Table 3 Homeologous chromosome pairs identified for Chinook salmon, Atlantic salmon, or both
Chinook Salmon HomeologsChinook Salmon Linkage GroupsNumber of Marker Pairs Supporting Homeolog PairingsHomeology in Atlantic SalmonNumber of Markers and Type of Support for the Homeology in Lien et al. (2011)Rainbow Trout Homeologs
1. High numbers of duplicated markers in Chinook and Atlantic salmon
 Ots03p-Ots23Ck05-Ck2511Ssa02p-Ssa05q39 MSV5Omy03p-Omy02p
 Ots15p-Ots17Ck23-Ck0113Ssa07q-Ssa17qb33 MSV5Omy21p-Omy15q
 Ots09q-Ots27Ck02-Ck319Ssa03q-Ssa06q7 MSV5Omy12q-Omy13q
 Ots11p-Ots34Ck15-Ck323Ssa04p-Ssa08q14 MSV5Omy19p-Omy10q
2. Higher numbers of duplicated markers in Chinook salmon compared with Atlantic salmon
 Ots01q-Ots06qCk13-Ck1711Ssa01qa-Ssa18qaBLASTOmy23-Omy01q
 Ots02q-Ots32Ck12-Ck3015Ssa02q-Ssa12qa1 MSV5Omy17p-Omy13p
 Ots04q-Ots12qCk08-Ck1819Ssa26-Ssa11qaa2 MSV5Omy06q-Omy26
 Ots07p-Ots14pCk16-Ck1017Ssa17qa-Ssa16qbaBLASTOmy07p-Omy18p
3. Homeologies not observed in Chinook salmon and supported by only one duplicated marker in Atlantic salmon
 Ots22-Ots16qaCk34-Ck040Ssa13qa-Ssa15qba1 MSV5Omy16q-Omy09q
 Ots24-Ots29aCk27-Ck030Ssa19qb-Ssa29a1 MSV5Omy16p-Omy15p
  • Chinook salmon linkage groups, number of pairs of markers supporting the homeologies, corresponding homeologs in Atlantic salmon and type of support for the homeologies in Lien et al. (2011), and corresponding homeologies in rainbow trout are represented. Support for the homeologies in Lien et al. (2011): duplicated SNP loci with both paralog polymorphic (MSV5) or alignment-based using BLAST within Atlantic salmon or with stickleback. Note: we have corrected the homeology between Omy15q and Omy21p that was incorrectly reported as being between Omy15q and Omy21q in Phillips et al. (2006) and in subsequent studies (Phillips, personal communication). SNP, single-nucleotide polymorphism.

  • a Homeology between two acrocentric chromosomes.