AS 332 Exam 4

Heritability can be estimated by the ____ between genetic values and phenotypes

squared correlation, regression

Repeatbility can be measured by the ___ between producing abilities and phenotypes

squared correlation, regression

Heritability ccan be definaed as ratio of what two variance components?

heritability = BV variance/Phenotype variance

Repeatability can be defined as a ratio of what two variance components

repeatability = PA variance/Phenotype variance

Give an example of a trait with low, moderate, and high heritability

Low - fertility

Moderate - weight

high - carcass

List 2 ways to increase heritability and repeatability. How would this benefit you as a producer?

Measure traits as accurately as possible

Treat animals as uniformly as possible

-increase accuracy of selection and culling decisions

____ contemporary groups provide a better estimate of the group average

Large

What range of value is possible for heritability

0-1

Calculate the ratio of the following calves for birth weight

1 - BW = 80 lbs

2 - BW = 75 lbs

3 - BW = 105 lbs

4 - BW = 95 lbs

5 - BW = 86 lbs

6 - BW = 82 lbs

(Xi/X mean) * 100

Mean = 87.17

1 = (80/87.17) *100 = 91.77%

2 = 86..01%

3 = 120.41%

4 = 108.94%

5 = 98.62%

6 = 94.04%

As a general rule ____ traits have high heritabilities and ____ have low heritabilities

high = carcass

low = survivability, fertility

define contemporary group

group of biologically similar animals raised in the same environment

twinning rate has a hieritability of about 0.10 and loin eye area has a heritability of about 0.50, as measured by ultrasound. If you were selecting only on an individual’s phenotype, which trait vvore accurately estimate breeding values? Why

LEA - phenotype for LEa is a more accurate predictor of LEA breeding values

Define heritability

percentage of phenotype variation explained by differences in breeding values

strength of the relationship between phenotype and breeding value for a trait

what is an important use for heritability

allows you to determine which traits will be improved faster by genetic selection

why does the regression coooefficient increase as the number of records increases

decreasing temporary environmental variation

for traits with repeated records the regression of breeding value on average phenotypic performance is B(_BV,P) = (nh²) / 1+(n-1)r. This regression coefficient predicts the change in breeding value given a 1-unit change in phenotype. In this formula, n is the number of performance records, and h² and r is the heritability and repeatability of the trait, respectively. Calculate the regression coefficients for sheep fleece grade and staple length. The repeatability is 0.60 for both traits.

Fleece Grade (h² = 0.35)

Staple length (h² = 0.50)

Number of records = 1, 2, 3, 5, 10

Write a definition of the regression coefficient for staple length (mm: 1 record), including the units

Fleece grade

1 = 0.35

2 = 0.44

3 = 0.48

5 = 0.52

10 = 0.55

Staple Length

1 = 0.50

2 = 0.63

3 = 0.68

5 = 0.74

10 = 0.78

Regression coefficient = We expect a 0.5 mm increase in BV for every 1 mm increase in staple llength phenotype

for traits with repeated records the regression of producing ability on average phenotypic performance is b_PA,P = (nr) / 1+ (n-1)r. Thisr regression coefficient predicts the change in producing ability given a 1-unit change in the phenotype. Calculate the regression coefficients for calving interval and milk yield in dairy cattle.

Calving interval (r = 0.15)

Milk yield (r = 0.50)

Numbers = 1, 2, 3, 5, 10

Write a definition of the regression coefficient for milk yield (lbs: 1 record) including the units

Calving interval

1 = 0.15

2 = 0.45

3 = 0.75

5 = 1.35

10 = 2.85

Milk Yield

1 = 0.50

2 = 1.50

3 = 2.50

5 = 4.50

10 = 9.50

Regression coefficient = We expect a 0.5lb increase in BV for every 1lb increase in milk yield phenotype

What is the essential principle involved in the several approaches to increasing heritability and repeatability

Decreasing environmental variation

animal breeders ofttthemical adjustment factors to data to account for “known” environmental effects. A “known” environmental effect is an effect that we can estimate. For example, we can estimate the average weight gain difference between heifers and steersss, so therefore we can “adjust'“ weights for gender of the calf. Why do we use these adjustment factors?

