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Commercial Genetic Test Validation

Pfizer GeneSTAR Tenderness MVP:

Summary:

The GeneSTAR Tenderness MVP1 was found to be significantly associated with a decrease in Warner-Bratzler shear force (WBSF) measurements (i.e. increased tenderness) at 14 d postmortem in two Bos taurus sample populations. Additionally this test was found to be significantly associated with a decrease in Warner-Bratzler-shear force measurements at day 1 d postmortem, but not 14 d postmortem, in a Bos indicus-influenced population of 390 animals.

Significance of the GeneSTAR Tenderness MVP* (Molecular Value Prediction)

 * 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.

*** Warner-Bratzler shear force (WBSF) is the force required to shear a cooked steak after postmortem aging

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

Test Claims:

The GeneSTAR Tenderness MVP Molecular Value Prediction (MVP) provides a prediction of the genetic breeding value for tenderness (measured as Warner-Bratzler shear force) in all breeds of cattle.

Test Details:

The GeneSTAR Tenderness 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:

• North American Bos taurus “Pfizer A” validation population WBSF Tenderness = Shear force (kg) of longissimus dorsi 14 day post mortem
• North American Angus validation population
• North American Bos indicus-influenced “Pfizer C” validation population

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

Quantiles for GeneSTAR Tenderness Molecular Value Prediction*

Population	Panel	Mean	Max	75% (Q3)	Median  (Q2)	25%     (Q1)	Min
North American Bos taurus “Pfizer A” validation population	Tenderness	n/a	0.192	0.102	0.012	-0.023	-0.444
North American Angus validation population	Tenderness	-0.133	0.738	0.04	-0.156	-0.329	-0.87
North American Bos indicus-influenced “Pfizer C” validation population	Tenderness	0.128	1.387	0.349	0.125	-0.127	-0.656

 *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 Tenderness MVP* (Molecular Value Prediction)

Population	TRAIT	Panel	b**	F	p	N
North American Bos taurus “Pfizer A” validation population	WBSF Tenderness        (day 14 postmortem;kg)	Tenderness	0.0665	4.2	0.021	462
North American Angus validation population	WBSF Tenderness        (day 14 postmortem;lb)	Tenderness	0.328	14.33	0.00008	760
North American Bos indicus-influenced “Pfizer C” validation population	WBSF Tenderness        (day 1 postmortem;kg)	Tenderness	0.358	6.227	0.007	390
	WBSF Tenderness        (day 14 postmortem;kg)	Tenderness	0.037	0.189	0.332	388

 *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 F test is based on a model including fixed contemporary group, random sire, and the regression of GeneSTAR tenderness MVP for the trait in question (January 2009).

**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 validation population A was performed by Gordon VanderVoort, Matt Kelly, Duc Lu and Stephen Miller, University of Guelph (July 2008) using the following model:

Trait=aet+tty+heterosis+AN+PI+SM+CH+sex+mbv
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)
Sex –heifer, bull or steer
MBV – Prediction of genetic merit based on SNP provided by Bovigen.

The remaining populations were analyzed by NBCEC using on a model including fixed contemporary group, random sire, and the regression of GeneSTAR tenderness MVP for the trait in question (January 2009).

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