Exam 1 Flashcards
Part of the chromosomes, that usually codifies a protein
Gene
Location on the chromosomes
Locus
Double helix made up of nucleotides
DNA
Specific form of the gene
Allele
What are the components for genes
Introns
Exons
regulatory areas
All of the DNA in chromosomes
Genomes
How many alleles does a individual have
2
What is homozygous
The 2 alleles are the same
What is heterozygous
The 2 alleles are different
Individual in the population have different sequences of nucleotides in their DNA
Polymorphism
Locations on the DNA where single nucleotides are different
Single Nucleotides Polymorphism (SNP_
Any part of the genome that affects traits of interest, Can be in coding or non coding regions
Quantitative trait loci (QTL)
What is the three Mendel’s Laws
Dominance and uniformity
Segregation
Independent assortment
What is dominance in Mendel First Law
Pure traits are crossed, only one form of trait appears in the next generation
What is Segregation in Mendel Laws
Mom and Dad two alleles
One of the allele from each is given to the offspring
What is Independent Assortment in Mendel’s Law
Alleles assort independently if possible
Do genes always assort independently?
NO because of linkage
loci located close together on a chromosomes
Linkage
The new combination of genes
Recombination
T or F More crossing over allow more genetic diversity
True
When do loci recombine, far apart or closely linked
far apart
The specific alleles the animal has at a locus
Genotype
the characteristic of the animal we are looking at
Trait
what we see when we look at an animal (measurement)
Phenotype
The black calf weight 85 lbs when it was born
trait: the color and the weight
Phenotype: the color black and 85 lbs
alleles interaction at two different location
Epistasis
What about endangered species or zoo animals?
Have small effective population size
4 Ways to change gene Frequencies in a population
Mutation
Migration
Selection
Random Drift
random change due to chance
Random drift
Why do We need to have a large population size
avoid the risk due to chance
a biochemical event causing a change in the DNA sequence
Mutation
Impact of mutation on animal improvement is very small or big
small
Gene editing Issues
- Regulations
- Do it before the animal is born
- Do it for a few animals
bring in alleles from outside the population - bring breeding animals into your herd
Migration
Why use migration (outside, native)
- Outside animals have higher frequency of desired alleles
- Native populations becoming too inbred and having problems
What is the most powerful gene frequency
Migration is the most powerful force for changing gene frequency.
choosing animals with high numbers of desired allele to be parents
Selection
what are the two types of selection
Natural Selection
Artificial Selection
animals which are unfit will die or fail to reproduce
Natural selection
selection imposed by human
artificial selection
The ability of animals of that genotype to reproduce
Fitness
If we are doing selection, we are changing what
frequency
Whenever q is large or small, you’ll see more changes in q
large
As s increase or decrease, change of q increase
increase
When we change gene frequency
We change the mean
Move the population in a desired direction
What animal breeders do?
Make decisions, select the parent of the next generation based on the traits of interest.
Do not need a numeric definition to accurately describe the trait
Qualitative traits
Traits are in a few phenotypic classes
Qualitative traits
Are categorical
Qualitative
Qualititave traits tend to
Be controlled by few or a lot of loci with large effects
Have little or a lot of effect of the environment
Be relatively easy or hard to manipulate through genetic management - relatively easy or hard to identify desired animals
Be controlled by FEW loci with large effects
Have LITTLE or NO effect of the environment
Be relatively EASY to manipulate through genetic management - relatively EASY to identify desired animals
What law does qualitative follow
Follow Mendels law
we know the genotype by looking at the phenotype
Single locus with co dominance, partial dominance, overdominance
the dominant allele completely masks the effect of the recessive allele. Heterozygous are the same as Homozygous dominant
Complete dominance
Why heterozygous animal sometimes bad
Heterozygous animal in a herd can be a carrier for a disease that is not desired
Why test males? Why not females?
