Table 5. Summary of genetic characteristics and deduced population structure.
A. Genetic characteristics for three sample categories.
| Feature | Sample | N50 | N25 | N75 | Mean | S-W P | B-F P | K-W P | Sig | Pairs | 95% CI | Padj | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ng | IV | 9.0 | 6.0 | 17.0 | 12.0 | 1.5.E-10 | 2.05E-15 | 1.30E-11 | A | IV-HV | 0.267 | - | 0.381 | 4.94E-09 |
| HV | 6.0 | 4.0 | 10.0 | 7.1 | 1.8.E-09 | B | IV-SL | 0.241 | - | 0.352 | 8.98E-12 | |||
| SL | 6.0 | 3.0 | 9.0 | 6.4 | 1.3.E-08 | B | HV-SL | 0.404 | - | 0.527 | 0.268 | |||
| ALL | 10.0 | 6.0 | 18.0 | 13.4 | 8.4.E-11 | — | — | — | — | — | — | |||
| Na | IV | 5.0 | 3.0 | 7.0 | 5.6 | 2.5.E-09 | 7.05E-07 | 2.20E-09 | A | IV-HV | 0.291 | - | 0.406 | 5.38E-07 |
| HV | 3.5 | 3.0 | 5.0 | 4.1 | 3.7.E-09 | B | IV-SL | 0.263 | - | 0.374 | 1.29E-09 | |||
| SL | 3.0 | 2.0 | 5.0 | 3.8 | 1.2.E-08 | B | HV-SL | 0.403 | - | 0.524 | 0.231 | |||
| ALL | 5.0 | 4.0 | 8.0 | 5.9 | 3.4.E-09 | — | — | — | — | — | — | |||
| Ho | IV | 0.567 | 0.455 | 0.703 | 0.567 | 1.0.E-03 | 0.4994 | 0.005462 | A | IV-HV | 0.350 | - | 0.472 | 7.99E-03 |
| HV | 0.507 | 0.373 | 0.653 | 0.500 | 1.6.E-03 | B | IV-SL | 0.353 | - | 0.474 | 7.99E-03 | |||
| SL | 0.529 | 0.388 | 0.647 | 0.504 | 5.5.E-04 | B | HV-SL | 0.443 | - | 0.567 | 0.868 | |||
| ALL | 0.548 | 0.425 | 0.659 | 0.534 | 6.1.E-04 | — | — | — | — | — | — | |||
| He | IV | 0.567 | 0.478 | 0.716 | 0.570 | 2.4.E-05 | 0.8272 | 2.43E-09 | A | IV-HV | 0.295 | - | 0.412 | 2.06E-06 |
| HV | 0.499 | 0.870 | 0.602 | 0.484 | 3.5.E-04 | B | IV-SL | 0.255 | - | 0.368 | 6.24E-10 | |||
| SL | 0.489 | 0.361 | 0.572 | 0.461 | 1.8.E-04 | B | HV-SL | 0.397 | - | 0.520 | 0.159 | |||
| ALL | 0.529 | 0.439 | 0.643 | 0.527 | 3.4.E-05 | — | — | — | — | — | — | |||
| PIC | IV | 0.495 | 0.385 | 0.668 | 0.512 | 1.1.E-02 | 0.03945 | 1.08E-09 | A | IV-HV | 0.290 | - | 0.406 | 7.98E-07 |
| HV | 0.394 | 0.324 | 0.541 | 0.421 | 1.0.E-02 | B | IV-SL | 0.253 | - | 0.366 | 3.81E-10 | |||
| SL | 0.375 | 0.318 | 0.506 | 0.397 | 2.6.E-03 | B | HV-SL | 0.396 | - | 0.519 | 0.1793 | |||
| ALL | 0.460 | 0.366 | 0.589 | 0.468 | 1.8.E-03 | — | — | — | — | — | — | |||
| PM | IV | 0.261 | 0.132 | 0.361 | 0.279 | 7.8.E-10 | 0.8338 | 2.89E-13 | A | IV-HV | 0.623 | - | 0.737 | 2.34E-09 |
| HV | 0.364 | 0.232 | 0.471 | 0.381 | 1.5.E-07 | B | IV-SL | 0.672 | - | 0.780 | 1.47E-14 | |||
| SL | 0.403 | 0.277 | 0.489 | 0.408 | 3.4.E-08 | B | HV-SL | 0.488 | - | 0.611 | 0.117 | |||
| ALL | 0.307 | 0.184 | 0.404 | 0.323 | 2.4.E-09 | — | — | — | — | — | — | |||
| FW | IV | 0.004 | -0.052 | 0.075 | 0.008 | 0.01428 | 8.94E-05 | 2.23E-13 | A | IV-HV | 0.298 | - | 0.420 | 1.21E-05 |
| HV | -0.055 | -0.106 | 0.004 | -0.019 | 1.2E-10 | B | IV-SL | 0.213 | - | 0.324 | 4.32E-14 | |||
| SL | 0.090 | -0.169 | 0.000 | -0.083 | 5.9.E-03 | C | HV-SL | 0.325 | - | 0.446 | 2.29E-04 | |||
| ALL | -0.021 | -0.067 | -0.043 | -0.005 | 4.4.E-04 | — | — | — | — | — | — | |||
Average value of genetic characteristics with standard deviation for each sample category obtained with the 169 certified DNA markers. IV: 101 indigenous varieties, HV: 78 hybrid varieties, SL: 85 selected strains, ALL: 261 representative samples of these three categories.
Ng: number of unique genotypes, Na: number of unique alleles, Ho: observed heterozygosity, He: expected heterozygosity, PIC: polymorphic information content, PM: probability of match, Fw: fixation index.
N50, N25, N75: 50th, 25th and 75th percentile values.
S-W P: p-value of the normal distribution for each sample estimated by Shapiro–Wilk test.
B-F P: p-value of homogeneity of variance among the three sample categories estimated by Brown–Forsythe test.
K-W P: p-value of one-way ANOVA among the three sample categories estimated by Kruskal–Wallis test.
Sig: different letters represent significance between them at p < .01.
95% CI and Padj: The adjusted 95% confidence interval and p-value for each sample pair by Brunner–Munzel test. The p-value was adjusted by Benjamini–Hochberg (BH) correction for multiple sample comparison.
Pairs: combinations for the pairwise Brunner–Munzel test or G''ST analysis.