Animal Genetics Exam 3

Qualitative

Types of Traits

• _________ (SIMPLE)

  • Discrete phenotypes

    • Black/White

    • Horns/No Horns

  • Few genes (usually 1)

  • Little or no effect of the enviornment

    • EX: coat color

Quantitative

Types of Traits

• ___________(COMPLEX)

  • Measured phenotypes

    • weight, height

    • litter size

  • Many genes (>1) → hundreds or thousands of genes contribute

  • Enviornmental effect can be large

    • EX: growth rate

• Many genes

• Measured traits

• Enviornmental influence

Quantitaive traits (3 characteristics)

1. ________

2. _______

3. _______

continuous scale

Quantitative Traits - Measured traits

• Measured on a ________

  • # of progeny born/weaned

  • weight height

• Nutrition

• Climate

• Disease

Quantitative Traits - Enviornmental Influence

• ______

• ______

• _____

single gene

Quantative Traits - Consequences

• Can’t see the effect of a _______ among the many involved (Masks genes)

• Must separate genotypic effect from enviornmental effect → want to know WHAT can be passed down and what is soley due to the enviornment

Phenotypes

________: the sum of a genetic effect (that an individual inherits) and an enviornmental effect (that an individual recieves)

normally distributed

Quantiative Traits are (usually) ____________.

• This is due to:

  • an underlying genetic distribution

  • an underlying enviornmental distribution

Normal distribution

__________- can be described by a mean and standard deviation

selection

It is the genetic variance in quantitative traits that allows ____ of (genetically) superior animals

arithmetic average

Population

• Mean (mu) - _________

  • Population measure - no singular individual, need at least two individuals

  • Distribution of records? don’t know the range

• spread

• standard deviation

Weaning weight in cattle

• Both populations have the same average BUT THEY ARE NOT THE SAME → _____/_____ are different

variance

Statistics describing variation

• ________ (sigma squared)

  • describes the spread of a normal distribution

greater

Variance

• Must be greater than zero

• The greater the deviations, the _____ the variance (more spread)

squared

Example: mean and variance

• Note that the units are ______

square root

Standard deviation - ______ of variance

symmetric

Normal Distribution

1. The curve is _____ about its mean

• 50% of the population is above the mean and 50% is below the mean

Review

Normal distribution

Review

Example 1

Review

Example 2

Using the normal distribution

relationships

Covariance and Correlation → measures of ________ between traits

• How are two traits related?

  • Height & Weight

  • Milk yield & %protein

    • Trait X and Trait Y

Covariance (________)

• How traits vary together

Review

Covariance calculation example

Review

_____ Covariance

Review

______ Covariance

• positive

• negative

Positive Covariance

• Variation - deviation from the mean

• ______ deviations in one trait tend to be paired with positive deviations in the other trait.

• ______ deviations in one trait tend to be paired with negative deviations in the other trait

Negative

_____ Covariance

• inverse relationship

• negative

• positive

Negative Covariance

• positive deviations in one trait tend to be paired with _____ deviations in the other trait.

• negative deviations in one trait tend to be paired with _____ deviations in te other trait.

Zero

Covariance of ___ occurs when two traits are independent.

• NO RELATIONSHIP BETWEEN 2 TRAITS

correlation

Units of covariance are difficult to interpret so we more often utilize ______

association

Correlation (Corx,y) - standardized measure of the degree of _____ between two traits

Review

Correlarion calculation example

• positive

• negative

Correlation

• It can range from -1 to +1

• A ____ value means that an increase in one value is associated with an increase in the other value.

• A ____ value means that an increase in one value is associated with a decrease in the other value.

strength

Correlation

• The absolute value of the number is a measure of the _____ of the correlation

  • The higher the number the stronger the association (Closer to 1)

    • Ex: A correlation of -0.7 indicates a stronger degree of association than does one of 0.5 (don’t care about size)

• Direction

• Strength

• Amount of Change

Correlation

• 3 basic aspects:

  • _______(sign of the relationship)

    • Positive, negative, nonexistent

  • ________ of relationship

    • Strong (>.7), moderate (.4-.7), weak (<0.4)

  • __________ expected → stronger correlation the more I move one trait that more I move the other (depends on strength)

causation

Correlation does not mean __________!

