Table 3.
Counts of markers used for the second round of the linkage analysis
| Chromosome | Possible AOxBO nulls | Total No. of markers in JM input file | No. carried to MDS analysis | Mapped markers | Latham (ABxAA) | Moy (AAxAB) | Both (ABxAB +ABxCD) | Null (AOxAB or ABxAO) | Null (AOxBO) | Length (cM) | HMM_mean for MDS order | HMM_mean after swaps |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LG1 | 25 | 471 | 331 | 295 | 223 | 33 | 7 + 1 | 19 | 12 | 114.1 | 1.48 | 1.25 |
| LG2 | 65 | 737 | 494 | 456 | 286 | 90 | 10 + 4 | 34 | 32 | 107.1 | 1.65 | 1.42 |
| LG3 | 21 | 933 | 603 | 557 | 447 | 45 | 9 + 4 | 39 | 13 | 128.2 | 1.77 | 1.67 |
| LG4a | 79 | 667 | 448 | 435 | 253 | 70 | 25 + 5 | 39 | 43 | 91.5 | 1.29 | 1.25 |
| LG5 | 83 | 739 | 509 | 486 | 287 | 66 | 18 + 8 | 63 | 44 | 85.4 | 1.42 | 1.27 |
| LG6 | 12 | 514 | 369 | 315 | 284 | 15 | 1 + 1 | 9 | 5 | 88.6 | 1.95 | 1.52 |
| LG7 | 16 | 396 | 252 | 243 | 216 | 11 | 0 | 10 | 6 | 100.2 | 1.93 | 1.55 |
HMM_mean denotes the mean number of recombinations inferred using a HMM
a The LG4 map is fitted using LOD2 weighting and 2d MDS, which fitted better than LOD2 weighting and 3d MDS