Phenotypic variation in South African beef bulls genotyped with the Illumina® BovineHD SNP array

This dataset determines the detailed, accurate phenotypes for growth, carcass and beef quality traits under carefully controlled conditions (listed here), to minimize variations in finishing, slaughter procedures, post-mortem carcass handling and laboratory analyses. SNPs of the Illumina® BovineHD SNP BeadChip (total 777,962 variants) were characterised in South African purebred beef bulls and the level of linkage between SNPs of the genes of the calpain-cast system determined (134 SNPs of the reference transcripts). The haplotype block structure of these genes, across and within breed types were compared and SNPs of the calpain-calpastatin system were validated for growth, carcass and beef quality traits, measured under carefully controlled protocols to minimize environmental variation. The aim was to determine whether extended meat ageing diluted the genetic effects of genomic markers (SNPs), or whether the accelerated meat ageing rate induced by electrical stimulation of carcasses, attenuated SNP effects on beef quality traits.