Increases selection accuracy

1. If the phenotype was 500 lbs, approximately what would be the estimated breeding value for this trait?

2. What is the cause of prediction errors for estimated breeding value? Rephrased, why do the actual breeding values not line up exactly on the regression line

3. How is heritability depicted in this figure

4. In what region of the graph are true breeding values under-estimated by the EBV

1. -75

2. environmental and GCV

3. regression

4. above the line

When defining heritability as a regression coefficient, fill in the missing quantities in the numerator and denominator of the equation:

h² = cov (__ , __) / ___

h² = cov ( P , BV ) / S²_P

When defining repeatability as a regression coefficient, fill in the missing quantities in the numerator and denominator of the equation:

r = cov (__ , __) / ___

r = cov ( P , PA ) / S²_P

When defining heritability as a correlation coefficient, fill in the missing quantities in the numerator and denominator of the equation:

h² = cov (__ , __) / ___

h² = cov ( BV , P ) / S²_BV * S²_P

When defining repeatability as a correlation coefficient, fill in the missing quantities in the numerator and denominator of the equation:

r = cov (__ , __) / ___

r = cov ( BV , P ) / S²_PA * S²_P

explain why heritability for a trait is not constant among different groups of individuals

environment differs among groups of animals

genetics differs among groups of animals

explain why producers should use contemporary groups when possible

increases selection accuracy

why would livestock producers calculate ratios of trait values

ratios help breeders quickly identify above and below average animals for a trait

why data on all of producers animals should be reported to breed associations

the reported animals will receive worse genetic evaluations

increased overall selection accuracy for the breed

what are the four factors that affect rates of genetic gain in a herd or breed

selection intensity, selection risk, genetic variation, generation interval

What does the equation estimate

r_{BV, BV}i o_BV

rate of genetic change

why is the two path version of the genetic change equation usually more appropriate than the one path version

often males and females differ in selection accuracy, selection intensity, and generation interval

what quantity in the genetic change equation is measured by the correlation between true breeding values and estimated breeding values

selection risk

with truncation selection, the selection intensity can be found in a table. what piece of information is needed to find the appropriate selection intensity in the table

proportion saved

Interpret the genetic trend graph below. Does the Duroc breed appear to be making genetic progress for days to 250 pounds?

Yes - decline = less days to match weight (250 lbs)

adjustment factors increase rate of genetic change by increasing selection ____

accuracy

give a practical example in the livestock industry of high selection intensity vs low selection intensity

high - top 5% of sires for a trait

low - ignoring a trait when selecting animals

give a practical example in the livestock industry of high selection accuracy vs low selection accuracy

high - proven sire

low - young sire

give a practical example in the livestock industry of large genetic variation vs small genetic variation

large - herd with mix of breed compositions

small - inbred or linebred herd

give a practical example in the livestock industry of a small generation interval vs a large generation interval

large - cattle

small - chickens

in terms of the rate of genetic change equation discuss the typical differences between males and females relative to accuracy, intensity, and generation interval

selection accuracy - males often have more offspring than females

selection intensity - fewer males are often needed and I can select more intensely on males as a result

generation interval - often differ between males and females

list two trade-offs of the rate of genetic change equation and why they are important

increased selection accuracy often leads to increased generation intervals

increasing female selection intensity often leads to increased generation intervals

what is the expected rate of genetic gain for yearling weight in a beef cattle herd with the following characteristics and selection policies? assume the phenotypic standard deviation for yearling weight is 60 lbs and heritability is 0.40. animals will be selected on their own yeling weight only with adjustments recommended by the BIF. sires will be selected as yearlings and selected bulls will be the best one of every 20 bulls weighed. Dams will be selected as yearligs and used 4 seasons. Selected cowswill be the best one of every 5 yearling females weighed

generation interval (L)

males - 2 year

females - 4 year

accuracy

males -

females -

intensity

males -

females -

expected yearling increase in BV -

generation interval (L)

males - 2 year

females - 4 year

accuracy

males - 0.63

females - 0.63

intensity

males - 2.06 (1/20 - table)

females -1.40 (1/5 - table)

expected yearling increase in BV - 13.84 lbs/year ((0.40(2.06+1.40)60)/(2/4)

r = sq rt .4 = 0.63

a rancher runs a closed herd of breeding cattle. he norally keeps ad breeds the top 3% of his bull calves based on individual preformance for yearling weight (YW). his sires average three years of age when their offspring are born. he is trying to decide between two female replacement strategies:

