Animal Breeding Genetics: BLUP, EPDs, and Sire Evaluation

Direct genetic effect

Effect of an individual's own genes on its performance.

Maternal genetic effect

Effect of the dam's genes on the environment she provides for offspring.

Direct component of weaning weight

Calf's own genetic ability to grow.

Maternal component of weaning weight

Dam's milk production and mothering ability.

BLUP

Best Linear Unbiased Prediction.

Purpose of BLUP

Predict genetic merit while accounting for environmental and other effects.

BLUE

Best Linear Unbiased Estimation.

What does BLUE estimate?

Fixed effects such as sex and management groups.

What does BLUP predict?

Random effects such as animal breeding values.

When did BLUP become widely used?

1980s.

EBV

Estimated Breeding Value.

EPD

Expected Progeny Difference.

MPPA

Most Probable Producing Ability.

What animals can contribute to BLUP evaluations?

Living, deceased, and animals without their own performance records.

What is a sire summary?

A list of genetic predictions, accuracies, and other information about sires.

What information is found in sire summaries?

EPDs, accuracy values, and genetic trait information.

Why are sire summaries important?

Improve selection effectiveness and allow comparison of more sires.

Why focus on sires rather than dams?

Sires can produce more offspring and influence many herds through AI.

What is artificial insemination (AI)?

Breeding using semen collected from a sire without natural mating.

How does AI improve genetic evaluation?

Increases connectedness between herds through shared sires.

What were central tests used for?

Comparing growth and feed efficiency among animals from different herds.

Limitations of central tests

Few traits, emphasis on individual performance, and location effects.

What is a direct EPD?

Predicts genetic differences in offspring's own performance.

What is a maternal Milk EPD?

Predicts daughters' maternal contribution to their calves' weaning weight.

What is Total Maternal EPD?

Combines maternal Milk EPD with half the direct weaning weight EPD.

EPD equation

EPD = EBV / 2.

EBV equation

EBV = 2 × EPD.

Difference between two EPDs

EPD difference = EPD A − EPD B.

Total Maternal EPD equation

TM = Milk EPD + (WW EPD / 2).

Accuracy equation using reliability

Accuracy = square root of reliability.

EBV +60: calculate EPD

+30 because 60 / 2 = 30.

EPD +15: calculate EBV

+30 because 15 × 2 = 30.

Bull A EPD +20 and Bull B EPD −5: difference?

25 lb; A's progeny average 25 lb heavier under comparable conditions.

Milk EPD +10 and WW EPD +30: Total Maternal?

+25 because 10 + (30 / 2) = 25.

Milk EPD +15 and WW EPD +40: Total Maternal?

+35 because 15 + (40 / 2) = 35.

Reliability 0.64: calculate accuracy

0.80 because square root of 0.64 = 0.80.

How should EPD differences be interpreted?

As expected differences in progeny performance on average.

Two important phrases when interpreting EPDs

On average and progeny.

Do EPDs predict an animal's own exact performance?

No; they predict expected differences in offspring averages.

What does an EPD of zero mean?

It represents the genetic base of that evaluation.

What is a base year?

A reference year used to establish the zero point for genetic predictions.

Can EPDs from different breeds be compared directly?

Usually no; breed bases differ and adjustments may be needed.

What does accuracy measure?

Reliability or confidence in a genetic prediction.

High accuracy means what?

Lower uncertainty and lower selection risk.

Low accuracy means what?

Higher uncertainty and higher selection risk.

What can increase EPD accuracy?

Additional informative pedigree, progeny, performance, or genomic data.

What is selection intensity?

How selective breeders are when choosing breeding animals.

How does increased selection intensity affect genetic change?

Can increase the rate of genetic improvement.

What is a contemporary group?

Animals raised under similar management and environmental conditions.

Why are contemporary groups important?

Help separate genetic differences from environmental differences.

What is connectedness?

Genetic relationships linking animals across different herds or groups.

Why is connectedness important?

Improves accuracy of genetic comparisons across herds.

How does AI increase connectedness?

The same sire can have offspring in multiple herds.

What is genotype by environment interaction (G × E)?

When genetic differences in performance depend on the environment.

What traits are often strongly influenced by environment?

Low-heritability traits.

What is parental misidentification?

Incorrectly recording an animal's sire or dam.

What is falsification of performance records?

Deliberately reporting inaccurate animal performance data.

Most common performance-record problem in class notes

Incomplete reporting.

What is an incorrect environmental adjustment?

Using inaccurate environmental information when adjusting performance records.

What is a contemporary-group error?

Placing animals in incorrect comparison groups or ignoring treatment differences.

What are major problems in genetic evaluation?

Faulty pedigrees, incomplete records, incorrect adjustments, poor grouping, weak connectedness, and G × E.

What is the main goal of large-scale genetic evaluation?

Compare genetic merit across large populations and improve selection.

Who commonly organizes breed-wide genetic evaluations?

Breed associations and genetic evaluation organizations.

How does large-scale evaluation improve selection?

Expands the available pool of breeding animals and improves genetic comparisons.