• It is important to remember that correlations, even strong ones, do not imply cause-and-effect!

  • Correlations may exist for many reasons.

simple

Types of Traits

• Qualitative Traits (_______)

  • Traits that we observe (categories)

  • Black or red coat, horns or no horns

Complex

Types of Traits

• Quantitative Traits (______)

  • Milk production, weaning weight

  • Many genes influene trait → normal distribution

Average

Quantitative Traits

• Mean

  • _______ performance in a population

Variance

Quantitive Traits

• Variance, standard deviation

  • Measure of ____

  • How much individuals vary from each other (and from mean)

Relationship

Quantative Traits

• Covariance, correlation

  • ________ between two traits

Covariance

Relationships between traits

• ______

  • How 2 traits vary together

Standardized

Relationships between traits

• Correlation

  • _________ measure of covariance

  • Measures the strength/degree of association

  • It can range from -1 to +1

• Direction

• Strength

• Change

Correlation

• 3 basic aspects:

  • ______ (sign of the relationship)

    • Positive, negative, nonexistent

  • ______ of the relationship

    • Strong, moderate, weak

  • Amount of ____ expected

    • by changing one trait how much does the other change

**Need to know more precisley the relationship between traits

predict

Regression:

• If one trait changes, can we _______ how much the other one will change?

Regression

_________: the change in one variable per unit change in the other

• Dependent

• Independent

Regression

• Y = _______ variable

• X = _______ variable

first

Regression X/Y

• X will be the trait you measure ____ in an animals life

• same

• opposite

Regression

• (+) traits go in the _____direction → increase in one increase in other

• (-) traits go in the ____ direction → increase in one causes a decrease in other

regression equation

How do we use regression?

• Regression: useful statistic, gives the units of change in one trait for every unit change in another

• Most useful when used to predict the value of one variable (trait) using the value of another variable (trait): _______

innacurate

Prediction

• Predictions are just predictions!

• Some are very accurate (usually from large amounts of data) some are wildly __________!

accuracy

Accuracy and Correlation

• The stronger the correlation, the higher the _____ (better prediction → shorter range)

• Weak correlation: expect great deviation from your prediction

Many genes

Quantiative Trait: trait that is affected by _______

• Each gene has a small effect → because there are many genes

• Many economically important traits in animals

Breeding Value

BV = _______ - value of indivdual alleles (contribution of each allele)

Dominance Value

DOM = _____- Value of allele combination (value of pair)

Epistatic Value

EPI = ______ value of allele interaction across loci

Genetic Value (BV, DOM, EPI)

Animal → Own Performance → _________

Breeding Value (BV)

Animal → Own Performance → _______

combinations

Parents can only pass on individual genes not _______

Breeding Value

• _______ (or additive genetic value)

  • value of individual alleles

  • value of an indiviudal as a parent

  • the value of genes to progeny

• Dominance

• Epistasis

Genetic Value

• The value of genes to self

• Includes _____ and _____ (Cannot be passed on to progeny)

  • depends on combination of alleles, cannot be inherited

Own Performance

Focus: ________

Progeny’s Performance

Focus: _________

genetics

Heritability

• How much of the variation in a population is due to ________

Genetic Variation

Heritability is the proporiton of phenotypic variation that is caused by ______

• Not controlled by genetics → controlled by enviornment

Broad sense

Heritability (h²**)

• _____: proportion of the phenotypic variation that is due to genetic variation

Narrow sense

Heritability (h²**)

• _____: proportion of the phenotypic variation that is due to breeding value variation

• Genetic

• Enviornmental

Heritability

• 0 < H²b < 1

  • Closer to 1 (greater heritability) more _____ influence

  • Closer to 0 (less heritability) less genetics more ____ contibution

• Reproductive

• Growth

• Carcass

0.6

Few traits have h² > ____

breeding value

h² - proportion of the phenotypic variation that is due to ______ variation

Review

Example - review interpretations

NO UNIVERSAL

There is _______ heritability for any trait

• Specific to one population, in one enviornment

enviornments

Heritabilities for the same traits can differ if animals are producing in different ________

over time

Heritabilities can change _______ (as genetic variance changes in response to selection)

BV

What do we use heritability for?

