Estimated gene frequencies of GeneSTAR markers and their size of effects on meat tenderness, marbling, and feed efficiency in temperate and tropical beef cattle breeds across a range of production systems

Abstract

The objectives of this study were to use genotypes for 12 commercially available GeneSTAR gene markers on 12,330 animals to estimate gene frequencies of the markers across a range of beef cattle breeds and to determine the effects of these markers on target traits using a subset of animals with both genotypic and phenotypic data (n = 9,414) for at least one trait. Tenderness markers (T1, T2, T3, T4) were assessed against shear force of 2 muscles, marbling markers (M1, M2, M3, M4) were assessed against intramuscular fat percent and marbling score, and the feed-efficiency markers (N1, N2, N3, N4) were assessed on daily feed intake and residual feed intake. Animals used were from 5 beef cattle research populations: Beef Cooperative Research Centre 1 (CRC1) temperate breeds (Angus, Hereford, Murray Grey, Shorthorn; n = 3,721), Beef CRC1 tropical breeds (Brahman, Santa Gertrudis, Belmont Red; n = 3,899), Beef CRC2 tropically adapted genotypes (Brahman and Tropical Composite; n = 4,446), and progeny test programs in Angus (n = 742) and Shorthorn (n = 347). Gene frequencies varied significantly across breeds and markers, with 86% of the markers estimated to be in Hardy-Weinberg equilibrium. Tenderness markers T1 and T2 had significant effects (P < 0.0001) on shear force, with the size and direction of effects consistent across the range of breeds for the 3 populations with phenotypes. However, sizes of marker effects differed across muscles and reduced upon tenderstretch hanging. Marker T3 was not significant (P > 0.05) in CRC1 temperate breeds but was significant (P < 0.0001) in tropically adapted breeds, with a large effect in Brahman. Marker T4 was significant for shear force in 2 CRC1 tropical breeds but with a different favorable allele. The 4 marbling markers were generally not significantly associated with intramuscular fat percent or marbling score across the 5 populations studied. Feed-efficiency markers N3 and N4 were significantly associated with residual feed intake and daily feed intake in the CRC1 temperate data set, in which a subset of the CRC1 data was used in their discovery, but were not significant in the other 4 populations. Markers N1 and N2 were generally not significant, but when they were significant, their direction of effects differed. The 12 GeneSTAR markers were studied in populations consisting of different breeds and genetic variability and showed gene frequencies and estimated effects that varied greatly across traits, suggesting large differences between the markers for their utility as selection tools in these populations.