Table 2.
Analysis of molecular variance (AMOVA) for the extraction of SNP variation among and within groups (populations) based on 28,798 polymorphic SNPs.
| Categorical variable | Source of variation | Degree of freedom | Sum of squares | Variance components | Percentage variation | FST |
|---|---|---|---|---|---|---|
| All 28,798 SNPs | ||||||
| STRUCTURE groups at K = 2 | Between predicted groups | 1 | 76,815.8 | 844.1 | 19.6 | 0.196 |
| Within groups | 194 | 673,966.1 | 3474.1 | 80.5 | ||
| STRUCTURE groups at K = 3 | Among predicted groups | 3 | 131,327.8 | 888.9 | 21.6 | 0.216 |
| Within groups | 192 | 619,454.1 | 3226.3 | 78.4 | ||
| STRUCTURE groups at K = 4 | Among predicted groups | 4 | 161,762.3 | 1010.5 | 24.7 | 0.247 |
| Within groups | 191 | 589,019.5 | 3083.9 | 75.3 | ||
| Eight wheat classes | Among wheat classes | 7 | 139,984.3 | 813.6 | 20.0 | 0.200 |
| Within groups | 188 | 610,797.6 | 3248.9 | 80.0 | ||
| Six breeding periods | Among six breeding periods | 5 | 33,152.2 | 98.8 | 2.6 | 0.026 |
| Within groups | 188 | 710,193.1 | 3777.6 | 97.5 | ||
| Four breeding periods | Among 4 breeding periods | 3 | 27,653.3 | 118.3 | 3.1 | 0.031 |
| Within groups | 190 | 715,692.0 | 3766.8 | 97.0 | ||
| Six breeding programs | Among 6 breeding programs | 5 | 30,563.9 | 93.3 | 2.5 | 0.025 |
| Within groups | 168 | 622,755.7 | 3706.9 | 97.6 | ||
| SNPs under selection | ||||||
| STRUCTURE groups at K = 3 (524 SNPs) | Among predicted groups | 3 | 8556.9 | 61.6 | 58.7 | 0.587 |
| Within groups | 192 | 8315.2 | 43.3 | 41.3 | ||
| Eight wheat classes (1520 SNPs) | Among wheat classes | 7 | 19,877.7 | 132.8 | 55.8 | 0.558 |
| Within groups | 188 | 19,758.5 | 105.1 | 44.2 | ||
| Six breeding periods | Among six breeding periods | 5 | 8242.4 | 47.7 | 14.9 | 0.149 |
| Within groups | 188 | 51,010.9 | 271.3 | 85.1 | ||
| Four breeding periods | Among six breeding periods | 3 | 7437.9 | 47.9 | 14.9 | 0.149 |
| Within groups | 190 | 51,815.3 | 272.7 | 85.1 | ||
For comparison purpose, the results computed from the 524, 1520, and 2314 outlier SNPs associated with the three predicted groups, 8 wheat classes, and six breeding periods, respectively are included.