Genomic–polygenic evaluation of multibreed Angus–Brahman cattle for postweaning ultrasound and weight traits with actual and imputed Illumina50k SNP genotypes

Abstract

The objectives were to estimate additive genetic variance fractions for 4 postweaning ultrasound and weight traits explained by 46,839 actual and imputed SNP genotypes, to compare rankings of calf additive genetic predictions from genomic–polygenic (GP), genomic (G), and polygenic (P) models, and to assess trends for GP, G, and P predicted additive genetic values as functions of calf Brahman fractions in a multibreed Angus–Brahman population. Traits were postweaning ultrasound ribeye area (UREA), backfat thickness (UBF), and percent intramuscular fat (UPIMF), and weight (UW). Phenotypes and Illumina3k genotypes were from 812 bull, heifer, and steer calves housed at the Feed Efficiency Facility of the University of Florida from 2006 to 2010. Program Findhap2 was used to impute from 2899 Illumina3k SNP to 46,839 Illumina50k SNP using a reference population of 828 Brangus heifers. Fixed effects for all models were contemporary group (year-pen), age of dam, sex of calf, age of calf, Brahman fraction of calf, and heterozygosity of calf. Random effects were additive SNP (GP and G models), additive polygenic (GP and P models), and residual. Software GS3 was used to compute variance components and heritabilities, and additive genetic predictions. Additive genetic variance fractions explained by the 46,839 actual and imputed SNP were 0.17 for UREA, 0.32 for UBF, 0.25 for UPIMF, and 0.19 for UW. Heritabilities were 0.33 for UREA, 0.22 for UBF, 0.43 for UPIMF, and 0.54 for UW. These additive genetic variance fractions were 1.8, 1.0, 4.4, and 2.1 times greater and heritabilities were 1.0, 1.2, 1.0, and 1.2 times greater than those obtained for these 4 traits using only the 2899 Illumina3k SNP. Rank correlations between EBV from GP and P models were the highest (0.93 to 0.96), followed by those between EBV from GP and G models (0.81 to 0.94), and by those between EBV from G and P models (0.66 to 0.81). Regression coefficients of EVB on Brahman fraction were small for all traits and models indicating that animals of comparable EBV existed in all breed groups. Imputation from Illumina3k to 50k increased the explained fraction of additive SNP variance resulting in higher rank correlations between additive genetic predictions from G and GP, and from G and P models for all ultrasound traits in this Angus–Brahman multibreed population.