Table 1. QTL identified with the combined analysis and their inferred phylogenetic partitions.
| Phenotype | Chr. | Position (cM) | LOD score | Position (Mb) | 1.5 LOD int. (Mb) | Partition | Posterior probability |
|---|---|---|---|---|---|---|---|
| Amorphous sperm head | 2 | 66.0 | 4.70 | 168.3 | 131.9–178.7 | C|MD | 1.00 |
| 5a | 50.0 | 3.95 | 120.5 | 88.3–135.7 | D|MC | 0.94 | |
| 9 | 2.0 | 7.73 | 13.3 | 3.1–30.2 | C|MD | 1.00 | |
| X | 20.0 | 11.46 | 60.8 | 46.9–95.2 | D|MC | 0.97 | |
| PAR | 4.0c | 3.87 | — | — | C|MD | 0.99 | |
| Distal bent tail | 3 | 16.0 | 5.58 | 42.3 | 16.2–67.9 | M|CD | 1.00 |
| 5 | 72.0 | 8.64 | 147.3 | 133.7–148.4 | M|CD | 1.00 | |
| X | 23.0 | 8.68 | 67.7 | 56.2–93.3 | M|CD | 1.00 | |
| Headless/tailless | 15 | 0.0 | 3.96 | 16.5 | 16.5–46.7 | M|CD | 0.96 |
| X | 23.0 | 10.10 | 67.7 | 51.5–97.1 | D|MC | 0.99 | |
| PAR | 0.0 | 3.95 | — | — | C|MD | 0.98 | |
| Proximal bent tail | 10 | 8.0 | 4.86 | 48.5 | 33.8–81.9 | M|CD | 0.97 |
| X | 31.5 | 10.05 | 90.8 | 56.2–97.1 | M|CD | 0.98 | |
| Xb | 58.0 | 3.36 | 146.9 | 95.2–62.9 | C|MD | — | |
| Testis weight | 2 | 28.6 | 8.29 | 80.6 | 69.7–08.3 | D|MC | 1.00 |
| 4 | 47.1 | 11.51 | 108.9 | 57.8–114.3 | D|MC | 0.98 | |
| 10 | 16.0 | 7.21 | 67.8 | 58.3–88.1 | M|CD | 0.94 | |
| PAR | 2.0 | 4.51 | — | — | C|MD | 0.99 | |
| Sperm density | 17 | 13.5 | 6.02 | 29.9 | 3.1–64.8 | M|CD | 1.00 |
| X | 4.0 | 4.22 | 20.7 | 10.2–56.2 | D|MC | 0.92 | |
| Xb | 56.0 | 3.82 | 142.4 | 86.6–162.9 | C|MD | — | |
| PAR | 2.0 | 6.06 | — | — | C|MD | 1.00 | |
| Sperm head PC1 | 2b | 76.0 | 4.00 | 177.0 | 143.8–179.0 | C|MD | — |
| 14a | 46.0 | 10.26 | 96.8 | 89.4–104.1 | M|CD | 1.00 | |
| 19a | 30.0 | 17.94 | 39.1 | 33.2–44.9 | M|CD | 1.00 | |
| Xb | 12.0 | 4.18 | 41.9 | 10.2–162.9 | C|MD | — | |
| X | 20.0 | 85.32 | 60.8 | 51.5–65.5 | M|CD | 1.00 | |
| PAR | 6.0 | 8.52 | — | — | C|MDd | 0.93 | |
| Sperm head PC2 | X | 18.0 | 10.80 | 56.2 | 45.1–70.3 | D|MC | 1.00 |
| PAR | 0.0 | 8.35 | — | — | C|MD | 0.51 | |
| Seminiferous tubule area | 2 | 26.0 | 7.25 | 76.3 | 57.7–102.4 | C|MD | 0.99 |
| 8 | 51.1 | 4.33 | 125.0 | 113.0–130.8 | C|MD | 0.96 | |
| 16a | 24.4 | 4.09 | 97.2 | 90.4–97.2 | D|MC | 0.93 | |
| 18 | 26.0 | 4.62 | 68.3 | 57.8–73.4 | M|CD | 0.97 | |
| X | 65.2 | 4.46 | 162.9 | 142.4–162.9 | C|MD | 1.00 | |
| PAR | 0.0 | 8.29 | — | — | C|MD | 1.00 | |
| Total abnormal sperm | 5 | 64.0 | 4.96 | 137.7 | 123.6–148.4 | M|CD | 0.75 |
| 15 | 4.0 | 4.66 | 28.6 | 16.5–68.7 | M|CD | 0.99 | |
| X | 34.0 | 15.98 | 93.3 | 56.2–99.1 | D|MC | 1.00 | |
| PAR | 0.0 | 5.44 | — | — | C|MD | 1.00 |
Posterior probabilities of the partitions were calculated using the approximate Bayes procedure in Broman et al. (2012). D|MC, M|CD, and C|MD describe the domesticus|musculus,castaneus; musculus|castaneus,domesticus; and castaneus|musculus,domesticus partitions, respectively. PAR, pseudoautosomal region.
a
QTL newly identified by the combined analysis.
b
QTL detected in separate analyses of the two crosses but not detected by the combined analysis.
c
PAR genetic positions are relative to the beginning of the region, not the X chromosome.
d
Sperm morphology PC1 assigned to D|MC in PhyloQTL, but likely in error due to the high LOD score of QTL on the X in the musculus × domesticus cross (see text).