Calpastatin and μ-calpain differ in their control of genotype specific residual variance of beef tenderness in Angus and MARC III steers

Abstract Text: Genotype variant effects of calpastatin (CAST) and μ-calpain (CAPN1) on mean beef tenderness have been widely characterized.  We have tested whether these genetic variants also control residual (non-genetic) variation, and subsequently total phenotypic variation, of tenderness.  Observation of rare genotypes is important for understanding the role of these genetic markers on beef tenderness.  Two populations at USMARC (Angus and MARC III) were subjected to marker-assisted selection for multiple years to equalize allele (CAST) and haplotype (CAPN1; CAPN1_316 with CAPN1_4751) frequencies.  Within each population, analyses were conducted for 14-d slice shear force (SSF) in steers (Angus, n = 199; MARC III, n = 254) to estimate genotypic effect size, mode of inheritance, and polygenic effects utilizing 5-generation pedigrees.  Beyond the traditional analyses with a single residual variance (Angus, σ_e = 1.79 kg; MARC III, σ_e = 3.58 kg), CAST and CAPN1 genotype specific residual variance models were tested.  In both populations, CAST genotype specific residual variance models fit significantly better (Angus, P < 0.001; MARC III, P < 0.001) than single residual variance models and were progressive in their effect.  Across populations, CAST genotype specific residual variance models identified the homozygous tender genotype as having the smallest residual variance (Angus, σ_e-TT = 1.22 kg; MARC III, σ_e-TT = 2.54 kg), the heterozygous genotype had intermediate residual variance (Angus, σ_e-CT = 1.99 kg; MARC III, σ_e-CT = 3.98 kg), and the homozygous tough genotype had the largest residual variance (Angus, σ_e-CC = 2.82 kg; MARC III σ_e-CC = 4.86 kg).  In comparison, CAPN1 genotype specific residual variance models were not as well supported (Angus, P = 0.05; MARC III, P = 0.03) and in both populations the effects were not progressive, with a heterozygous CAPN1 genotype (having an intermediate effect on mean) having the smallest residual variance.  Effects of CAST and CAPN1 on mean tenderness were maintained under all genotype specific residual variance analyses.  These results indicate that beyond changes in the mean, CAST also influences phenotypic variation in beef tenderness, which may be important for management and marketing of beef.  USDA is an equal opportunity provider and employer. 

Keywords: carcass quality, marker effects, tenderness