• saving the top 20% of his heifers based on YW (L = 6 years)

• saving the top 60% of his heifers based on YW (L = 3 yeras)

  1. If h² = 0.4 and o_P(YW)= 50 lb, calculate the expected rate of genetic change in YW for each strategy

  2. which strategy would you choose and why

     1. which elements of the key equation is the rancher experimenting with

1. a. 20% = 0.4(2.27+1.40)50/(3+6) = 8.16 lb /yr

   b. 60% = 0.4(2.27+0.64)50/(3+3) = 9.70 lb / yr

2. 2 - faster genetic change

3. female selection intensity and female generation interval

What is the expected rate of genetic gain for days to 280 lbs with the following characteristics and selection polices? Assume that the standard deviation of breeding values is 6 days and that accuracy of selection is 0.32 for females and 0.60 for boars. The average number of days to reach 280 lbs is 180 days. Selected boars reached 280 lbs at an average of 175 days. Selected females reached 280 lbs at an average of 178 das. The phenotypic standard deviation for this trait is 12 days. Complete the following table

generation interval (L)

males - 2 year

females - 3 year

intensity

males -

females -

expected change in BV for days to 280 lbs per year -

generation interval (L)

males - 2 year

females - 3 year

intensity

males - 0.42

females -0.17

expected number born alive increase in BV per year - 0.37 days/yr

Im = |(175-180)/12| = 0.42

If = |(178-190)/12| = 0.17

(0.60×0.42+0.32×0.17)6 / (3+2) = 0.367 days/yr

list three ways that can be used to increase accuracy of a breeding value

increase number of progeny records

increase h²

DNA test

What are 2 general methods for predicting breeding values

selection index

best linear unbiased prediction

what does it mean when we say the EBV is an unbiased estimate of true breeding value

as we collect more data, the EBV is equally likely to increase or decrease

BLUP and selection index are 2 methods for estimating breeding values from phenotypic data

1. which method is used by breed associations

2. why

1. best linear unbiased prediction

   1. accounts for genetic trends, accounts for culling for poor performance, accounts for non-random mating

accuracy of an EBV (or EPD) can be defined as a measure of ____ taken by breeders and producers

selection risk

accuracy of EBV based on progeny performance can reach close to 100% regardless of a trait’s heritability, but accuracy of EBV based on an individual’sss own performance may only reach 30 to 70% depending on heritabiliity. Why?

An individual’s own phenotype is affected by its BV, GCV, and Ep. No matter how many records of own performance we collect, GCV and Ep never go away, preventing us from reaching 100% accuracy.

Each individual progeny record is also affected by GCV and E, along with dam and Mendelian Sampling effects. However, if we collect a large number of offspring records on an animal, all of these effects start to cancel each other out, leaving only ½ * BV of the parent. Accuracy can now reach close to 100%

in the procdures for calculating EBV, what is meant by “regression for the amount of information”

when accuracy of an EBV is low, the EBVs are regressed closer to the mean EBV in the breed

A commercial cow-calf producer wishes to calculate within-herd weaning weight EPDs for 2 of his or her herd bulls. The senior herd sire “Sure Thing “ has sired four calf crops, and his 80 progeny average 10 pounds heavier than their contemporary group mates. he also purchased a yearling bull “Long Shot” with no progeny, but who (himself) weighed 40 pounds heavier than his contemporary gropu average. Assume heritability of weaning weight is 0.30

