View Full Table | Close Full ViewTable 1.

Heritability estimates and summary statistics for the traits used in this study. Cross-validation (CRV) and external validation (EXV) are data splits representing cross-validation and validation datasets, respectively

 
Trait H2 Animals EPD1 Mean EPD SD Mean BIF2 accuracy Mean BIF accuracy in CRV Mean BIF accuracy in EXV
Birth wt, kg 0.42 7,804 0.81 0.73 0.39 0.43 0.31
Calving ease direct, % 0.20 6,905 6.24 3.81 0.31 0.34 0.24
Calving ease maternal, % 0.12 6,905 7.64 2.97 0.18 0.22 0.10
Carcass wt, kg 0.28 7,976 9.25 4.00 0.17 0.21 0.10
Docility, % 0.37 2,012 11.31 10.27 0.36 0.42 0.24
Fat thickness, cm 0.42 7,974 0.03 0.05 0.19 0.23 0.13
DMI, kg/d 0.31 2,570 0.08 0.08 0.29 0.33 0.23
Heifer pregnancy, % 0.13 573 8.26 2.1 0.26 0.32 0.13
Marbling score 0.37 7,975 0.51 0.28 0.22 0.25 0.16
Mature height, cm 0.64 676 0.86 1.17 0.47 0.57 0.27
Maternal milking ability, kg 0.14 7,804 11.08 2.74 0.21 0.26 0.13
Mature wt, kg 0.37 676 33.4 29.6 0.45 0.53 0.29
Rib eye area, cm2 0.37 7,976 1.94 1.35 0.26 0.30 0.19
Scrotal circumference, cm 0.47 4,610 0.43 0.54 0.39 0.44 0.31
Weaning wt, kg 0.20 7,804 23.38 4.38 0.31 0.34 0.23
Yearling height, cm 0.50 3,103 0.81 0.81 0.44 0.50 0.34
Yearling wt, kg 0.20 7,804 42.27 7.29 0.27 0.31 0.18
1EPD = expected progeny differences.
2BIF = Beef Improvement Federation.



View Full Table | Close Full ViewTable 2.

Number of observations and summary statistics for several traits used in the year 2010 study1. Cross-validation (CRV) and external validation (EXV) are data splits representing cross-validation and validation datasets, respectively

 
Trait H2 Animals EPD2 mean EPD SD Mean BIF3 accuracy Mean BIF accuracy in CRV Mean BIF accuracy in EXV
Birth wt, kg 0.31 1,783 0.98 0.37 0.39 0.42 0.32
Calving ease direct, % 0.10 1,722 4.67 1.95 0.30 0.32 0.22
Calving ease maternal, % 0.14 1,722 5.67 1.42 0.16 0.18 0.09
Carcass wt, kg 0.29 1,812 4.63 0.73 0.14 0.18 0.08
DMI, kg/d 0.48 2,253 0.12 0.14 0.28
Fat thickness, cm 0.42 1,844 0.03 0.03 0.20 0.23 0.13
Marbling score 0.37 1,844 0.27 0.1 0.20 0.24 0.14
Maternal milking ability, kg 0.12 1,783 9.80 1.15 0.30 0.32 0.21
Rib eye area, cm2 0.37 1,844 0.90 0.58 0.23 0.27 0.17
Weaning wt, kg 0.25 1,783 21.41 1.96 0.30 0.33 0.23
1This dataset refers to a subset data of the current study that was analyzed in year 2010.
2EPD = expected progeny differences.
3BIF = Beef Improvement Federation.



View Full Table | Close Full ViewTable 3.

Accuracies of direct genomic values (DGV), regression coefficients, and percent genetic variation explained by DGV with EBV and deregressed EBV (DEBV) response variables

