Reliability of molecular breeding values for Warner-Bratzler shear force and carcass traits of beef cattle – An independent validation study1

Abstract

Interest in genetic improvement of carcass and tenderness traits of beef cattle using genome-based selection (GS) and marker-assisted management programs is increasing. The success of such a program depends on the presence of linkage disequilibrium between the observed markers and the underlying QTL as well as on the relationship between the discovery, validation, and target populations. For molecular breeding values (MBV) predicted for a target population using SNP markers, reliabilities of these MBV can be obtained from validation analyses conducted in an independent population distinct from the discovery set. The objective of this study was to test MBV predicted for carcass and tenderness traits of beef cattle in a Canadian-based validation population that is largely independent of a United States-based discovery set. The discovery data set comprised of genotypes and phenotypes from >2,900 multibreed beef cattle while the validation population consisted of 802 crossbred feeder heifers and steers. A bivariate animal model that fitted actual phenotype and MBV was used for validation analyses. The reliability of MBV was defined as square of the genetic correlation (R(2) g) that represents the proportion of the additive genetic variance explained by the SNP markers. Several scenarios involving different starting marker panels (384, 3K, 7K, and 50K) and different sets of SNP selected to compute MBV (50, 100, 200, 375, 400, 600, and 800) were investigated. Validation results showed that the most reliable MBV (R(2) g) were 0.34 for HCW, 0.36 for back fat thickness, 0.28 for rib eye area, 0.30 for marbling score, 0.25 for yield grade, and 0.38 for Warner-Bratzler shear force across the different scenarios explored. The results indicate that smaller SNP panels can be developed for use in genetic improvement of beef carcass and tenderness traits to exploit GS benefits.

Genomic prediction of breed composition and heterosis effects in Angus, Charolais and Hereford crosses using 50K genotypes

“…The numbers of observations, phenotypic means, and standard deviations for the studied traits are summarized in Table 2. Consistent with previous studies, there was substantial phenotypic variation in this sample of crossbred beef cattle (Akanno et al 2014a(Akanno et al , 2014b. The proportions of total phenotypic variance explained by all genetic effects according to the model defined for Fig.…”

Genomic selection: A paradigm shift in animal breeding

“…Bolormaa et al (2013b) found that this increased accuracy slightly (0.33 to 0.38) but not as much as if the same number of animals had been from the same breed. When Akanno et al (2014) used a reference population of several pure breeds in USA to predict within a crossbred population in Canada, the accuracy was low. If the target breed is not included in the reference population, the accuracy is very low.…”

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

“…For slaughter, animals were first stunned by captive bolt and then exsanguinated. Collection of carcass data was previously described [53,55,[59][60][61][62]. Briefly, hot carcass weight (HCW) in kg was obtained by summing up the weight of each side of the carcass that was split during dressing, about 45 min post-mortem.…”