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Commercial Genetic Test Validation

Pfizer GeneSTAR Feed Efficiency MVP:

Summary:

The GeneSTAR feed efficiency MVP[1] was found to be significantly and positively associated with residual feed intake (RFI) in a North American population of 671 Bos taurus cattle. No significant association was found between this MVP and feed efficiency in a North American population of 395 Bos indicus-influenced cattle.

Significance of the GeneSTAR Feed Efficiency MVP* (Molecular Value Prediction)

Population

TRAIT

Panel

b**

F

p

N

Bos taurus “Pfizer A” validation population

Residual Feed Intake (RFI;kg)***

Feed Efficiency

0.4

n/a

0.02

671

Bos indicus- influenced “Pfizer C” validation population

Residual Feed Intake (RFI;kg)

Feed Efficiency

-0.019

0.017

0.55

395

* Molecular prediction values (MVP) were provided by Pfizer Animal Genetics based on their 56 SNP panel for Marbling Score, Tenderness and Net Feed intake (residual feed intake).

**The column labeled ‘b’ is the regression of phenotypes in the test population on the MVPs reported for the DNA test. It is a measure of how well the MVP scales with the phenotype. There are many reasons that this value would differ from its nominally expected value of 1. Traits scale differently in different environments, management scenarios and methods of measurement. Therefore, we would not practically expect this value to be exactly 1. However, values substantially less than 1 suggest that differences in phenotypes observed in other cattle managed under conditions representative of U.S. beef production are likely to be less than those predicted by the MVP. This would not affect how animals would be ranked by the MVP, but would impact the weighting given to differences in MVPs relative to differences in EPDs based on phenotypic data.

***RFI is the difference between an animal’s actual and expected feed intake based on its body weight and growth rate.

1MVP (Molecular Value Prediction) is equivalent to the term Molecular Breeding Value (MBV) used by the NBCEC.

Test Claims:

The GeneSTAR Molecular Value Predictions (MVP) provide a prediction of the genetic breeding value for feed efficiency (measured as net feed intake) in all breeds of cattle.

Test Details:

The GeneSTAR Feed Efficiency MVP is derived from analysis of a 56 SNP marker panel designed to provide MVPs for tenderness, marbling score and net feed intake (residual feed intake).

Sample Populations*:

Bos taurus “Pfizer A” validation population RFI: Residual feed intake (RFI) was calculated from the difference between average of actual daily dry matter intake of the animal and the expected daily dry matter intake. A multiple phenotypic regression model of daily dry matter intake on mid-test metabolic weight (MMW) and average daily gain including the overall mean was used to determine the expected daily dry matter intake.

Where, yi is the daily dry matter intake for animal i, µ is the overall mean, b1 is the regression on x1, actual average daily gain, b2 is the regression on x2, actual midpoint metabolic weight, tty (year, trial and treatment within trial) is the test group effect and ei is the residual effect. The RFI equation accounted for 75% of the variation in feed intake.

Bos indicus-influenced “Pfizer C” validation population. Average RFI based on a 70 day test.

* Letter-designations for validation populations as described in Pfizer Technical Summary (February 2009). Feed efficiency data was not available for "Pfizer B" population

Quantiles for GeneSTAR Feed Efficiency Molecular Value Prediction (MVP)*

Population

Panel

Mean

Max

 75% (Q3)

Median  (Q2)

25%   (Q1)

Min

Bos taurus “Pfizer A” validation population

Feed Efficiency

n/a

0.516

0.125

0.022

-0.116

-0.822

North
American
Bos indicus
-influenced “Pfizer C” validation
population

Feed Efficiency

-0.113

0.606

0.153

-0.094

-0.309

- 1.101

* Molecular value predictions (MVPs) were provided by Pfizer Animal Genetics based on their 56 SNP panel for Marbling Score, Tenderness and Net Feed intake (residual feed intake). These were the MVP distributions in the data analyzed and are not necessarily reflective of those of any other population.

Significance of the GeneSTAR Feed Efficiency MVP* (Molecular Value Prediction)

Population

TRAIT

Panel

b**

F

p

N

Bos taurus “A” validation population

Residual Feed Intake (RFI;kg)

Feed Efficiency

0.4

n/a

0.02

671

Bos indicus- influenced “C” validation population

Residual Feed Intake (RFI;kg)

Feed Efficiency

-0.019

0.017

0.55

395

*Molecular value predictions (MVPs) were provided by Pfizer Animal Genetics based on their 56 SNP panel for Marbling Score, Tenderness and Net Feed intake (residual feed intake).

**The column labeled ‘b’ is the regression of phenotypes in the test population on the MVPs reported for the DNA test. It is a measure of how well the MVP scales with the phenotype. There are many reasons that this value would differ from its nominally expected value of 1. Traits scale differently in different environments, management scenarios and methods of measurement. Therefore, we would not practically expect this value to be exactly 1. However, values substantially less than 1 suggest that differences in phenotypes observed in other cattle managed under conditions representative of U.S. beef production are likely to be less than those predicted by the MVP. This would not affect how animals would be ranked by the MVP, but would impact the weighting given to differences in MVPs relative to differences in EPDs based on phenotypic data.

Analysis of Bos taurus “A” validation population was performed by Gordon VanderVoort, Matt Kelly, Duc Lu and Stephen Miller, University of Guelph (July 2008) as follows:

  • The animal model for MVP validation was fit in Asreml:
    • Trait=aet+tty+heterosis+AN+PI+SM+CH+MVP +random(animal)
    • Where: aet = linear regression of the age at end of test
    • tty – effect of contemporary group including year, trial and treatment within trial
    • heterosis – linear regression of degree of breed heterozygosity based on parental breed composition AN+PI+SM+CH – linear regression coefficients on the proportion of the most prominent breeds represented (in animal i)
    • MVP – Feed Efficiency MVP prediction of genetic merit provided by Pfizer.
    • Random(animal) – Animal (additive genetic) random effect
  • Analysis of Bos indicus- influenced “C” validation population was performed by NBCEC using a model

  • Where b1 is the regression on MBV, breed and contemporary group (cg) were fixed and sire was random. Contemporary group was defined by pen within test group.