Table 2.
Summary of Y1 and PSY2 DNA Sequence Variation
| Loci | Sites | π (×10−3) | θw (×10−3) | Tajima's D |
|---|---|---|---|---|
| Y1a | ||||
| All | Total | 8.41 | 6.44 | 1.04 (NS) |
| Silent | 10.86 | 8.39 | ||
| Nonsynonymous | 2.68 | 1.88 | ||
| Yellow | Total | 0.54 | 1.79 | −2.39b |
| Silent | 0.57 | 2.09 | ||
| Nonsynonymous | 0.44 | 0.79 | ||
| White | Total | 10.19 | 7.14 | 1.60 (NS) |
| Silent | 13.20 | 9.25 | ||
| Nonsynonymous | 3.20 | 2.23 | ||
| PSY2c | ||||
| All | Total | 8.49 | 7.75 | 0.30 (NS) |
| Silent | 11.62 | 10.49 | ||
| Nonsynonymous | – | – | ||
| Yellow | Total | 7.59 | 6.70 | 0.45 (NS) |
| Silent | 10.52 | 9.23 | ||
| Nonsynonymous | 0.88 | 0.91 | ||
| White | Total | 8.59 | 8.80 | −0.08 (NS) |
| Silent | 11.90 | 11.87 | ||
| Nonsynonymous | – | – |
π, nucleotide diversity/site; θw, Watterson's estimator (calculated using the no-recombination assumption); NS, not significant (P > 0.10). Estimates are based on all nucleotide sites. Dashes indicate that the measure of diversity for that particular set of lines cannot be calculated.
a
One orange/yellow endosperm line, Ames 24575, and one white endosperm line, PI595547, were excluded because of missing data.
b
0.001 < P < 0.01.
c
Two orange/yellow endosperm lines, Y-4 and PI595559, were excluded from analysis because of excessive missing data.