Abstract
Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein–protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders’ visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p-value lower than 1 × 10–3 were included. The genes identified as associated were included in a protein–protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655–44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein–protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection.
Highlights
Consumption studies suggest that quality is more important compared to other factors such as product price in the consumer’ purchasing decision (Henchion et al, 2014)
Warner-Bratzler shear force had a total of 3,181 significant single nucleotide polymorphism (SNP) (Figure 1 and Supplementary Table S1), and 74% of these SNPs were assigned to a gene using all four marker-gene distance
A total of 1,867, 3,181, 3,926, and 3,678 associated markers were identified for marbling, Warner-Bratzler Shear Force (WBSF), tenderness, and connective tissue, respectively
Summary
Consumption studies suggest that quality is more important compared to other factors such as product price in the consumer’ purchasing decision (Henchion et al, 2014). Like all other meat quality attributes, these are complex traits controlled by genetics and influenced to a large degree by environmental factors (Leal-Gutiérrez and Mateescu, 2019) They are difficult and expensive to measure on a large number of animals and might require progeny testing which makes them perfect candidates for genomic research aimed at identifying genetic markers accounting for variability in meat quality and the causative mutations responsible for this variation. These findings would be highly beneficial for the beef industry since consumers are willing to pay a higher price if higher meat quality can be guaranteed (Lyford et al, 2010; Polkinghorne and Thompson, 2010)
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