 
Training (cross-validation)
External validation
EBV DEBV EBV DEBV
Trait r1 b1 %GV1 r b %GV r b %GV r b %GV
Birth wt, kg 0.55 0.90 30 0.54 1.01 29 0.57 0.86 32 0.44 1.02 19
Calving ease direct, % 0.59 0.91 34 0.70 1.20 49 0.59 0.99 35 0.54 1.31 30
Calving ease maternal, % 0.65 0.92 42 0.62 0.92 39
Carcass wt, kg 0.74 0.91 55 0.43 0.95 18 0.62 0.88 39 0.54 1.75 30
Docility, % 0.64 0.80 41 0.71 0.78 50 0.69 0.91 48 0.58 1.22 34
Fat thickness, cm 0.74 1.19 54 0.48 1.12 23 0.61 1.19 37 0.46 1.44 21
DMI, kg/d 0.44 1.01 19 0.34 0.95 12 0.39 0.99 15 0.22 0.86 5
Heifer pregnancy, % 0.57 0.95 31 0.54 2.22 29 0.71 0.87 51 0.12 1.25 2
Marbling score 0.76 1.00 58 0.51 1.05 26 0.78 1.01 61 0.48 1.24 23
Mature height, cm 0.56 1.04 31 0.52 0.97 27 0.66 1.11 43 0.34 1.12 11
Maternal milking ability, kg 0.72 0.91 52 0.72 0.87 52
Mature wt, kg 0.47 0.73 22 0.28 0.21 8 0.55 0.90 30 0.24 0.35 6
Rib eye area, cm2 0.71 0.97 50 0.62 0.95 38 0.65 0.97 42 0.50 1.17 25
Scrotal circumference, cm 0.62 0.91 38 0.60 1.03 36 0.63 0.94 40 0.41 1.11 17
Weaning wt, kg 0.71 0.92 50 0.77 1.16 59 0.68 0.88 46 0.62 1.21 39
Yearling height, cm 0.62 0.94 37 0.57 1.05 32 0.61 0.85 37 0.41 1.00 16
Yearling wt, kg 0.74 0.93 55 0.91 1.15 83 0.68 0.83 47 0.71 1.20 51
AVG 0.64 0.94 41 0.57 1.05 35 0.63 0.94 41 0.44 1.15 22
1r = accuracy of DGV estimated as correlation between DEBV or EBV and DGV; b = regression of DEBV or EBV on DGV; %GV = percent genetic variance explained by DGV.



View Full Table | Close Full ViewTable 4.

Accuracies of direct genomic values (DGV), regression coefficients of deregressed EBV (DEBV) or EBVon DGV and percent genetic variation explained by DGV with EBV and DEBV as response variables comparing identical by state (IBS)-based and K-means cross-validation methods

 
Trait IBS based (EBV) K-means (EBV) IBS based (DEBV) K-means (DEBV)
r1 b1 %GV1 r b %GV r b %GV r b %GV
Birth wt, kg 0.55 0.9 30 0.49 0.87 24 0.54 1.01 29 0.47 0.99 22
Calving ease direct, % 0.59 0.91 34 0.51 0.86 26 0.70 1.20 49 0.61 1.21 38
Calving ease maternal, % 0.65 0.92 42 0.59 0.84 34
Carcass wt, kg 0.74 0.91 55 0.68 0.91 46 0.43 0.95 18 0.38 0.95 15
Docility, % 0.64 0.80 41 0.63 0.79 39 0.71 0.78 50 0.70 0.79 50
Fat thickness, cm 0.74 1.19 54 0.70 1.21 49 0.48 1.12 23 0.42 1.00 18
DMI, kg/d 0.44 1.01 19 0.41 0.92 17 0.34 0.95 12 0.33 0.95 11
Heifer pregnancy, % 0.57 0.95 31 0.54 0.97 29 0.54 2.22 29 0.58 4.64 34
Marbling score 0.76 1.00 58 0.77 0.95 60 0.51 1.05 26 0.55 1.12 30
Mature height, cm 0.56 1.04 31 0.43 0.97 18 0.52 0.97 27 0.36 0.83 13
Maternal milking ability, kg 0.72 0.91 52 0.66 0.87 44
Mature wt, kg 0.47 0.73 22 0.33 0.62 11 0.28 0.21 8 0.14 0.12 2
Rib eye area, cm2 0.71 0.97 50 0.69 0.94 48 0.62 0.95 38 0.58 0.89 34
Scrotal circumference, cm 0.62 0.91 38 0.55 0.90 30 0.60 1.03 36 0.52 1.01 27
Weaning wt, kg 0.71 0.92 50 0.62 0.87 39 0.77 1.16 59 0.68 1.22 47
Yearling height, cm 0.62 0.94 37 0.58 0.94 33 0.57 1.05 32 0.55 1.07 30
Yearling wt, kg 0.74 0.93 55 0.66 0.87 44 0.91 1.15 83 0.81 1.16 65
AVG 0.64 0.94 42 0.58 0.9 35 0.57 1.05 35 0.51 1.2 29
1r = accuracy of DGV estimated as correlation between DEBV or EBV and DGV; b = regression of DEBV or EBV on DGV; %GV = percent genetic variance explained by DGV.



