Table 2.
Open in new tab

Summary of male and female linkage maps for sockeye salmon. Arms for each LG were assigned based on centromere location. LG type denotes acrocentric (A) and metacentric (M) LGs. Orthology support is the number of loci shared between sockeye salmon and Chinook salmon for each orthologous relationship. See Brieuc et al. (2014) and Kodama et al. (2014) for additional information on orthologous relationships between Chinook salmon, coho salmon, rainbow trout, and Atlantic salmon. LG arm designations and cM positions for markers in this map do not correspond to Limborg et al. (2015), but markers are named the same

Sockeye LGLength (cM)# markersLG typeSockeye LG armChinook chromosomeCoho LGRainbow trout chromosomeAtlantic salmon chromosomeOrthology support
FemaleMaleFemaleMale
So182.8842.5717044ASo1aOts26Co26Omy22Ssa2112
So2200.0626.4429071MSo2aOts07pCo05aOmy07pSsa17qb6
MSo2bOts07qCo05bOmy07qSsa2211
So3155.99144.9628864MSo3aOts03qCo02bOmy03qSsa259
MSo3bOts03pCo02aOmy03pSsa02p7
So4129.91214.42272110MSo4aOts13pCo17aOmy18qSsa2710
MSo4bOts20Co23Omy05pSsa01qb8
So5150.684.7924667MSo5aOts08qCo15aOmy25q(Omy29)Ssa09qb8
MSo5bOts14pCo16bOmy18pSsa16qb7
So6137.72101.1519279MSo6aOts29Co11bOmy15pSsa295
MSo6bOts21Co19bOmy14qSsa05p5
So7133.68155.1523580MSo7aOts31Co14bOmy14pSsa14qb5
MSo7bOts16qCo17bOmy09qSsa15qb3
So8167.7992.9618660MSo8aOts15qCo09bOmy21qSsa07q3
MSo8bOts15pCo09aOmy21pSsa07p4
So9a78.12168ASo9aOts19Co22Omy02qSsa10qb13
So9.5a71.26116ASo9.5aOts10qCo30Omy08qSsa14qa9
So10169.6965.3326382MSo10aOts06qCo04bOmy01qSsa18qa4
MSo10bOts30Co28Omy10pSsa04q7
So11167.6133.7522667MSo11aOts13qCo15bOmy27Ssa20qb3
MSo11bOts34Co12bOmy10qSsa08q5
So12139.0184.1223282MSo12aOts08pCo14aOmy25pSsa09qa12
MSo12bOts10pCo16aOmy09pSsa18qb8
So13143.45117.44237123MSo13aOts18Co21Omy04qSsa06p6
MSo13bOts12pCo08aOmy11p&qSsa20qa9
So14161.9452.9627191MSo14aOts23Co13bOmy02pSsa05q1
MSo14bOts14qCo18aOmy24Ssa09qc8
So15169.4688.0929397MSo15aOts02pCo01aOmy17pSsa02q6
MSo15bOts02qCo01bOmy17qSsa12qb3
So1668.6180.0612653ASo16aOts25Co25Omy20p+qSSa08p&Ssa287
So17b138.9560.5317361MSo17aOts01pCo10aOmy04pSsa232
MSo17bOts01pCo10aOmy04pSsa2315
So18c150.1931.2423960MSo18aOts11qCo07bOmy19qSsa01p14
MSo18bOts11pCo07aOmy19pSsa04p5
So19107.9441.6215657MSo19aOts33pCo29OmySexSsa11qa9
MSo19bOts33qCo29OmySexSsa11qa3
So20144.99105.9227108MSo20aOts22Co24Omy16qSsa13qa7
MSo20bOts28Co27Omy28Ssa03p9
So21130.0125.8818964MSo21aOts32Co20bOmy13pSsa12qa4
MSo21bOts27Co10bOmy13qSsa06q3
So22152.3769.2224882MSo22aOts16pCo18bOmy11pSsa19qa6
MSo22bOts09pCo06aOmy12pSsa13qb9
So23152.6790.5522275MSo23aOts17Co19aOmy15qSsa17qa3
MSo23bOts24Co20aOmy16pSsa19qb5
So24129.68181.1122196MSo24aOts05qCo13aOmy05qSsa10qa9
MSo24bOts05pCo12aOmy08pSsa15qa4
So2584.565.8614563ASo25aOts06pCo04aOmy01pSsa16qa10
So26159.9398.0817051ASo26aOts09qCo06bOmy12qSsa03q4
So27225.3512.0028177MSo27aOts04qCo03bOmy06qSsa264
MSo27bOts04pCo03aOmy06pSsa2413
