Lecture 6 - Milk production data (II)

ANSCI 4940 - Spring 2026

Meike van Leerdam

monitoring milk yield

• What is the goal of the farm
  
• What is the size of the farm
• What management system do they use > seasonal, grazing, free stall etc.

Things to take into account looking at data

• Test day average vs rolling averages
• What are you trying to optimize?

Bias

Past/Present/Future

Past: Rolling average

Present: Test day average

Future: Production < 100 DIM

Far Future: Heifer production

What dictates milk production

phenotype = genotype + environment

Genetics

\[ \Delta G_{year} = \frac{ \sqrt{\text{reliability}} \times \text{selection intensity} \times \sqrt{\text{genetic variance}} }{ \text{generation interval} } \]

Effect of selection differs

• Traits associated with physical shape and size
  • High heritability (≥ 40%)
• Traits related to milk and solids yield
  • Moderate heritability (15–30%)
• Traits associated with health and fertility
  • Low heritability (≤ 10%)

Calculation of Breeding Values

\[ y = Xb + Zu + e \]

• y = observed phenotypes
  
• b = fixed effects (e.g., sex, management)
  
• u = random genetic effects (breeding values)
  
• e = residual error
  
• X, Z = link observations to effects

What do we get from this?

• Each animal receives an estimate of genetic merit
  
• Called Predicted Transmitting Ability (PTA)
  
• PTA = breeding value ÷ 2

Note:
Real U.S. animal models are more complex and include: - Contemporary groups
- Herd-by-sire effects
- Permanent environmental effects

Genomic prediction

What is genomic prediction? - Uses DNA information + phenotypes + pedigree to estimate genetic merit - DNA markers = SNP (positions in the genome with two variants)

Why use genomics? - DNA is not influenced by environment - Improvs accuracy of breeding value estimation - Allows evaluation of young animals without records

How are genomic PTA calculated?

• Estimate SNP effects using a predictor population with reliable PTA
• Combine:
  • Genomic predictions from SNP
  • Parent averages (PA)
  • Traditional pedigree + phenotype evaluations

Net merit dollar value

The expected difference in lifetime profit (in USD) of a cow (or bull’s daughters) compared to a reference animal, due solely to genetics, assuming typical U.S. management and prices.

“If I replace one genetically average cow with this one, how much more (or less) money will I make over her lifetime?”

What is in it?

Different indexes

Shift to prezi

presentation