Males usually produce more offspring
Importance/advantages of DNA testing
Heterozygous animal in a herd can be a carrier for a disease that is not desired, by sending sample and money you can find that out
Why do deleterious alleles tend to be recessive
Hiding in the heterozygous, not expressed when bred with a dominant allele
how to know if Is it Genetic or Environment
Prior knowledge about the defect
Look at housing and management groups
Look for family tendencies
What is already known, we may not know the mode of inheritance
Prior knowledge about the defect
Was there anything different in the way the animals were treated
Look at housing and management groups
Example of Look at housing and management groups
Issue with feed
Vaccination
Contamination
Check for carrier sire was in the past generation
Look for family tendencies
which one requires more work and which one is easier
environmental and genetics
environmental is easier
genetics requires more work
T or F Difference breed association have different policies
True
Offspring of carriers can’t be register until they are DNA tested
True
AI bulls must be tested for defects
True
AI sire needed to be tested free due to BLAD
holstein cattle
17% are carriers of hydrocephalus, cant get rid of this
Friesien horse
Does recessive always mean bad
no
Must be defined numerically to be accurately described
Quantitative traits
A range of values
Quantitative traits
quantitative traits that phenotypically look like qualitative traits
Threshold traits
they are discrete (qualitative)
Phenotypic scales
they are continuous (quantitative)
Genetic scale
Quantitative traits tend to
Be controlled by many or little to no loci, each with small effects
Have a large or small effect of the environment
Are less or more easily manipulated and controlled
Be controlled by MANY loci, each with small effects
Have a LARGE effect of the environment
Are LESS easily manipulated and controlled
The genetic model
P = G + E
G expressed in some E
Phenotype
Total effect of all genes, the value of an animal’s gene to itself
Genetic Value
Everything non genetic
Environment
Genetic value equation
G = A + D + I
A = additives
D = dominance
I = Epistasis
Why is Genetic value different from breeding value
Can’t transmit dominance and epistasis ONLY additive values to breeding value
When changing the frequencies of genotypes, you are also changing the frequency of what
phenotypes
The value of an animal’s genes to its progeny
Breeding Value
Only additives value
Breeding Value
how does a higher breeding value affect genetic frequency
Higher breeding value. The higher the genetic frequency of the populations
What does the Mean, Genetic Value and Breeding value depend on?
The gene frequencies in the populations
Why are national evaluations important
It is easier for us to compare the animals when they are together, not from an single herd
How do we predict the future, Mains tools available for animal breeders
Selection
Mating System
Animal disposal
decide which animals become parents of the next generations
Selection
decide which animals are mated to each other
Mating system
remove animals based on current performance (remove worst ones, to improve current herd)
Animal disposal
Two effects important when working in cross breeding
Dominance and epistasis
Interactions of the allele at the same loci, not transmittable
Dominance
the interaction among allele at different loci
Epistasis
When is it transmittable in Epistasis
loci on the same chromosomes and are linked
What should you look for when buying a cow
The breeding value
The environment it was raised
What causes differences in performance
Environment
affects group of animals
Macro environment
affects individual uniquely
Micro environment
Example of macroenvironment
Feed Quality
Climate
Housing
Example of microenvironment
Age
Disease
Social Order
affect the animal for the remainder of its life
Permanent Environment
affects a single record
Temporary Environment
We want to use phenotype to predict Genetic value but what complicates things
Environment
How do we account for E
Adjust records
Deviated from contemporary group mean
2 types of adjust records
additive factors
Multiplicative factors
add a constant
additive factors
multiply by a percent
Multiplicative factors
Bring everyone to the same scale, like age, so it is easier to compare
Adjust record
Known source of variation when adjusting
Age
Sex
Age of dam
Parity of dam
Location
All records should be adjusted by the same or different method
All records should be adjusted by the SAME method
Compare animals to other in the same group
Deviated from contemporary group mean
A group of animals with an equal opportunity to perform
Deviated from contemporary group mean
What makes a good contemporary group?
