From: Evaluation of approaches for identifying population informative markers from high density SNP Chips
 |  | Delta |  |  |  | pairwise Wright's FST | pairwise W&C's FST | PCA |  |  |  | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Breed | Markers | log0 | log1 | log2 | log3 | log0 | log1 | log2 | log3 | log0 | log1 | log2 | log3 | log0 | log1 | log2 | log3 |
Angus | 50 | 100 | 79.17 | 66.67 | 33.33 | 85.4 | 64.58 | 43.75 | 18.75 | 93.8 | 81.25 | 37.5 | 16.67 | 85.4 | 68.75 | 52.08 | 20.83 |
 | 100 | 100 | 91.67 | 77.08 | 72.92 | 97.9 | 91.67 | 89.58 | 87.5 | 100 | 100 | 95.83 | 91.67 | 89.6 | 79.17 | 77.08 | 60.42 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 97.92 | 97.92 | 100 | 97.92 | 97.92 | 97.92 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 97.92 | 97.92 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Brown Swiss | 50 | 100 | 95.8 | 95.8 | 95.8 | 100 | 100 | 100 | 95.8 | 100 | 100 | 100 | 91.7 | 100 | 100 | 100 | 100 |
 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Charolais | 50 | 72 | 56 | 24 | 0 | 92 | 76 | 60 | 24 | 92 | 60 | 44 | 16 | 88 | 68 | 20 | 4 |
 | 100 | 88 | 76 | 56 | 24 | 96 | 96 | 84 | 60 | 96 | 88 | 80 | 44 | 92 | 92 | 84 | 52 |
 | 200 | 96 | 96 | 96 | 92 | 96 | 96 | 92 | 92 | 96 | 96 | 96 | 92 | 96 | 96 | 92 | 84 |
 | 300 | 100 | 96 | 96 | 96 | 96 | 96 | 96 | 92 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 |
 | 400 | 100 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 | 96 |
Finnish Ayrshire | 50 | 100 | 60 | 20 | 10 | 100 | 90 | 60 | 40 | 70 | 70 | 60 | 50 | 100 | 100 | 70 | 40 |
 | 100 | 100 | 100 | 90 | 90 | 100 | 90 | 80 | 50 | 90 | 90 | 80 | 50 | 100 | 100 | 100 | 80 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 80 | 100 | 100 | 100 | 90 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Guernsey | 50 | 100 | 100 | 95.2 | 95.2 | 95.2 | 95.2 | 95.2 | 95.2 | 100 | 95.2 | 95.2 | 95.2 | 95.2 | 95.2 | 95.2 | 95.2 |
 | 100 | 100 | 100 | 100 | 95.2 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 95.2 | 95.2 | 95.2 | 95.2 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Hereford | 50 | 68 | 60 | 36 | 24 | 92 | 80 | 60 | 48 | 100 | 92 | 84 | 68 | 96 | 88 | 76 | 72 |
 | 100 | 100 | 88 | 88 | 84 | 100 | 100 | 96 | 84 | 100 | 100 | 100 | 96 | 100 | 100 | 100 | 100 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Holstein | 50 | 96 | 72 | 48 | 24 | 92 | 72 | 64 | 40 | 96 | 96 | 96 | 96 | 96 | 96 | 88 | 84 |
 | 100 | 100 | 96 | 96 | 92 | 100 | 100 | 100 | 100 | 100 | 100 | 92 | 88 | 100 | 100 | 92 | 92 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Jersey | 50 | 100 | 100 | 100 | 92.9 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 96.4 |
 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Limousin | 50 | 92 | 84 | 56 | 40 | 96 | 92 | 84 | 48 | 88 | 80 | 72 | 44 | 84 | 60 | 20 | 12 |
