TABLE 2.
Statistical analyses of recombination across a1–sh2
| Informative subintervals | Genetic backgrounds | Comparisons to the average of a1–sh2a | Comparisons to the genome's averagea | Recombination activitiesb |
|---|---|---|---|---|
| II | A632/LC | 2.8e−156↑ (22×) | 4.2e−63↑ (10×) | Hot spot (global, local) |
| Oh43/LC | 8.8e−77↑ (14×) | 5.9e−13↑ (3.6×) | Hot spot (global, local) | |
| W64A/LC | 3.5e−100↑ (15×) | 3.0e−32↑ (5.8×) | Hot spot (global, local) | |
| III | A632/LC | 0.28 | 0.10 | Average spot |
| Oh43/LC | 0.73 | 0.094 | Average spot | |
| W64A/LC | 0.41 | 0.41 | Average spot | |
| VI | A632/LC | 6.8e−104↑ (17×) | 2.1e−40↑ (7.5×) | Hot spot (global, local) |
| Oh43/LC | 8.0e−49↑ (10×) | 6.3e−07↑ (2.6×) | Hot spot (global, local) | |
| W64A/LC | 0↑ (23×) | 3.1e−110↑ (9.2×) | Hot spot (global, local) | |
| VII | A632/LC | 7.1e−6↑ (6.9×) | 0.018↑ (3.1×) | Hot spot (global, local) |
| Oh43/LC | 0.16 | 0.55 | Average spot | |
| W64A/LC | 0.030↑ (3.3×) | 0.66 | Hot spot (local) | |
| VIII | A632/LC | 4.4e−137↑ (16×) | 3.3e−52↑ (7.1×) | Hot spot (global, local) |
| Oh43/LC | 0↑ (23×) | 9.7e−81↑ (5.8×) | Hot spot (global, local) | |
| W64A/LC | 4.9e−175↑ (14×) | 1.2e−54↑ (5.4×) | Hot spot (global, local) | |
| IX | A632/LC | 3.1e−8↓ (NA)c | 1.1e−16↓ (NA) | Cold spot (global, local) |
| Oh43/LC | 5.1e−10↓ (40×) | 1.5e−36↓ (160×) | Cold spot (global, local) | |
| W64A/LC | 3.1e−12↓ (NA) | 9.2e−29↓ (NA) | Cold spot (global, local) | |
| X | A632/LC | 0.74 | 0.23 | Average spot |
| Oh43/LC | 0.40 | 0.11 | Average spot | |
| W64A/LC | 0.011 ↑(2.7×) | 0.89 | Hot spot (local) | |
| XI–XIII | A632/LC | 4.1e−17↓ (NA) | 2.9e−38↓ (NA) | Cold spot (global, local) |
| Oh43/LC | 2.8e−21↓ (51×) | 2.1e−86↓ (200×) | Cold spot (global, local) | |
| W64A/LC | 3.9e−25↓ (59×) | 1.6e−66↓ (150×) | Cold spot (global, local) |
P-values are shown for χ2 goodness-of-fit tests used to compare the observed recombination rate in each subinterval with (a) the average rate of recombination (cM/Mb) across the a1-sh2 interval in each genetic background and (b) the average rate of recombination in the genome (2.4 cM/Mb). This genome rate of 2.4 cM/Mb is an updated estimate based on a new maize genetic map that consists of 5917 cM (Lee et al. 2002) compared to the rate previously used (Yao et al. 2002). Arrows (↑ and ↓) denote a significantly higher or lower rate of recombination (P-value < 0.05), respectively, than the rate to which it was compared. For subintervals with significant P-values, the fold difference between rates is shown in parentheses.
Hot and cold spots are intervals that have higher and lower rates of recombination, respectively, than the rates to which they are compared. Global and local spots significantly differ from the average genome and the a1–sh2 interval rates of recombination, respectively. Average spots do not significantly differ from either the global or local rates.
For genetic backgrounds that have no recombination in a given subinterval, the fold difference with the rate to which it is compared cannot be calculated. NA, not applicable.