title: Validation of commercial DNA tests for quantitative beef quality traits.
abstract: Associations between 3 commercially available genetic marker panels (GeneSTAR Quality Grade, GeneSTAR Tenderness, and Igenity Tender-GENE) and quantitative beef traits were validated by the US National Beef Cattle Evaluation Consortium. Validation was interpreted to be the independent confirmation of the associations between genetic tests and phenotypes, as claimed by the commercial genotyping companies. Validation of the quality grade test (GeneSTAR Quality Grade) was carried out on 400 Charolais x Angus crossbred cattle, and validation of the tenderness tests (GeneSTAR Tenderness and Igenity Tender-GENE) was carried out on over 1,000 Bos taurus and Bos indicus cattle. The GeneSTAR Quality Grade marker panel is composed of 2 markers (TG5, a SNP upstream from the start of the first exon of thyroglobulin, and QG2, an anonymous SNP) and is being marketed as a test associated with marbling and quality grade. In this validation study, the genotype results from this test were not associated with marbling score; however, the association of substituting favorable alleles of the marker panel with increased quality grade (percentage of cattle grading Choice or Prime) approached significance (P < or = 0.06), mainly due to the effect of 1 of the 2 markers. The GeneSTAR Tenderness and Igenity TenderGENE marker panels are being marketed as tests associated with meat tenderness, as assessed by Warner-Bratzler shear force. These marker panels share 2 common mu-calpain SNP, but each has a different calpastatin SNP. In both panels, there were highly significant (P < 0.001) associations of the calpastatin marker and the mu-calpain haplotype with tenderness. The genotypic effects of the 2 tenderness panels were similar to each other, with a 1 kg difference in Warner-Bratzler shear force being observed between the most and least tender genotypes. Unbiased and independent validation studies are important to help build confidence in marker technology and also as a potential source of data required to enable the integration of marker data into genetic evaluations. As DNA tests associated with more beef production traits enter the marketplace, it will become increasingly important, and likely more difficult, to find independent populations with suitable phenotypes for validation studies.
authors.affiliation: University of California, Davis 95616, USA. alvaneenennaam@ucdavis.edu
authors.forename: A L
authors.initials: AL
authors.lastname: Van Eenennaam
authors.forename: J
authors.initials: J
authors.lastname: Li
authors.forename: R M
authors.initials: RM
authors.lastname: Thallman
authors.forename: R L
authors.initials: RL
authors.lastname: Quaas
authors.forename: M E
authors.initials: ME
authors.lastname: Dikeman
authors.forename: C A
authors.initials: CA
authors.lastname: Gill
authors.forename: D E
authors.initials: DE
authors.lastname: Franke
authors.forename: M G
authors.initials: MG
authors.lastname: Thomas
mesh_terms: D000483:Alleles; D000818:Animals; D001823:Body Composition / Q000235:genetics*; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005819:Genetic Markers; D005820:Genetic Testing / Q000592:standards*; D005838:Genotype; D008460:Meat / Q000592:standards*; D020641:Polymorphism, Single Nucleotide; D011933:Reagent Kits, Diagnostic / Q000662:veterinary*; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers; D011933:Reagent Kits, Diagnostic