Table 3. Allele counts of the two homeolog pairs displaying pseudolinkage within females.
| Marker Pair | Genotypes | Linkage Group | Parental Phases (Marker A/Marker B) | Recombinant Phases (Marker A/Marker B) | Chi-Squared | P-value | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker A | Marker B | Marker A | Marker B | Marker A | Marker B | Alleles | Count | Alleles | Count | ||
| TP47181 | TP21253 | G,C | A,G | AC13 | Pseudolink | G/A | 32 | C/A | 23 | 18.7 | 3.20E−04 |
| C/G | 25 | G/G | 5 | ||||||||
| TP21253 | TP30908 | A,G | T,C | Pseudolink | AC34 | A/T | 43 | A/C | 12 | 36 | 7.50E−08 |
| G/C | 23 | G/T | 7 | ||||||||
| TP47181 | TP30908 | G,C | T,C | AC13 | AC34 | G/T | 23 | C/T | 27 | 4.2 | 0.243 |
| C/C | 21 | G/C | 14 | ||||||||
| TP10591 | TP15996 | T,G | G,A | AC21 | Pseudolink | T/G | 14 | G/G | 4 | 15.8 | 0.0013 |
| G/A | 13 | T/A | 1 | ||||||||
| TP15996 | TP32826 | G,A | A,T | Pseudolink | AC01 | G/A | 18 | A/A | 0 | 33 | 3.20E−07 |
| A/T | 14 | G/T | 0 | ||||||||
| TP10591 | TP32826 | T,G | A,T | AC21 | AC01 | T/A | 22 | G/A | 23 | 7.9 | 0.049 |
| G/T | 27 | T/T | 10 | ||||||||
These instances appear to result from an excess of parental phase genotypes. Flanking markers from both linkage groups with the most complete genotypes, along with the principle marker causing pseudolinkage, are displayed. Note, for AC21/AC01, the marker causing pseudolinkage (TP15996) was heterozygous in both parents (ab X ab cross). Therefore, the phases for half of the progeny could not be ascertained. Chi-squared goodness of fit tests were performed for each pair of alleles, comparing the observed genotype frequencies to a null hypothesis of a 1:1:1:1 genotype distribution.