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Table 1 Distribution of the top 100 most significant SNP effects for predicted transmitting abilities for 13 production, health, and reproduction traits of contemporary U.S. Holsteins by chromosome.

From: Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

Chr MY FY PY FPC PPC PL SCS DPR SCE DCE SSB DSB NM All traits
1 2 4 4 4 5 15 4 17 7 6 7 3 15 93
2 3 0 0 0 1 1 11 2 0 0 0 2 0 20
3 10 4 1 4 1 9 7 17 4 0 4 6 1 68
4 3 2 2 0 0 4 0 0 2 0 3 0 0 16
5 2 2 2 7 13 0 4 0 7 3 10 0 2 52
6 2 2 5 1 6 2 9 0 0 6 0 1 5 39
7 0 6 1 1 2 11 13 15 4 11 0 6 4 74
8 2 1 0 0 0 4 1 3 0 0 0 3 1 15
9 7 6 1 1 2 0 0 0 4 3 1 6 4 35
10 5 0 0 0 3 0 2 6 1 0 4 0 0 21
11 3 3 3 1 3 0 1 0 1 0 0 5 0 20
12 2 1 1 2 3 0 6 0 8 2 6 1 1 33
13 13 12 8 4 1 0 1 2 1 0 0 7 4 53
14 2 1 1 24 2 0 0 2 0 0 6 4 0 42
15 1 2 1 2 0 1 0 0 1 1 4 5 1 19
16 1 0 0 0 0 2 11 1 0 0 3 3 0 21
17 4 7 6 11 14 9 1 5 20 21 7 2 14 121
18 8 4 6 5 4 8 2 5 9 12 6 4 10 83
19 2 3 2 0 0 0 0 0 0 0 0 3 0 10
20 0 2 11 0 2 0 2 0 1 1 1 5 0 25
21 4 1 5 0 5 0 0 0 2 1 6 5 1 30
22 1 0 0 0 0 3 2 3 0 1 0 2 1 13
23 5 5 9 2 3 0 1 0 2 1 1 16 3 48
24 2 1 2 2 2 1 1 0 1 1 3 0 2 18
25 0 2 0 3 0 0 5 1 0 0 1 0 0 12
26 0 7 6 6 10 9 3 4 6 10 9 1 11 82
27 5 6 7 0 1 1 1 0 3 1 0 1 3 29
28 0 0 5 0 1 2 0 3 3 1 1 1 3 20
29 0 0 0 0 0 1 2 1 0 2 1 3 1 11
X 11 16 11 19 16 15 9 12 12 16 15 3 12 167
U 0 0 0 1 0 2 1 1 1 0 1 2 1 10
P* 10-12 10-24 10-23 10-17 10-22 10-29 10-23 10-25 10-38 10-23 10-24 10-21 10-34  
R2 0.42 0.43 0.42 0.45 0.40 0.54 0.54 0.53 0.52 0.42 0.56 0.55 0.49  
  1. SNP, single nucleotide polymorphism; Chr, chromosome; MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; PL, productive life; SCS, somatic cell score; DPR, daughter pregnancy rate; SCE, service-sire calving ease; DCE, daughter calving ease; SSB, service-sire stillbirth; DSB, daughter stillbirth; NM, net merit; U, unknown. Boldface indicates ≥10 significant SNP effects. *Rounded cutoff for P value for top 100 most significant SNPs for trait. R2, variation accounted for by the top 100 SNPs for the trait.