 | 100 | 100 | 100 | 96 | 76 | 100 | 92 | 88 | 84 | 88 | 88 | 72 | 72 | 92 | 92 | 72 | 48 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 96 | 92 | 92 | 92 | 92 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 96 | 96 | 100 | 96 | 96 | 96 | 96 | 96 | 96 | 92 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 96 | 96 | 96 | 100 | 96 | 96 | 96 | 100 | 100 | 100 | 100 |
Norwegian Red | 50 | 90.5 | 71.4 | 61.9 | 33.3 | 90.5 | 71.4 | 57.1 | 28.6 | 90.5 | 81 | 71.4 | 57.1 | 85.7 | 76.2 | 61.9 | 28.6 |
 | 100 | 100 | 95.2 | 90.5 | 85.7 | 95.2 | 90.5 | 85.7 | 76.2 | 90.5 | 90.5 | 76.2 | 71.4 | 95.2 | 95.2 | 90.5 | 85.7 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 95.2 | 100 | 100 | 100 | 95.2 | 95.2 | 100 | 100 | 95.2 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Piedmontese | 50 | 100 | 94.7 | 94.7 | 78.9 | 100 | 100 | 100 | 94.7 | 100 | 94.7 | 94.7 | 73.7 | 94.7 | 84.2 | 73.7 | 47.4 |
 | 100 | 100 | 100 | 100 | 94.7 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 94.7 | 94.7 | 94.7 | 68.4 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Red Angus | 50 | 93 | 73.3 | 46.7 | 26.7 | 86.7 | 53.3 | 33.3 | 20 | 80 | 53.3 | 46.7 | 13.3 | 93.3 | 53.3 | 46.7 | 20 |
 | 100 | 93 | 80 | 66.7 | 60 | 86.7 | 86.7 | 80 | 66.7 | 100 | 93.3 | 93.3 | 73.3 | 93.3 | 80 | 73.3 | 60 |
 | 200 | 93 | 93.3 | 93.3 | 93.3 | 100 | 100 | 100 | 93.3 | 100 | 100 | 93.3 | 93.3 | 100 | 93.3 | 80 | 80 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 86.7 | 86.7 | 86.7 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 93.3 | 93.3 | 93.3 |
Red Poll | 50 | 88.9 | 88.9 | 83.3 | 72.2 | 100 | 100 | 83.3 | 77.8 | 94.4 | 88.9 | 77.8 | 66.7 | 100 | 94.4 | 94.4 | 94.4 |
 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 94.4 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Shorthorn | 50 | 80 | 76 | 68 | 56 | 92 | 92 | 92 | 80 | 92 | 92 | 92 | 88 | 96 | 92 | 80 | 80 |
 | 100 | 92 | 88 | 88 | 88 | 92 | 92 | 92 | 88 | 96 | 96 | 92 | 92 | 100 | 96 | 96 | 92 |
 | 200 | 96 | 96 | 92 | 92 | 100 | 96 | 96 | 96 | 100 | 96 | 96 | 96 | 100 | 100 | 100 | 100 |
 | 300 | 96 | 100 | 100 | 100 | 100 | 96 | 96 | 96 | 100 | 96 | 96 | 96 | 100 | 100 | 100 | 100 |
 | 400 | 100 | 100 | 100 | 96 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
Simmental | 50 | 100 | 92 | 68 | 36 | 92 | 92 | 80 | 60 | 96 | 84 | 68 | 40 | 88 | 68 | 44 | 32 |
 | 100 | 100 | 92 | 84 | 80 | 96 | 100 | 96 | 96 | 100 | 100 | 88 | 76 | 92 | 92 | 76 | 56 |
 | 200 | 100 | 100 | 100 | 96 | 100 | 100 | 100 | 100 | 100 | 100 | 96 | 92 | 92 | 88 | 76 | 68 |
 | 300 | 100 | 100 | 100 | 96 | 100 | 100 | 100 | 100 | 100 | 96 | 96 | 96 | 96 | 92 | 88 | 76 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 96 | 92 |
Welsh Black | 50 | 100 | 100 | 93.3 | 76.7 | 96.7 | 93.3 | 83.3 | 80 | 100 | 96.7 | 90 | 83.3 | 96.7 | 96.7 | 90 | 83.3 |
 | 100 | 100 | 100 | 100 | 100 | 96.7 | 93.3 | 93.3 | 93.3 | 100 | 100 | 100 | 100 | 96.7 | 96.7 | 96.7 | 96.7 |
 | 200 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 96.7 | 100 | 100 | 96.7 | 96.7 |
 | 300 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 96.7 | 96.7 | 96.7 |
 | 400 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |