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Evaluation phase genotype frequency by trait category for CAPN1, CAST, and GHR in an Angus population selected to increase minor genotype and haplotype frequencies

 
Genotype Preweaning traits, n = 465 (%) Carcass quality traits, n = 199 (%)
CAPN11
CAPN1hCC:CAPN1hCC 166 (35.7) 77 (38.7)
CAPN1hCC:CAPN1hGT 228 (49.0) 94 (47.2)
CAPN1hGT:CAPN1hGT 71 (15.3) 28 (14.1)
CAST2
CASTaC:CASTaC 49 (10.5) 22 (11.1)
CASTaC:CASTaT 238 (51.2) 82 (41.2)
CASTaT:CASTaT 178 (38.3) 95 (47.7)
GHR3
GHRaA:GHRaA 153 (32.9) 78 (39.2)
GHRaA:GHRaT 240 (51.6) 88 (44.2)
GHRaT:GHRaT 72 (15.5) 33 (16.6)
1Haplotype of 2 SNP within the CAPN1 gene. CAPN1hCC = CAPN1-316 C allele with CAPN1-4751 C allele and CAPN1hGT = CAPN1-316 G allele with CAPN1-4751 T allele.
2CASTaC = C allele of CAST SNP and CASTaT = T allele of CAST SNP
3GHRaA = A allele of GHR SNP and GHRaT = T allele of GHR SNP



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Angus cattle evaluation phase performance and carcass quality trait means and SD

 
Trait n Mean SD
Birth BW, kg 465 34.7 4.8
Weaning BW, kg 464 196.5 25.3
Yearling BW, kg 199 474.6 50.5
Final BW, kg 199 567.2 43.1
Dressing percent, % 199 61.6 1.7
HCW, kg 199 349.8 30.4
Adjusted fat thickness, mm 199 15.6 4.2
Marbling score1 199 5.67 0.85
LM area, sq. cm 199 73.0 6.1
Vision yield grade 199 3.77 0.65
Slice shear force, kg 199 11.94 2.39
VISNIR2 predicted shear force, kg 199 13.03 1.65
14.00 = Slight00; 5.00 = Small00; 6.00 = Modest00 (USDA, 1997; BIF, 2010).
2Visible and near-infrared reflectance spectroscopy (VISNIR; Shackelford et al., 2012a,b).



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Significance (P-values) for sources of variation and heritability estimates for performance and carcass quality traitswith values ≤ 0.05 in bold

 
Trait Year Dam age Calf age1 Calf sex CAPN1 CAST GHR h2 ± SE
Birth BW < 0.001 < 0.001 < 0.001 < 0.001 0.19 0.31 0.54 0.54 ± 0.14
Weaning BW < 0.001 < 0.001 < 0.001 < 0.001 0.72 0.09 0.58 0.24 ± 0.14
Yearling BW 0.03 < 0.001 < 0.001 2 0.71 0.32 0.40 0.203 ± 0.18
Final BW 0.01 < 0.001 < 0.001 0.33 0.48 0.23 0.24 ± 0.17
Dressing percent < 0.001 0.72 < 0.01 0.43 0.24 0.82 0.34 ± 0.20
Hot carcass weight < 0.01 < 0.001 < 0.001 0.57 0.31 0.24 0.22 ± 0.17
Adjusted fat thickness < 0.001 0.14 < 0.001 0.59 0.06 0.35 0.26 ± 0.21
Marbling score < 0.001 0.52 < 0.01 0.31 0.91 0.53 0.26 ± 0.22
LM area < 0.001 0.38 0.21 0.69 0.16 0.82 0.703 ± 0.22
Vision yield grade 0.03 0.07 < 0.001 0.77 0.02 0.33 0.37 ± 0.22
Slice shear force < 0.01 0.43 0.52 < 0.001 < 0.001 0.56 0.32 ± 0.22
VISNIR4 predicted shear force 0.03 0.86 0.54 0.53 0.16 0.27 0.203 ± 0.20
1Julian birth day linear covariate used for birth BW; linear age (d) covariate used for all other traits.
2Postweaning traits were only measured on steers, so sex effect was not included in the model.
3Constrained to 0.20 ≤ h2 ≤ 0.70.
4Visible and near-infrared reflectance spectroscopy (VISNIR; Shackelford et al., 2012a,b)



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Significance (P-Values) for additive or dominance effects of CAPN1 or CAST on traits where either marker had significant effect with values ≤ 0.05 in bold

 
CAPN1
CAPN1
CAST
CAST
Trait Additive effect Dominance effect Additive effect Dominance effect
Vision Yield Grade cNS1 NS1 < 0.01 0.45
Slice shear force < 0.001 0.19 < 0.001 0.43
1NS = Nonsignificant (P = 0.77) effect.



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Significant estimated additive effects and SE for CAPN1 and CAST genetic markers on carcass quality traits

 
CAPN1
CAST
Trait additive effect/GT haplotype additive effect/T allele
Vision yield grade NS1 -0.198 ± 0.071
Slice shear force, kg 1.049 ± 0.246 -1.257 ± 0.261
1NS = Nonsignificant (P = 0.77) genetic effect.



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Estimated additive effects and SE for CAPN1 and CAST genetic markers on slice shear force with either single residual variance or genotype specific residual variance models

 
Type of residual variance model CAPN1
CAST
additive effect/GT haplotype additive effect/T allele
Single
Slice shear force, kg 1.049 ± 0.246 -1.257 ± 0.261
CAPN1 genotype specific
Slice shear force, kg 1.040 ± 0.279 -1.209 ± 0.251
CAST genotype specific
Slice shear force, kg 1.080 ± 0.224 -1.240 ± 0.341



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Back transformed average additive effects and SE for CAPN1 and CAST genetic markers on log transformed slice shear force with either single residual variance or CAPN1 genotype specific residual variances or CAST genotype specific residual variances

 
Type of residual variance model CAPN1
CAST
additive effect/GT haplotype additive effect/T allele
Single
Slice shear force, kg 1.081 ± 0.242 -1.218 ± 0.255
CAPN1 genotype specific
Slice shear force, kg 1.068 ± 0.268 -1.181 ± 0.242
CAST genotype specific
Slice shear force, kg 1.105 ± 0.229 -1.204 ± 0.305



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Estimated effect of CAPN1 GT haplotype relative to CAPN1 CC haplotype for additive and dominance modes of inheritance

 
Trait Additive Dominance
Birth BW, kg -0.04 ± 0.29 -0.63 ± 0.37
Weaning BW, kg -0.27 ± 1.40 1.50 ± 1.84
Yearling BW, kg 2.49 ± 3.65 1.20 ± 4.87
Final BW, kg 5.57 ± 4.47 2.37 ± 5.96
Dressing percent, % -0.06 ± 0.15 -0.22 ± 0.21
Hot carcass weight, kg 3.00 ± 3.03 0.34 ± 4.05
Adjusted fat thickness, mm 0.31 ± 0.42 0.25 ± 0.56
Marbling score1 0.125 ± 0.084 -0.088 ± 0.112
LM area, sq. cm 0.41 ± 0.65 0.33 ± 0.85
Vision yield grade 0.041 ± 0.067 0.017 ± 0.089
Slice shear force, kg 1.049 ± 0.246 -0.432 ± 0.327
VISNIR2 predicted shear force, kg -0.205 ± 0.187 0.144 ± 0.250
14.00 = Slight00; 5.00 = Small00; 6.00 = Modest00 (USDA, 1997; BIF, 2010).
2Visible and near-infrared reflectance spectroscopy (VISNIR; Shackelford et al., 2012a,b).



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Estimated effect of CAST T allele relative to CAST C allele for additive and dominance modes of inheritance

 
Trait Additive Dominance
Birth BW, kg -0.10 ± 0.32 -0.55 ± 0.39
Weaning BW, kg -1.90 ± 1.58 2.26 ± 1.97
Yearling BW, kg -3.77 ± 3.88 3.31 ± 5.32
Final BW, kg −5.23 ± 4.75 -0.14 ± 6.51
Dressing percent, % -0.27 ± 0.16 -0.09 ± 0.22
Hot carcass weight, kg −4.70 ± 3.22 -0.99 ± 4.42
Adjusted fat thickness, mm -1.05 ± 0.44 -0.80 ± 0.61
Marbling score1 0.034 ± 0.089 0.000 ± 0.122
LM area, sq. cm 1.09 ± 0.68 -0.26 ± 0.93
Vision yield grade -0.198 ± 0.071 -0.073 ± 0.097
Slice shear force, kg -1.257 ± 0.261 -0.281 ± 0.357
VISNIR2 predicted shear force, kg 0.006 ± 0.199 0.473 ± 0.273
14.00 = Slight00; 5.00 = Small00; 6.00 = Modest00 (USDA, 1997; BIF, 2010).
2Visible and near-infrared reflectance spectroscopy (VISNIR; Shackelford et al., 2012a,b).



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Estimated effect of GHR T allele relative to GHR A allele for additive and dominance modes of inheritance

 
Trait Additive Dominance
Birth BW, kg -0.07 ± 0.29 -0.36 ± 0.36
Weaning BW, kg -0.20 ± 1.42 -1.77 ± 1.83
Yearling BW, kg 4.71 ± 3.46 -1.52 ± 4.84
Final BW, kg 7.34 ± 4.25 -3.60 ± 5.92
Dressing percent, % 0.08 ± 0.15 0.02 ± 0.20
Hot carcass weight, kg 4.90 ± 2.88 -2.08 ± 4.02
Adjusted fat thickness, mm 0.57 ± 0.40 -0.35 ± 0.55
Marbling score1 -0.089 ± 0.080 0.053 ± 0.111
LM area, sq. cm 0.39 ± 0.62 -0.23 ± 0.84
Vision yield grade 0.095 ± 0.064 -0.046 ± 0.088
Slice shear force, kg 0.254 ± 0.234 -0.086 ± 0.324
VISNIR2 predicted shear force, kg 0.029 ± 0.177 -0.395 ± 0.248
14.00 = Slight00; 5.00 = Small00; 6.00 = Modest00 (USDA, 1997; BIF, 2010).
2Visible and near-infrared reflectance spectroscopy (VISNIR; Shackelford et al., 2012a,b).