Table 4.
Analysis of molecular variance (AMOVA) for the extraction of SNP variation among and within groups (populations) based on 2,179 O. glaberrima accessions genotyped with 3,834 polymorphic SNPs.
| Category | Source of variation | d.f. | Sum of squares | Variance components | Percentage of variation |
|---|---|---|---|---|---|
| Country of origin* | Among groups | 13 | 202,566.7 | 54.5 | 18.1 |
| Within groups | 4,344 | 1,072,188.8 | 246.8 | 81.9 | |
| Total | 4,357 | 1,274,755.5 | 301.3 | 100.0 | |
| Ecology* | Among groups | 7 | 107,343.2 | 32.4 | 10.8 |
| Within groups | 4,350 | 1,167,789.9 | 268.5 | 89.2 | |
| Total | 4,357 | 1,275,133.1 | 300.9 | 100.0 | |
| Groups based on STRUCTURE at K = 5 | Among groups | 5 | 316,630.5 | 89.6 | 28.9 |
| Within groups | 4,352 | 958,124.9 | 220.2 | 71.1 | |
| Total | 4,357 | 1,274,755.4 | 309.8 | 100.0 | |
| Groups based on cluster analysis | Among groups | 4 | 289,596.6 | 84.8 | 27.3 |
| Within groups | 4,353 | 985,158.8 | 226.3 | 72.7 | |
| Total | 4,357 | 1,274,755.4 | 311.1 | 100.0 |
*
Countries of origin: Burkina Faso, Cameroon, Chad, Gambia, Ghana, Guinea Conakry, Guinea Bissau, Ivory Coast, Liberia, Mali, Nigeria, Senegal, Togo, and “others,” which consisted of all other countries with <10 accessions. Ecologies of origin: Floating, Hydromorphic, Irrigated lowland, Lowland irrigated/rainfed, Rainfed lowland, Mangrove, Swamp, and upland.