Table 3.
Analysis of molecular variance (AMOVA) of 298 inbred lines grouped on different categorical variables for the extraction of SNP variation among and within groups (populations) based on 235,019 SNPs.
| Category | Source of variation | Degree of freedom | Sum of squares | Variance components | Percentage of variation |
|---|---|---|---|---|---|
| Groups based on STRUCTURE at K = 3 | Among groups | 2 | 1,396,725.3 | 8,954.0 | 29.6 |
| Within groups | 293 | 6,233,282.8 | 21,274.0 | 70.4 | |
| Total | 295 | 7,630,008.0 | 30,228.0 | 100.0 | |
| Groups based on neighbor-joining method | Among groups | 4 | 1,676,030.9 | 6,964.1 | 25.3 |
| Within groups | 291 | 5,969,328.7 | 20,513.2 | 74.7 | |
| Total | 295 | 7,645,359.6 | 27,477.3 | 100.0 | |
| Groups based on genetic backgrounds of recurrent parents | Among groups | 6 | 1,194,314.2 | 5,066.3 | 18.8 |
| Within groups | 280 | 6,144,305.6 | 21,943.9 | 81.2 | |
| Total | 286 | 7,338,619.8 | 27,010.2 | 100.0 | |
| Groups based on genetic backgrounds of recurrent parents, excluding “Others” in Table 2 | Among groups | 7 | 1,495,876.8 | 5,759.3 | 21.6 |
| Within groups | 279 | 5,842,743.0 | 20,941.7 | 78.4 | |
| Total | 286 | 7,338,619.8 | 26,701.0 | 100.0 | |
| Groups based on genetic backgrounds of CML donor parents | Among groups | 2 | 509,151.8 | 5,532.8 | 20.2 |
| Within groups | 157 | 3,436,444.4 | 21,888.2 | 79.8 | |
| Total | 159 | 3,945,596.1 | 27,421.0 | 100.0 | |
| Heterotic groups | Among groups | 1.0 | 371,556.3 | 3,244.0 | 12.0 |
| Within groups | 216.0 | 5,139,101.0 | 23,792.1 | 88.0 | |
| Total | 217.0 | 5,510,657.3 | 27,036.1 | 100.0 | |
| Groups based on germplasm type | Among groups | 1 | 330,070.6 | 2,191.0 | 8.1 |
| Within groups | 296 | 7,353,918.8 | 24,844.3 | 91.9 | |
| Total | 297 | 7,683,989.5 | 27,035.3 | 100.0 |