Animal Breeding Final Exam

what is our goal as animal breeders?

select the best to improve the next generation → IMPROVE BREEDING GOAL

how can we select animals?

1.) own performance

2.) relatives

• because of shared genes

selection

the process that determines which individuals become parents, how many offspring they produce, and how long they remain in the breeding population

single vs multiple trait selection examples - cattle

• fertility

• precocity

• weight gain

• carcass quality

• health

• disease resistance

single vs multiple trait selection examples - swine

• litter size

• feed efficiency

• % of lean meat

• meat quality

• health

• disease resistance

selection should target ________ important traits

economic

3 basis of selection

1.) individual

2.) between families

3.) within families

individual selection (mass selection)

animals are selected based on their own performance

between family selection

the entire best family/families (are) selected

within family selection

the best individuals within the families are selected

selection is more effective when ________ is high

heritability (h2)

2 advantages of individual selection (mass selection)

1.) information on individuals to be selected is easily available

2.) used when pedigree information is not available

2 disadvantages of individual selection (mass selection)

1.) not applied for sex-limited traits

2.) not applied when traits have low heritability

family selection

animals are selected based on the performance of their family (within/between)

key to family selection

pedigree

2 advantages of family selection

1.) improve traits with low h2 with high reproductive traits

2.) it supports individual selection

2 disadvantages of family selection

1.) it’s costly

2.) requires a large family size-genetic relationship

progeny test

selection of the individuals based on the average performance of their progeny

each progeny of an individual inherits _____ of the genes

1/2

2 advantages of progeny test

1.) the BEST method for sex-limited traits

2.) identification of carriers

2 disadvantages of progeny test

1.) high cost + time required

2.) increases generation interval

progeny test is based on ______ siblings

half

3 methods of multi-trait selection

1.) tandem selection

2.) independent culling levels

3.) total score or selection index

tandem selection

to improve a breeding population for several traits by selecting ONE TRAIT at ONE TIME

• use in the presence of an unfavorable correlation between two traits

2 disadvantages for tandem selection

1.) less efficient method of selection

2.) requires more time for improvement

independent culling levels

a minimum cutoff for each trait is fixed, and every animal to be selected must MEET THIS MINIMAL LEVEL

total score or selection index

the ranking of animals is based on a value calculated by giving each selected trait a “RELATIVE WEIGHT”

match the _____ to the ______ _____

index; breeding goal

2 advantages of selection index

1.) allows the identification of animals that best fit the overall genetic goal

2.) evaluate the traits to emphasize and formulate a specific plan for maximizing them in the herd

2 disadvantages of selection index

1.) they are difficult to build

2.) traits vary in importance from time to time and the index built at one time may not be applicable for all times

3 factors that affect EBV

1.) performance

2.) pedigree

3.) environment

breeding value

the value of an individual as a genetic parent

• estimate of an animals genetic merit for a particular trait

• define the superiority or inferiority of the offspring of an animal

heritability

the extent of differences observed in animal performance are due to variations in genetics

mass selection

is based on ranking the animals on their own performance

• h2 = b

animal model

• no performance

• meat quality

• dairy bulls

• relatives = additive genetic relationship

animal model (definition)

represents a method that makes use of phenotypic information of relatives to estimate the breeding value of an animal

• if your trying to pick a dairy bull, look at female relatives for their milk production to select the males

for sex-limited traits what model would you use?

animal model

• performance

• pedigree

• environment

you want _____ heritability with _____ offspring

high; less

multi-traits

• selection index

• culling level

selection index

a linear combination of phenotypic information and weighting factors that is used for genetic prediction when performance data come from genetically similar contemporary groups

lenoy hazel

developed selection index

• 1943

• genetic prediction

• method to combine traits

• economically optimal way

disadvantages of selection index

1.) does NOT deal with adequately with records from animals reared in diff. environments

2.) phenotypes MUST be from genetically similar groups

advantage of selection index

good for within herds or flocks

best linear unbiased prediction - BLUP

a method of genetic prediction that is particularly appropriate when performance data come from genetically diverse contemporary groups

• simulatenous equations to solve for breeding value predictions

charles R. henderson

came up with BLUP

• need performance data

• pedigree

• environment

2 advantages of BLUP

1.) accounts for genetic and environmental differences in the performance data used to predict BV

2.) uses all data available

difference between EPV and EBV

EPV = look at individual

EBV = look at progeny

• both consider additive values

accuracy of selection/reliabilities of PTA

a measure of the strength of the relationship between the true breeding values and their predictions for a trait under selection

why not use true breeding value?