So28177.7414.96240108MSo28aOts12qCo08bOmy26Ssa11qb3
MSo28bOts01qCo011aOmy23Ssa01qa8
Total4082229163222179353
Sockeye LGLength (cM)# markersLG typeSockeye LG armChinook chromosomeCoho LGRainbow trout chromosomeAtlantic salmon chromosomeOrthology support
FemaleMaleFemaleMale
So182.8842.5717044ASo1aOts26Co26Omy22Ssa2112
So2200.0626.4429071MSo2aOts07pCo05aOmy07pSsa17qb6
MSo2bOts07qCo05bOmy07qSsa2211
So3155.99144.9628864MSo3aOts03qCo02bOmy03qSsa259
MSo3bOts03pCo02aOmy03pSsa02p7
So4129.91214.42272110MSo4aOts13pCo17aOmy18qSsa2710
MSo4bOts20Co23Omy05pSsa01qb8
So5150.684.7924667MSo5aOts08qCo15aOmy25q(Omy29)Ssa09qb8
MSo5bOts14pCo16bOmy18pSsa16qb7
So6137.72101.1519279MSo6aOts29Co11bOmy15pSsa295
MSo6bOts21Co19bOmy14qSsa05p5
So7133.68155.1523580MSo7aOts31Co14bOmy14pSsa14qb5
MSo7bOts16qCo17bOmy09qSsa15qb3
So8167.7992.9618660MSo8aOts15qCo09bOmy21qSsa07q3
MSo8bOts15pCo09aOmy21pSsa07p4
So9a78.12168ASo9aOts19Co22Omy02qSsa10qb13
So9.5a71.26116ASo9.5aOts10qCo30Omy08qSsa14qa9
So10169.6965.3326382MSo10aOts06qCo04bOmy01qSsa18qa4
MSo10bOts30Co28Omy10pSsa04q7
So11167.6133.7522667MSo11aOts13qCo15bOmy27Ssa20qb3
MSo11bOts34Co12bOmy10qSsa08q5
So12139.0184.1223282MSo12aOts08pCo14aOmy25pSsa09qa12
MSo12bOts10pCo16aOmy09pSsa18qb8
So13143.45117.44237123MSo13aOts18Co21Omy04qSsa06p6
MSo13bOts12pCo08aOmy11p&qSsa20qa9
So14161.9452.9627191MSo14aOts23Co13bOmy02pSsa05q1
MSo14bOts14qCo18aOmy24Ssa09qc8
So15169.4688.0929397MSo15aOts02pCo01aOmy17pSsa02q6
MSo15bOts02qCo01bOmy17qSsa12qb3
So1668.6180.0612653ASo16aOts25Co25Omy20p+qSSa08p&Ssa287
So17b138.9560.5317361MSo17aOts01pCo10aOmy04pSsa232
MSo17bOts01pCo10aOmy04pSsa2315
So18c150.1931.2423960MSo18aOts11qCo07bOmy19qSsa01p14
MSo18bOts11pCo07aOmy19pSsa04p5
So19107.9441.6215657MSo19aOts33pCo29OmySexSsa11qa9
MSo19bOts33qCo29OmySexSsa11qa3
So20144.99105.9227108MSo20aOts22Co24Omy16qSsa13qa7
MSo20bOts28Co27Omy28Ssa03p9
So21130.0125.8818964MSo21aOts32Co20bOmy13pSsa12qa4
MSo21bOts27Co10bOmy13qSsa06q3
So22152.3769.2224882MSo22aOts16pCo18bOmy11pSsa19qa6
MSo22bOts09pCo06aOmy12pSsa13qb9
So23152.6790.5522275MSo23aOts17Co19aOmy15qSsa17qa3
MSo23bOts24Co20aOmy16pSsa19qb5
So24129.68181.1122196MSo24aOts05qCo13aOmy05qSsa10qa9
MSo24bOts05pCo12aOmy08pSsa15qa4
So2584.565.8614563ASo25aOts06pCo04aOmy01pSsa16qa10
So26159.9398.0817051ASo26aOts09qCo06bOmy12qSsa03q4
So27225.3512.0028177MSo27aOts04qCo03bOmy06qSsa264
MSo27bOts04pCo03aOmy06pSsa2413
So28177.7414.96240108MSo28aOts12qCo08bOmy26Ssa11qb3
MSo28bOts01qCo011aOmy23Ssa01qa8
Total4082229163222179353

aLG So9 is the sex chromosome for sockeye salmon and was represented by 2 acrocentric LGs in the female (So9, So9.5) and a single metacentric LG in the male (So9). LG So9 in the male contained 107 markers and was 109.5 cM long. LG So9 is denoted as 9A_(X2) in (Limborg et al. 2015), and So9.5a is denoted as 9B_(X1).

bDesignated as acrocentric in Limborg et al. (2015).

cAssembled as separate LGs in Limborg et al. (2015).