1. calculate weaning weight EPD and accuracy of Sure Thing

2. calculate weaning weight EPD and accuracy of Long Shot

3. Which sire would you expect to sire the heaviest calves in the future

1. b = (2(80)(0.3)) / (4+(80-1)*0.3) = 48 / 27.7 = 1.73

   EBV = 1.73 × 10 = 17.3 lbs

   EPD = ½ * 17.3 lbs = 8.65 lbs

   Accuracy = sq rt ((80×0.3) / (4+(80-1)*0.3)) = 0.93

2. b = 0.3

   EBV = 0.3 × 40 = 12 lbs

   EPD = ½ * 12 lbs = 6 lbs

   Accuracy = sq rt (0.3) = 0.55

   1. Sure thing - Better EPD

The EPDs for yearling weight for 2 bulls are 115 lbs for Trendsetter and 75 lbs for Desperado

1. by itself, whaat does the fact that Trendsetter has an EPd = 115 lbs mean

2. how much heavier should Trendsetter’s progeny be, on average, relative to Desperao’s progeny

1. nothing

2. 40 lbs

what is one strategy a producer could use to mitigate selection risk when using young sires (or sires with lowly acccurate breeding values)

use more young sires

in large-scale genetic evaluations, what is the base

0

why are large scale genetic evaluations more often focused on sire summaries than on dam summaries

sires often produce more offspring over their lifetimes than dams

a bull has a milk EPD = +30 lbs and a weaning weight EPD = +47 lbs. the milk EPD is the maternal effect on weaning weight and weaning weight EPD is the direct effect on weaning weight. what is this bull’s total maternal EPD for weaning weight

30 + (1/2 × 47) = 53.5 lbs

yearling bulls are the SDSU cow-calf unit in 2009. BD = birth date. MGS = maternal grandsire, BW = birth weight, adh WW = adjusted 205 d weaning weight, YW = yearling weight

1. the progeny of 888 is xpected to be ____ lbs heavier than progeny sires by 889

2. which bulls have below average 205 d weaning weights for this herd

3. bull 887 has the highest adjusted 205 d weaning weight, but bull 859 has the highest weaning weight EPD. why would 887 have a smaller weaning weight EPD

4. which bulls would you select if you were only interested in purchasing 3b ulls based on weaning weight? why

1. 1.6

2. 866, 889

3. environment, gene combination value

   1. 859, 887, 892 - highest WW EPD
      

what % of current angus sires have a milk EPD higher than bull 859? (Milk EPD = 26)

45%

Is bull 875 above or below the average yearling weight EPD for current sires in the angus breed (YW EPD = 92)

below average

The weaning weight EPD for a SimAngus bull is 33 lbs. What is wrong with the following statement

• The angus bull 889 is expected to produce progeny at weaning that weigh 7 lbs heaiver, on average, than the SimAngus bull

Cannot directly compare EPDs across breeds

Fintry of Graham has a calving ease direct EPD = +4%, and the accuracy of this EPD = 0.50. therefore, we have 68% confidence that Graham’s true calving ease direct PD is between ____ % and ____ %

-1.1 - 9.1

a bull’s 68% confidence range for weaning weight EPD is +30 lbs and + 50 lbs. what does this mean

we are 68% confident that this bull’s true progeny difference for WW is between 30 and 50 lbs

if Graham’s 68% confidence range for calving ease direct is larger than Midland Empire’s 68% confidence range for the same trait, what does this mean

Graham’s EPD has a lower accuracy than Midland Empire’s EPD

the dairy industry reports accuracies of predicted transmitting abilities as _______ which are different from accuracy values reported in other species but should be interpreted similarly

reliabilitiy

T/F - progeny from a sire with a lowly accurate birth weight EPD will not have more variable bith weights than progeny from a sire with a higly accurae birth weight EPD

False

Choose 3 EPDs and explain what is being measured. Make sure to include the econoomic relevenace of the trait.

• Calving Ease Direct - Difference in percent of calves born unassisted to heifers - producers with first calf heifers

• Docility - difference in cattle temperament - raising seedstock cattle or cattle that will be around old or young people - you want cattle with favorable temperaments

• Marbling - difference in percent of intramuscular fat - raising terminal cattle, higher marbling scores can get you more money if sold on a grid