5 things
Large number of animals
From different families - have variability
Measure all animals
Similar ages
Placed on test in the same facility on the same day
To get a good average
Large number of animals
We want to compare animals for selection - dont want to reduce variability
From different families - have variability
ALL individual should be recorded so we don’t bias the family mean and group mean
Measure all animals
Don’t measure just the good ones. Use random sample if needed
Measure all animals
Equal environment = equal opportunity
Placed on test in the same facility on the same day
same group meaning same age
Similar age
Is there a perfect contemporary group
No
Proportions of genotypic variance to the phenotypic variance, what we see in the next generations
Heritability
How easily we can change the trait
Magnitude of heritability
Additional influence of a mother on the phenotype of offspring
Maternal effects
What are the two categories of maternal effects
Maternal genetics effects
Maternal environmental effects
Important in the early life but reduces over time
How good the Dam is, such as milk production. Good genetic component
Maternal genetics effects
Effects in the mum’s belly that effects, mother is receiving nutrition that helps the baby
Maternal environmental effects
Looking at future performance of the same animal
Repeatability
What is gonna be repeated for the next lactation (example) and so on
Repeatability
3 types of Animal fields
Low
Moderate
High
More difficult to be improved by selection, Need to keep them longer in your breeding plan
Low
Reproduction, health and survival
Low
There is opportunity for selection. Improvements are generations after generations
Moderate
Performance trait, growth traits (body weight)
Moderate
Selection is very effective. You can make lots of improvements in a few generations
High
Carcass trait, height, length, back fat
High
Should you Always include all the traits even though heritability is low?
Yes, you just need to keep them longer
Valuable traits tend to have low, moderate and high heritability
low
Making breeding decision
3 things
Select to produce replacements
Allow to produce market offspring
Culled from the herd
% of alleles in two individuals that are identical by descent
Relationship coefficient
% of loci in an individual that have both allele identical by descent
Inbreeding coefficient
Relationship between sire and the offspring is
0.5
Relationship between dam and the offspring is
0.5
Relationship between full siblings can, in theory, range from and average
range from 0 to 1
average 0.5
Relationship between half siblings can, in theory, range from
range from 0 to 0.5
average 0.25
Relationship between full sibling
0.5
Relationship between parent-offspring
0.5
Relationship between half siblings
0.25
Relationship between grandparents - grand progeny
0.25
Which ones are exact relationships and which ones are average?
exact relationship: parent offspring
Average: Full sibs, half sibs, and grandparents
Uses of relationship
Prediction of breeding valve
Calculating inbreeding of an animal
IBS
Alleles identical by state
IBD
Alleles identical by descents
looks the same because same allele but different parents
Allele by state
coming from the same parent
Identical by descent
If the parents of an individual are unrelated, the inbreeding coefficients of the individual is always
0
inbreeding coefficient
Parent-offspring
25%
inbreeding coefficient Mating full sibs
25%
inbreeding coefficient Mating half sibs
12.5%
inbreeding coefficient Animal with grandparent
3.1%
the mating of relative
Inbreeding
What is the potential relationship between inbreeding and selection:
The top selection are usually related
Inbreeding results
Establishment of uniform populations
Potential improvement of traits of interest
Lost of genetic diversity
Inbreeding depression
Is heterozygosity increase or decrease in inbreeding
decrease
is homozygosity increase or decrease in inbreeding
increase
Decrease heterozygosity = increase homozygosity
leads to what
lead to deleterious recessive alleles
Decrease performance of inbreds
Inbreeding depression
Inbreeding consenquences
Increase rate of homozygosity resulting in deleterious recessive allele
Loss of genetic variability
Reduced fitness and vigor of animals
Increased susceptibility to diseases
Decrease reproductive success
Main reason to inbred
To create uniformity within a line
Test potentially valuable sires that may be carriers of underside allele
Increase hybrid vigor
gives the expected values or average
Pedigree
give the realized values or real values
Genomic
Importance of genetic parentage testing
Determine/confirm parentage by analyzing the DNA
The greatest advantage of animal breeding compared to other
disciplines is that
Changes are cumulative, permanent and long term
any characteristic of an animal that can take on different values
variable or trait
record of information, such as
the weight of an animal
Observation (or phenotype)