Table 2.
Open in new tab

Summary of male and female linkage maps for sockeye salmon. Arms for each LG were assigned based on centromere location. LG type denotes acrocentric (A) and metacentric (M) LGs. Orthology support is the number of loci shared between sockeye salmon and Chinook salmon for each orthologous relationship. See Brieuc et al. (2014) and Kodama et al. (2014) for additional information on orthologous relationships between Chinook salmon, coho salmon, rainbow trout, and Atlantic salmon. LG arm designations and cM positions for markers in this map do not correspond to Limborg et al. (2015), but markers are named the same

Sockeye LGLength (cM)# markersLG typeSockeye LG armChinook chromosomeCoho LGRainbow trout chromosomeAtlantic salmon chromosomeOrthology support
FemaleMaleFemaleMale
So182.8842.5717044ASo1aOts26Co26Omy22Ssa2112
So2200.0626.4429071MSo2aOts07pCo05aOmy07pSsa17qb6
MSo2bOts07qCo05bOmy07qSsa2211
So3155.99144.9628864MSo3aOts03qCo02bOmy03qSsa259
MSo3bOts03pCo02aOmy03pSsa02p7
So4129.91214.42272110MSo4aOts13pCo17aOmy18qSsa2710
MSo4bOts20Co23Omy05pSsa01qb8
So5150.684.7924667MSo5aOts08qCo15aOmy25q(Omy29)Ssa09qb8
MSo5bOts14pCo16bOmy18pSsa16qb7
So6137.72101.1519279MSo6aOts29Co11bOmy15pSsa295
MSo6bOts21Co19bOmy14qSsa05p5
So7133.68155.1523580MSo7aOts31Co14bOmy14pSsa14qb5
MSo7bOts16qCo17bOmy09qSsa15qb3
So8167.7992.9618660MSo8aOts15qCo09bOmy21qSsa07q3
MSo8bOts15pCo09aOmy21pSsa07p4
So9a78.12168ASo9aOts19Co22Omy02qSsa10qb13
So9.5a71.26116ASo9.5aOts10qCo30Omy08qSsa14qa9
So10169.6965.3326382MSo10aOts06qCo04bOmy01qSsa18qa4
MSo10bOts30Co28Omy10pSsa04q7
So11167.6133.7522667MSo11aOts13qCo15bOmy27Ssa20qb3
MSo11bOts34Co12bOmy10qSsa08q5
So12139.0184.1223282MSo12aOts08pCo14aOmy25pSsa09qa12
MSo12bOts10pCo16aOmy09pSsa18qb8
So13143.45117.44237123MSo13aOts18Co21Omy04qSsa06p6
MSo13bOts12pCo08aOmy11p&qSsa20qa9
So14161.9452.9627191MSo14aOts23Co13bOmy02pSsa05q1
MSo14bOts14qCo18aOmy24Ssa09qc8
So15169.4688.0929397MSo15aOts02pCo01aOmy17pSsa02q6
MSo15bOts02qCo01bOmy17qSsa12qb3
So1668.6180.0612653ASo16aOts25Co25Omy20p+qSSa08p&Ssa287
So17b138.9560.5317361MSo17aOts01pCo10aOmy04pSsa232
MSo17bOts01pCo10aOmy04pSsa2315
So18c150.1931.2423960MSo18aOts11qCo07bOmy19qSsa01p14
MSo18bOts11pCo07aOmy19pSsa04p5
So19107.9441.6215657MSo19aOts33pCo29OmySexSsa11qa9
MSo19bOts33qCo29OmySexSsa11qa3
So20144.99105.9227108MSo20aOts22Co24Omy16qSsa13qa7
MSo20bOts28Co27Omy28Ssa03p9
So21130.0125.8818964MSo21aOts32Co20bOmy13pSsa12qa4
MSo21bOts27Co10bOmy13qSsa06q3
So22152.3769.2224882MSo22aOts16pCo18bOmy11pSsa19qa6
MSo22bOts09pCo06aOmy12pSsa13qb9
So23152.6790.5522275MSo23aOts17Co19aOmy15qSsa17qa3
MSo23bOts24Co20aOmy16pSsa19qb5
So24129.68181.1122196MSo24aOts05qCo13aOmy05qSsa10qa9
MSo24bOts05pCo12aOmy08pSsa15qa4
So2584.565.8614563ASo25aOts06pCo04aOmy01pSsa16qa10
So26159.9398.0817051ASo26aOts09qCo06bOmy12qSsa03q4
So27225.3512.0028177MSo27aOts04qCo03bOmy06qSsa264
MSo27bOts04pCo03aOmy06pSsa2413
So28177.7414.96240108MSo28aOts12qCo08bOmy26Ssa11qb3
