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Table 1 Allele frequency changes since 1964 in selected genes. (‘Allele 1’ is the lower-ranked letter of any pair of A, C, G, T)

From: Genome changes due to artificial selection in U.S. Holstein cattle

SNPa frequency of ‘allele 1’ in population
chr position (bp) gene I b II b III b Current c AFD d
X 114,995,979 ADGRG2 e 0.99 0.62 0.45 0.39 0.60
10 28,703,125 AVEN e 0.02 0.30 0.51 0.59 0.56
X 116,153,810 DMD f 0.05 0.46 0.53 0.58 0.53
3 98,450,919 SPATA6 e 0.08 0.53 0.57 0.59 0.51
2 100,376,419 ERBB4 e 0.08 0.29 0.47 0.56 0.48
23 27,215,001 SKIV2L e 0.37 0.58 0.78 0.84 0.47
1 88,050,696 USP13 g 0.22 0.57 0.63 0.64 0.42
11 6,724,678 IL1R2 g 0.68 0.33 0.29 0.26 0.42
13 76,932,968 SULF2 e 0.19 0.38 0.51 0.61 0.41
26 17,465,791 BLNK g 0.41 0.74 0.79 0.83 0.41
19 24,812,617 SPATA22 e 0.80 0.49 0.42 0.39 0.40
23 25,552,635 BOLA-DRB2 g 0.22 0.49 0.60 0.62 0.40
1 65,433,706 GSK3B g 0.54 0.21 0.17 0.16 0.38
12 35,934,370 LATS2 e, g 0.42 0.23 0.14 0.08 0.34
9 90,155,533 ESR1 e 0.45 0.24 0.16 0.13 0.32
20 32,030,332 GHR e 0.42 0.61 0.70 0.73 0.31
11 28,602,889 EPAS1 e, g 0.41 0.60 0.64 0.71 0.30
1 95,258,770 SPATA16 e 0.92 0.65 0.69 0.62 0.30
11 31,296,603 FSHR e 0.03 0.23 0.25 0.26 0.23
20 39,017,985 PRLR e 0.70 0.61 0.50 0.49 0.21
14 1,801,116 DGAT1 h 0.93 0.71 0.82 0.77 0.16
  1. a These SNPs were selected based on three criteria: AFD is large among all SNPs, the SNP is in a gene with known fertility or immunity function, or other well established functions (DGAT1 and DMD)
  2. b I, II, III represent Groups I, II and III respectively, where Group I was unselected, Group II was subjected to 20 years of selection, and Group III was subjected to 40 years of selection since 1964
  3. c The current population had 294,079 cows with 98% of the cows born in 2006–2015
  4. d This is the absolute allele frequency difference between Group I and the current population approximately due to 50 years of selection
  5. e Associated with fertility
  6. f Associated with muscle diseases
  7. g Associated with immunity
  8. h Widely confirmed to have the most significant effects on milk production traits in dairy cattle