NBCEC - National Beef Cattle Education Consortium - hosted by Iowa State University

Commercial Genetic Test Validation

Pfizer GeneSTAR Marbling MVP:

Summary
Test Claims
Test Details
Sample Populations

Summary:

There was no significant association of this test with the trait of Marbling Score in any of the validation populations. However, the GeneSTAR Marbling MVP[1] was found to be significantly associated with percent intramuscular fat (%IMF) in a Bos indicus- influenced, and one of two Bos Taurus populations. Additionally this test was found to be significantly associated with the quality grade (% choice or better) in the Bos indicus- influenced population o f 394 animals, but not the Bos taurus “B” validation population.

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

Population	TRAIT	Panel	b**	F	p	N
North American Bos taurus “Pfizer A” validation population	Marbling score***	Marbling	-0.267	3.15	0.961	595
	% IMF	Marbling	0.193	1.76	0.094	282
North American Bos taurus “PfizerB” validation population	Marbling score	Marbling	.120	1.1	0.147	723
	% Choice		-0.032	0.1	0.624	723
	% IMF		0.312	5.26	0.011	785
North American Bos indicus-influenced “Pfizer C” validation population	Marbling score	Marbling	0.367	1.73	0.096	392
	% Choice		0.276	3.68	0.028	392
	% IMF		0.659	9.83	0.001	394

* 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.

*** Degree of intramuscular fatness in the longissimus dorsi (ribeye muscle).

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

Test Claims:

The GeneSTAR Marbling MVP provides a prediction of the genetic breeding value for marbling (measured as marbling score) in all breeds of cattle.

Test Details:

The GeneSTAR Marbling 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
Subjective marbling score 1 to 10
Ultra-sound marbling estimate
North American Bos taurus “Pfizer B” validation population
North American Bos indicus-influenced “Pfizer C” validation population

*Letter-designations for validation populations as described in Pfizer Technical Summary (February 2009).

Quantiles for GeneSTAR Marbling Molecular Value Prediction*

Population	Panel	Mean	Max	75% (Q3)	Median (Q2)	25% (Q1)	Min
North American Bos taurus “Pfizer A” validation population	Marbling	n/a	0.729	0.107	0.0006	-0.112	-0.545
North American Bos taurus “Pfizer B”validation population	Marbling	-0.059	0.383	0.07	-0.054	-0.186	-0.596
North American Bos indicus-influenced “Pfizer C” validation population	Marbling	-0.13	0.415	0.003	-0.142	-0.271	-0.688

*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 Marbling MVP* (Molecular Value Prediction)

Population	TRAIT	Panel	b**	F	p	N
North American Bos taurus “Pfizer A” validation population	Marbling score	Marbling	-0.267	3.15	0.961	595
	% IMF	Marbling	0.193	1.76	0.094	282
North American Bos taurus “PfizerB” validation population	Marbling score	Marbling	.120	1.1	0.147	723
	% Choice		-0.032	0.1	0.624	723
	% IMF		0.312	5.26	0.011	785
North American Bos indicus-influenced “Pfizer C” validation population	Marbling Score	Marbling	0.367	1.73	0.096	392
	% Choice		0.276	3.68	0.028	392
	% IMF		0.659	9.83	0.001	394

*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 Marbling MVP for the trait in question (January 2009).

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:

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).

GENETIC TEST VALIDATION