic improvement
Understand different types of selection
Understand key components of response to selection
Breeding goal => specific traits with their desired direction of change over generations
Genetic model
Describe genetic quality
Phenotypic value = breeding value + environmental effect (+ µ)
Heritability => proportion of var(P) due to additive genetic effects
Other genetic models
- Repeated observations: repeatability (r)
Ep = permanent env effect
Et = temporary env effect
Repeated measurements model
- Multiple offspring: common env effects (c2)
Transmission model
Breeding value => prediction of genetic merit
- A≠G
- Gives an indication of performance of offspring
- Bull with A = +1000 kg milk daughters produce +500 kg more than average
Selection of parents = key to genetic improvement
Different types of selection