MSo28bOts01qCo011aOmy23Ssa01qa8
Total4082229163222179353
Sockeye LGLength (cM)# markersLG typeSockeye LG armChinook chromosomeCoho LGRainbow trout chromosomeAtlantic salmon chromosomeOrthology support
FemaleMaleFemaleMale
So182.8842.5717044ASo1aOts26Co26Omy22Ssa2112
So2200.0626.4429071MSo2aOts07pCo05aOmy07pSsa17qb6
MSo2bOts07qCo05bOmy07qSsa2211
So3155.99144.9628864MSo3aOts03qCo02bOmy03qSsa259
MSo3bOts03pCo02aOmy03pSsa02p7
So4129.91214.42272110MSo4aOts13pCo17aOmy18qSsa2710
MSo4bOts20Co23Omy05pSsa01qb8
So5150.684.7924667MSo5aOts08qCo15aOmy25q(Omy29)Ssa09qb8
MSo5bOts14pCo16bOmy18pSsa16qb7
So6137.72101.1519279MSo6aOts29Co11bOmy15pSsa295
MSo6bOts21Co19bOmy14qSsa05p5
So7133.68155.1523580MSo7aOts31Co14bOmy14pSsa14qb5
MSo7bOts16qCo17bOmy09qSsa15qb3
So8167.7992.9618660MSo8aOts15qCo09bOmy21qSsa07q3
MSo8bOts15pCo09aOmy21pSsa07p4
So9a78.12168ASo9aOts19Co22Omy02qSsa10qb13
So9.5a71.26116ASo9.5aOts10qCo30Omy08qSsa14qa9
So10169.6965.3326382MSo10aOts06qCo04bOmy01qSsa18qa4
MSo10bOts30Co28Omy10pSsa04q7
So11167.6133.7522667MSo11aOts13qCo15bOmy27Ssa20qb3
MSo11bOts34Co12bOmy10qSsa08q5
So12139.0184.1223282MSo12aOts08pCo14aOmy25pSsa09qa12
MSo12bOts10pCo16aOmy09pSsa18qb8
So13143.45117.44237123MSo13aOts18Co21Omy04qSsa06p6
MSo13bOts12pCo08aOmy11p&qSsa20qa9
So14161.9452.9627191MSo14aOts23Co13bOmy02pSsa05q1
MSo14bOts14qCo18aOmy24Ssa09qc8
So15169.4688.0929397MSo15aOts02pCo01aOmy17pSsa02q6
MSo15bOts02qCo01bOmy17qSsa12qb3
So1668.6180.0612653ASo16aOts25Co25Omy20p+qSSa08p&Ssa287
So17b138.9560.5317361MSo17aOts01pCo10aOmy04pSsa232
MSo17bOts01pCo10aOmy04pSsa2315
So18c150.1931.2423960MSo18aOts11qCo07bOmy19qSsa01p14
MSo18bOts11pCo07aOmy19pSsa04p5
So19107.9441.6215657MSo19aOts33pCo29OmySexSsa11qa9
MSo19bOts33qCo29OmySexSsa11qa3
So20144.99105.9227108MSo20aOts22Co24Omy16qSsa13qa7
MSo20bOts28Co27Omy28Ssa03p9
So21130.0125.8818964MSo21aOts32Co20bOmy13pSsa12qa4
MSo21bOts27Co10bOmy13qSsa06q3
So22152.3769.2224882MSo22aOts16pCo18bOmy11pSsa19qa6
MSo22bOts09pCo06aOmy12pSsa13qb9
So23152.6790.5522275MSo23aOts17Co19aOmy15qSsa17qa3
MSo23bOts24Co20aOmy16pSsa19qb5
So24129.68181.1122196MSo24aOts05qCo13aOmy05qSsa10qa9
MSo24bOts05pCo12aOmy08pSsa15qa4
So2584.565.8614563ASo25aOts06pCo04aOmy01pSsa16qa10
So26159.9398.0817051ASo26aOts09qCo06bOmy12qSsa03q4
So27225.3512.0028177MSo27aOts04qCo03bOmy06qSsa264
MSo27bOts04pCo03aOmy06pSsa2413
So28177.7414.96240108MSo28aOts12qCo08bOmy26Ssa11qb3
MSo28bOts01qCo011aOmy23Ssa01qa8
Total4082229163222179353

aLG So9 is the sex chromosome for sockeye salmon and was represented by 2 acrocentric LGs in the female (So9, So9.5) and a single metacentric LG in the male (So9). LG So9 in the male contained 107 markers and was 109.5 cM long. LG So9 is denoted as 9A_(X2) in (Limborg et al. 2015), and So9.5a is denoted as 9B_(X1).

bDesignated as acrocentric in Limborg et al. (2015).

cAssembled as separate LGs in Limborg et al. (2015).

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