View Full Table | Close Full ViewTable 5.

Comparison of relationship among animals within (amax_within) and across (amax_across) clusters in various methods

 
Method Cluster Animals amax_within amax_across amax_diff1 r2 CI3 of r
K-means Cluster 1 284 0.56 0.24 0.32 0.43 0.33 to 0.52
K-means Cluster 2 2,150 0.47 0.31 0.17 0.49 0.46 to 0.52
K-means Cluster 3 1,243 0.50 0.31 0.18 0.52 0.48 to 0.56
K-means Cluster 4 1,039 0.37 0.21 0.16 0.46 0.41 to 0.51
K-means Cluster 5 434 0.55 0.23 0.32 0.52 0.45 to 0.59
Average 0.49 0.26 0.23 0.48
IBS4based Cluster 1 1,030 0.55 0.28 0.27 0.50 0.45 to 0.54
IBS based Cluster 2 1,030 0.43 0.32 0.11 0.55 0.51 to 0.59
IBS based Cluster 3 1,030 0.38 0.32 0.06 0.55 0.51 to 0.59
IBS based Cluster 4 1,030 0.37 0.32 0.05 0.59 0.55 to 0.63
IBS based Cluster 5 1,030 0.45 0.30 0.15 0.58 0.54 to 0.62
Average 0.44 0.31 0.13 0.55
Random Cluster 1 1,093 0.38 0.39 –0.01 0.58 0.54 to 0.62
Random Cluster 2 999 0.37 0.37 0.00 0.62 0.58 to 0.66
Random Cluster 3 1,030 0.37 0.37 0.00 0.60 0.56 to 0.64
Random Cluster 4 1,032 0.37 0.38 –0.01 0.56 0.52 to 0.60
Random Cluster 5 996 0.40 0.39 0.01 0.60 0.56 to 0.64
Average 0.38 0.38 0.00 0.59
IBS_UnEqual5 Cluster 1 71 0.43 0.16 0.27 0.53 0.34 to 0.68
IBS_UnEqual Cluster 2 2,423 0.45 0.35 0.10 0.53 0.50 to 0.56
IBS_UnEqual Cluster 3 1,731 0.44 0.35 0.09 0.52 0.48 to 0.55
IBS_UnEqual Cluster 4 638 0.49 0.29 0.19 0.54 0.48 to 0.59
IBS_UnEqual Cluster 5 287 0.57 0.24 0.33 0.47 0.37 to 0.56
Average 0.48 0.28 0.20 0.52
1amax_diff = the difference between amax_within and amax_across.
2Training cross-validation correlations (r) between EBV and direct genomic values for birth weight.
3CI = confidence interval of correlations.
4IBS = identical by state.
5IBS_UnEqual = IBS-based methodology with unequal cluster sizes.



View Full Table | Close Full ViewTable 6.

Comparison of accuracies of direct genomic values (DGV) and percent genetic variation explained by DGV across the current study and year 2010 study in cross-validation (CRV) and external validation (EXV) datasets

 
Year 2010 study results Current results
Trait Animals r1 – CRV %GV1 – CRV r – EXV %GV – EXV Animals r – CRV %GV – CRV r – EXV %GV – EXV
Birth wt, kg 1,783 0.55 30 0.52 27 7,804 0.55 30 0.57 32
Calving ease direct, % 1,722 0.57 32 0.41 17 6,905 0.59 35 0.60 36
Calving ease maternal, % 1,722 0.53 40 0.67 45 6,905 0.65 43 0.62 39
Carcass wt, kg 1,812 0.63 40 0.50 25 7,976 0.74 55 0.73 53
Fat thickness, cm 1,844 0.70 49 0.61 37 7,974 0.74 55 0.74 55
DMI, kg/d 2,253 0.39 17 0.28 11 2,570 0.44 19 0.39 15
Marbling score 1,844 0.77 59 0.49 24 7,975 0.76 58 0.76 58
Maternal milking ability, kg 1,783 0.68 46 0.43 18 7,804 0.72 52 0.73 53
Rib eye area, cm2 1,844 0.65 42 0.48 23 7,976 0.71 50 0.70 49
Weaning wt, kg 1,783 0.64 41 0.53 28 7,804 0.71 50 0.70 49
AVG 1,839 0.61 40 0.49 26 7,169 0.66 45 0.65 44
1r = accuracy of DGV estimated as correlation between EBV and DGV; %GV = percent genetic variance explained by DGV.