• To determine the _____ of an animal

  • How much of an individual superiority is due to (additive) genetics versus enviornmental effects

selection

What do we use heritability for?

• To predict response to ______

  • How much of the superiority of a group of selected animals will be transmitted to the next generation

One

Types of Traits

• ________ measurement taken

  • Ex: birth weight → impossible to measure this twice

Multiple

Types of Traits

• _______ measurements taken

  • Ex: litter size, milk yield

• PE

• TE

Enviornmental Variation

• Enviornment (E) - permanent and temporary enviornment

  • ____- influences all records of an individual → injury that changes mammary gland: forever changes milk.

  • ____- influences a single record, different TE for each record → different foods, weather

Repeatability

Two definitions of ______

• The degree of association between repeated records (same trait being measured multiple times) on the SAME animal

• Correlation between repeated measures

Importance of repeatability

• Repeatability and ______

*Keep the animal with the best trait that has the highest repeatability (more likely that this animal will perfrom the same again and again)

h²

In a population, what values do we want for heritability and repeatability?

• ______= proportion of phenotypic variation due to BV

higher = any one record = good indicator of an animal’s BV (connection between phenotype and BV)

r

In a population, what values do we want for heritability and repeatability?

• ______= Correlation between repeated records on the same animal → could be negative

higher = any one record = good indicator of an animal’s producing ability (good indicator of NEXT production measuremnt)

uniform enviornment

Improving h² and r: _______

• Performance - not a good indicator of BV because of ENVIORNMENTAL differences

h²

Improving h² and r

• Increased ____ due to uniform training enviornment

*Not BEST enviornment just CONSISTENT enviornment

consistent

Improving h² and r

• Manage animals so that enviornmental effects are _____

• Examples

  • Thoroughbred- provide similar training

  • Dairy (milk production) - provide similar feed

  • Beef (weaning weight) - provide pastures of similar quality, same vaccinations

uniform

Minimize enviornmental differences

• Not making the enviornment better, making the enviornment more ___

n+1

Repeatability of N Records (rn)

• Repeatibility of n previous mesured records and the _____ record

decreases

Repeatability of N Records (rn)

• Adding more records: increased repeatability

• Reduced value from adding more records (rate of increasing repeatability ______)

n

Predicting Next Record

• Example: predicting the n+1 record from performance in ___ previous records

  • Using repeatability to predict the next performance

How do we campare records in a population?

Predicting Next Record

genetic diversity

Breeding Captive Populations

• What are the objectives and how do we achieve them?

  • to maintain _________ so they can survive.

sex limited

Domestic Animal Breeding

• Problem: want to improve milk yield through selection of male, how can this be done.

  • Milk yield is a _______ trait (males carry genes to produce milk but their physiology prevents milk production)

    • can select males to increase the productivity of the daughters

Breeding captive populations

• Objective: Maintain genetic diversity

  • Process

1. Sample wild population (founders)

2. Breed each generation to maintain as much of the original diversity sampled as possible

• do not mate individuals that are closley related → do not want to increase homozygosity

female relatives

Domestic Animal Breeding

• Male slection for a sex limited trait

• Utilize information from _______ to evaluate the potential of a male as a parent

• Works because of sharing of genes in common and the accuracy depends on how closley related the male is to the females with records

relatedness

Strategies

• All of these strategies are based on calculations of the degree of ______ of individuals in the population

additive genetic relationship

Relationships

• Related animals have genes in common

  • Causes → resemblance in appearance and similalrity in performance

• Use _________ (ax,y) to quanitify the degree to which two animals are related