Table 1. Assignment of Chinook genetic linkage groups to chromosomes.
| Chromosome | Arm | CK LG | Markers | BAC Clone | RT Chromosome | RT LGa |
|---|---|---|---|---|---|---|
| Ots1 | 1p | CK13 | BHMS577 | 102N02a | Omy4p | 24p |
| 1q | CarbE1 | 86E19o | Omy23 | 30 | ||
| Ots2 | 2p | CK12 | OMM1300 | 318G19s | Omy 17 | 29q |
| 2q | MHC2 | 4C02o | Omy 17 | 29p | ||
| Ots3 | 3p | CK05 | Oneu102 | 18G23a | Omy3p | 31p |
| Ots4 | 4p | CK8 | OMM1204 | 113I17s | Omy 6p | 10p |
| 4q | B6 | B6o | Omy6q | 10q | ||
| Ots5 | 5p | CK11 | TRSHA | 354I19s | Omy8p | 23p |
| 5q | OMM1195 | 107J7s | Omy5q | 8q | ||
| Ots6 | 6q | CK17 | FGF6 | 122J17o | Omy1q | 6q |
| Ots7 | 7p | CK16 | CD83 | 17c24o | Omy7p | 12p |
| 7q | NrampB | 146I11o | Omy7q | 12q | ||
| Ots8 | 8p | CK14 | G9 | G9o | Omy25 | 4 |
| 8q | TCRb | 270C12o | Omy29 | 25 | ||
| Ots9 | 9q | CK02 | GH1 | 167I21o | Omy12q | 9q |
| Ots10 | 10p | CK20 | CD4 | 275D24s | Omy9p | 21p |
| 10q | OMM1295 | 146Hs | Omy8q | 23q | ||
| Ots11 | 11p | CK15 | OMM1134a | 271M12s | Omy19p | 14p |
| 11q | BHMS281 | 198E23a | Omy19q | 14q | ||
| Ots12 | 12p | CK18 | OMM3042 | C9o | Omy11q | 19p |
| 12p | OMM3020 | F1o | Omy11p | 19p | ||
| 12q | B6a | B6o | Omy26 | 18 | ||
| Ots13 | 13p | CK7 | MHCIA | 24K3o | Omy18q | 16q |
| 13q | Somatolactin | 193J21o | Omy27 | 11 | ||
| Ots14 | 14q | CK10 | Omi66 | 366K10o | Omy24 | 26 |
| Ots15 | 15p | CK23 | LDHB | 176H21s | Omy21p | 15p |
| Ots16 | 16q | CK04 | OMM1145 | 520I2s | Omy9q | 21 |
| Ots17 | 17q | CKSex | Omy7INRA | 197M11s | Omy15q | 7q |
| Ots18 | CK33 | Ssa43 | 322O19a | Omy4q | 24q | |
| Ots19 | CK22 | MetB | 127C24o | Om2q | 27q | |
| Ots20 | CK28 | Ssa2 | 88023a | Omy5p | 8p | |
| Ots21 | CK09 | BHMS206 | 26A22a | Omy14q | 3q | |
| Ots22 | Ck34 | OMM1340 | 277k4o | Omy16q | 22q | |
| Ots23 | Ck25 | TAP1 | 34E19o | Omy2p | 27p | |
| Ots24 | CK27 | OMM5162 | 25G06o | Omy16p | 22p | |
| Ots25 | CK06 | OMM1199 | 33GD8o | Omy20q | 17q | |
| Ots26 | CK21 | OMM1010 | 231J20s | Omy22 | 5 | |
| Ots27 | Ck31 | OMM3006 | C11o | Omy13 | 2q | |
| Ots28 | CK24 | OMM1020 | 239K12s | Omy28 | 13 | |
| Ots29 | Ck03 | OMM1087 | 340I3s | Omy15p | 7p | |
| Ots30 | CK29 | OMM1348 | 117A19s | Omy10p | 20p | |
| Ots31 | CK26 | MHC1B | 20C13o | Omy14p | 3p | |
| Ots32 | CK30 | Omy27DU | 118G14o | Omy13p | 2p | |
| Ots33 | CK19 | SCAR163 | 171H7s | SEX | 1 | |
| Ots34 | CK32 | OMM1134a | 271M12s | 10q | 20q |
Chromosomes are listed from the largest to the smallest, with Ots1–16 being metacentric (bi-armed) chromosomes and Ots 17–34 being acrocentric (uni-armed) chromosomes. Linkage groups correspond to those on the genetic map in the companion article (Naish et al. 2013). In the future, the linkage groups will be renamed to correspond to the chromosome numbers. B6 was a random clone isolated from the RT library, which goes to two telomeres. Ots 18–34 are single-armed chromosomes. a, Atlantic salmon library (CHORIO); o, Oregon State University BAC library; s, Swanson BAC library; p, short arm of the metacentric (bi-armed) chromosomes; q, long arm of the metacentric (bi-centric) chromosomes.
The rainbow trout LGs were used before the genetic map was connected to the chromosomes. In the recent maps (Rexroad et al. 2008; Palti et al. 2004; Phillips et al. 2009), the linkage groups are numbered the same as the chromosomes. The p and q include Ots1–Ots16 for Chinook salmon and Omy1–Omy22 for rainbow trout. Chinook chromosomes Ots17–Ots34 and rainbow trout chromosomes Omy23–Omy30 are acrocentric single-armed chromosomes. o=OSU library, s=Swanson library, and a=Atlantic salmon CHORIO library. The BACs from the “a” library were previously used as probes on rainbow trout chromosomes.