Characterisation of muscle calpain system SNPs and associations with production and beef quality traits in South African beef cattle following electrical stimulation and extended ageing

Abstract

The genes of the muscle calpain system are the most important genes that affect beef tenderness and research on associations of these genotypes with beef quality traits in South African beef cattle is limited. Beef quality traits often have a large environmental component and it is important to minimize environmental biases for accurate analyses, while shorter distances between single nucleotide polymorphisms (SNPs) enable the identification of more informative variants across breeds. We therefore used the Illumina BovineHD (777K) SNP array to genotype bulls from five selected South African purebred beef breeds (Angus, Bonsmara, Brahman, Charolais and Nguni) for the capn1, capn2, capn3 and cast genes. Detailed carcass and beef quality traits were determined, while maintaining a constant environment for finishing, carcass handling and sample analyses. Characterization of the calpain system genes revealed a high proportion of alleles favourable for tenderness in Bonsmara cattle (originally a Sanga-type composite) and an opportunity to improve the average frequency of tender alleles in Nguni cattle (Sanga, Bos taurus africanus). Extensive linkage was identified in the cast and capn2 genes with regions of high linkage disequilibrium between breeds. This presents an opportunity for across-breed selection for candidate SNPs in overlapping haplotype blocks. The identification of candidate SNPs with mixed model association analyses (GCTA software) identified 62 putative associations with Warner-Bratzler shear force (WBSF) or myofibril fragment length (MFL), while only six of these SNPs (especially in the cast and capn2 genes) affected these tenderness phenotypes over extended meat ageing periods. Most candidate SNPs (>80% of associations) affected certain stages of the meat ageing period and were unable to sustain the genetic effect over the entire meat ageing period of 20 days, confirming that the altered physiological mechanisms of extended aging are subject to effects from different genetic markers. Several quantitative trait nucleotides (QTNs) were identified in both the non-electrically stimulated (NS) and the electrically stimulated (ES) treatment groups using a different mixed model approach, more suited to these data (GAPIT package in R software). Associations of SNPs with tenderization, estimated by MFL at various stages of meat ageing, were closely linked to associations of SNPs with decreased calpastatin inhibitory effects on proteases (in linkage blocks). All four genes of the calpain system contained QTNs for calpastatin inhibition of proteases (ten in total) and the tenderizing effects of the SNPs in these genes were primarily found for MFL, where 13 QTNs were identified in both control and ES groups, with some SNPs sustaining effects for extended meat ageing periods. The effects of electrical stimulation on SNP associations with traits failed to demonstrate a universal effect across SNPs or traits. Although many SNP effects were only slightly affected by treatment, other SNP effects were observed in only one of the treatment groups, where electrical stimulation either enhanced or eliminated genetic associations. Novel QTNs for intermediary energy metabolism were identified, with four of these SNPs located in the capn2 gene that could explain previous data linking pH to these genes. This provides the link between calpain protease activity (through energy metabolic pathways) and pH decline that will favour sarcoplasmic Ca2+ release, facilitating more rapid tenderization. These results validate the SNPs of the calpain-calpastatin system for selection to improve myofibril fragmentation in South African beef bulls and highlight the importance of tenderizing interventions, when determining genomic associations. Furthermore, these data confirmed the complex effects of calpain protease activity in cellular homeostasis that can also alter metabolic processes, though pleiotropic effects of these genetic markers.