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Table 5 Reliability gains when adding real sequence variants to HD or 60 K

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

Trait Reliability for PA (%) Gain for HD SNPs only Gain for HD SNPs + 481,904 candidate SNPsa Gain for HD SNPs + 481,904 candidate SNPs + indels Gain for 60 k SNPs only Gain for 60 k SNPs + 16,648 candidate SNPsb,c
Milk 37.9 34.1 33.9 (−0.2) 33.9 34.3 35.7 (1.4)
Fat 37.9 33.7 34.0 (0.3) 33.4 34.3 35.1 (0.8)
Protein 37.9 27.9 27.0 (−0.9) 26.7 27.5 28.2 (0.7)
Fat percentage 37.9 49.2 52.7 (3.5) 52.4 52.9 54.8 (1.9)
Protein percentage 37.9 42.1 41.6 (0.5) 43.0 41.6 44.3 (2.7)
Productive life 32.0 36.1 35.8 (−0.3) 36.4 35.6 38.2 (2.6)
Somatic cell score 34.7 35.9 36.1 (0.2) 37.1 35.1 37.0 (1.9)
Daughter pregnancy rate 31.5 30.8 30.0 (−0.8) 31.2 29.0 33.0 (4.0)
Cow conception rate 29.8 28.7 28.1 (−0.6) 28.8 28.9 31.8 (2.9)
Heifer conception rate 30.0 19.0 20.3 (1.3) 19.7 20.5 21.5 (1.0)
Sire calving ease 29.9 27.8 27.7 (−0.1) 25.2 24.5 28.5 (4.0)
Daughter calving ease 25.3 32.5 30.8 (−1.7) 29.9 31.5 31.4 (−0.1)
Sire stillbirth 29.0 7.6 7.3 (−0.3) 7.1 7.6 7.8 (0.2)
Daughter stillbirth 23.8 37.4 37.0 (−0.4) 35.8 35.4 38.0 (2.6)
Final score 36.2 24.7 25.5 (0.8) 25.8 24.6 27.8 (3.2)
Stature 38.2 30.4 32.4 (2.0) 32.8 30.3 34.7 (4.3)
Strength 37.4 29.9 31.8 (1.9) 31.8 29.9 34.5 (4.6)
Dairy form 37.4 33.8 35.3 (1.5) 35.8 35.0 38.2 (3.2)
Foot angle 36.7 17.3 17.6 (0.3) 18.2 17.2 19.6 (2.4)
Rear legs (side view) 37.3 21.9 22.7 (0.8) 22.0 22.1 24.1 (2.0)
Body depth 37.6 31.0 33.1 (2.1) 33.7 31.2 36.0 (4.8)
Rump angle 37.8 32.7 34.0 (1.3) 33.5 32.9 36.1 (3.2)
Rump width 37.1 29.2 30.4 (1.2) 30.2 29.1 32.5 (3.4)
Fore udder attachment 37.5 35.1 36.4 (1.3) 36.1 35.0 39.0 (4.0)
Rear udder height 37.3 24.7 25.7 (1.0) 25.8 24.1 27.3 (3.2)
Udder depth 38.0 40.2 42.6 (2.4) 42.8 40.6 44.6 (4.0)
Udder cleft 37.1 23.7 24.5 (0.8) 24.0 23.6 25.5 (1.9)
Front teat placement 37.6 32.6 33.4 (0.8) 32.3 30.9 35.0 (4.1)
Teat length 37.7 29.0 30.3 (1.3) 29.9 28.0 32.7 (4.7)
Rear legs (rear view) 36.0 20.7 20.3 (−0.4) 20.1 20.4 22.8 (2.4)
Feet and leg score 36.4 16.9 16.5 (−0.4) 16.6 15.9 18.3 (2.4)
Rear teat placement 37.4 33.1 33.6 (0.5) 32.1 32.9 35.2 (2.3)
Net merit 34.4 23.8 24.3 (0.5) 24.4 23.4 24.7 (1.3)
Average 35.2 28.8 29.4 (0.6) 29.2 29.5 32.2 (2.7)
  1. Reliability gains in percentage points over parent average reliability
  2. PA parent average
  3. aDifference from reliability gain for HD SNPS only in parentheses
  4. bDifference from reliability gain for 60 k SNPS only in parentheses
  5. cDoes not include 6584 60 k markers that were not available in sequence data