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Table 6 Coefficients for regression of validation data on genomic predictions when adding real sequence variants to HD or 60 k

From: Selecting sequence variants to improve genomic predictions for dairy cattle

Trait PA HD SNPs only HD SNPs + 481,904 candidate SNPs HD SNPs + 481,904 candidate SNPs + InDels 60 k SNPs only 60 k SNPs + 16,648 candidate SNPsa
Milk 0.81 1.03 1.06 1.06 1.04 1.05
Fat 0.68 0.92 0.95 0.94 0.94 0.93
Protein 0.75 0.93 0.96 0.95 0.94 0.95
Fat percentage 0.97 1.14 1.13 1.12 1.12 1.09
Protein percentage 0.77 0.96 0.98 0.97 0.95 0.96
Productive life 1.24 1.30 1.32 1.25 1.27 1.25
Somatic cell score 0.89 1.09 1.10 1.06 1.08 1.06
Daughter pregnancy rate 1.20 1.47 1.49 1.48 1.43 1.43
Cow conception rate 0.72 0.94 0.95 0.92 0.91 0.91
Heifer conception rate 0.75 0.97 1.03 0.98 0.94 0.92
Sire calving ease 0.65 0.83 0.83 0.81 0.82 0.84
Daughter calving ease 0.80 1.04 1.03 1.02 1.04 1.02
Sire stillbirth 0.84 0.75 0.76 0.78 0.77 0.76
Daughter stillbirth 0.77 1.15 1.16 1.15 1.12 1.16
Final score 0.71 0.93 0.92 0.92 0.91 0.88
Stature 0.84 1.04 1.02 1.01 1.01 1.00
Strength 0.80 1.05 1.03 1.02 1.01 0.99
Dairy form 0.82 1.10 1.08 1.08 1.07 1.05
Foot angle 0.71 0.84 0.82 0.82 0.81 0.79
Rear legs (side view) 0.87 1.01 0.99 0.99 0.98 0.96
Body depth 0.76 1.01 0.99 0.99 0.97 0.96
Rump angle 0.80 1.08 1.07 1.05 1.06 1.05
Rump width 0.78 1.01 0.99 0.98 0.98 0.96
Fore udder attachment 0.80 1.06 1.04 1.03 1.03 1.01
Rear udder height 0.78 0.97 0.96 0.96 0.94 0.93
Udder depth 0.76 1.11 1.09 1.08 1.07 1.06
Udder cleft 0.87 1.00 0.99 0.99 0.98 0.95
Front teat placement 0.80 1.05 1.03 1.01 1.02 0.99
Teat length 0.91 1.06 1.06 1.04 1.04 1.03
Rear legs (rear view) 0.58 0.86 0.85 0.83 0.83 0.80
Feet and leg score 0.54 0.74 0.72 0.72 0.71 0.68
Rear teat placement 0.90 1.13 1.10 1.09 1.09 1.04
Net merit 0.85 0.82 0.84 0.81 0.83 0.81
Average 0.81 1.01 1.01 1.00 0.99 0.98
  1. PA parent average
  2. aDoes not include 6584 60 k markers that were not available in sequence data