because we CAN’T measure

true breeding value

represents the genetic potential of that animal

• unknown value

• cannot be observed directly

the _____ the accuracy, the more likely the ____ is to predict that animals true breeding value

higher; EBV

the more information you have the more _________ you are and the more accurate your ______ is

accuratel; BV

4 factors that influence the accuracy of an EBV

1.) amount of information

2.) heritability of the trait

3.) information on correlated traits

4.) the accuracy of the parents

the higher the _______ of a trait, the higher the _____ accuracy

heritability, EBV

how to calculate accuracy

• heritability

• repeatability

• relationship

• performance

  • own or from relatives

as you increase in records your _______ also increases

heritability

accuracy increases as number or _______ increase

records

r is higher for higher h2 at the ____ number of progenies

same

same # of animals = accuracy _______ and heritability ________

increases; increases

the lower the h2 the _____ progeny needed

more

how to tell if an animal is young or old (accuracy based)

if they have a low accuracy = young animal

go for a higher EBV or higher accuracy?

EBV (then you look at the accuracy of those traits)

expected progeny difference (EPD)

the expected difference between the average performance of an individuals progeny and the average performance of ALL progeny

producers selling calves at _______ may prioritize EPD’s differently than producers wishing to ______ heifers

weaning; retain

the breeding goal has to match…

the goal of your production system and the target market you are adjusting/selecting for

direct vs. maternal EPD’s

how DAUGHTERS of a bull are expected to produce compared to other cows in a herd

genomic selection

refers to the use of genome-wide genetic markers to predict the breeding value of selection candidates → relies on linkage disequalibrium between the markers and polymorphisms that cause variation

genetic marker

DNA sequence with a known physical location on a chromosome

• can help link a trait with a responsible gene

single nucleotide polymorphism

change in a single nucleotide

2 approaches to SNP’s

1.) single-step

2.) multistep

genetically enhanced expected progeny differences (GE-EPD)

EPD’s the include information taken from the results of genomic testing

how do we use GE-EPD’s?

genomics DOES NOT change how we use EPD’s

does genomics change how we use EPD’s?

NO!!!

why do we use GE-EPD’s?

significant reduction of the generation interval

DNA information would boost the accuracy MOST for the _____ heritability trait, and LEAST for the _____ heritable trait

low, highly

accuracy of selection (reliabilities of PTA)

measure of the strength of the relationship between the true breeding values and their predictions for a trait under selection

what does accuracy of selection measure?

how well the BV of an animal is estimated

the _____ the accuracy, the more likely the _____ is to predict the animal’s true breeding value

higher, EBV

4 benefits of genomics

1.) increase the accuracy of EPD’s

2.) accelerate genetic progress

• decrease generation interval

3.) add “novel” traits to our suite of available EPD

4.) keep/cull devisions on bull calves earlier in life

selection response

the change in the average of a particular trait due to selection for that trait

what 2 things should you look at when selecting animals (in relation to selection reponse)

1.) breeding goal

2.) genetic prediction

4 factors that affect selection response**

1.) heritability

2.) selection intensity

3.) generation interval

4.) accuracy of selection

accuracy of selection

measure of the strength of the relationship between the true breeding values and their predictions for a trait under selection

selection intensity - i

represents the mean of the selected proportion in phenotypic standard deviations

• how “choosey” or picky we are in deciding which individuals are selected

why is selection intensity important?

help improve genetic gain + increase the frequency of the favorable alleles in the population

factors that affect selection intensity

high intensity - pick less animals

• parents far better than average

• superior offspring

• FAST genetic change

low intensity - pick more animals

• parents not much better than average

• offspring will be average

• SLOW genetic change

generation interval

amount of time required to replace one generation with the next

breeding equation

R = h² (S)

with generation intervals do you want a long or short interval?

short = max gain

a ______ in generation interval usually results in a ______ in accuracy

decrease; decrease

a ______ in accuracy usually results in a ______ selection intensity and vice versa

increase; decrease

a ______ in selection intensity means a ______ replacement rate

increase; low

different ________ _______ for males and female

selection intensity

males selection intensity considerations/factors

• # of offspring

• stringent selection

• selection risk

  • number of males needed

  • accuracy

• generation interval

  • males are mature earlier

  • progeny test, sex-limited traits

females selection intensity considerations/factors

• selection risk

  • large # of replacements

• reproductive capacity

  • # of offsprings

• selection

  • own performance (EBV)

  • accuracy

• generation interval

selection of males is ____ important than selecting females

MORE

correlation - r

measures the strength of the relationship between two variables

2 types of correlation

1.) genotypic

2.) phenotypic

phenotypic correlation

measures the degree and direction of the relationship between the phenotypes of the two traits

genetic correlation

measures the degree and direction of the relationship between the EBV’s/PTA of the two traits

• additive values (genes + alleles)

  • pleiotropy

  • GxE interaction

  • linkage