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Table 3 Summary of predicted locations of salinity tolerance candidate genes on linkage groups from three salmonids

From: Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss)

Gene Name

2R

3R

4R

S. alpinus

O. mykiss

G. aculeatus

S. salar

ATP1α1b

C

I

22a/23ab

4/12

12qa/16pa

CaSR

GH

VII

5/9

5

9p/20p

CFTRI & II

J/K

XIX

2/23

4d/19d

10q/18q/27q

cldn10e

C

I

22/23c

4/12

12q16q

COL1A1

E

XI

?

20

9q

 

E

V

17q/33

8

17q/22p

COL1A2

B

X

15

31

16q

GH1 & 2

E

XI

4q/11q

20a

2q/9qa/24

GHR

I

XIII

7/25

39

10p/19q

 

I

XIV

17q

28

8p

IGF1

K

IV

22/24a

3a/24a

7pa/15pa

IGF2

J/K

XIX

2a/23

4a/19a

10q/18q/27qa

NKCC1

I

XIII

7/25

?

10p/19q

 

I

XIV

17qa

28

?

SPARC

F/G

IV

10/12p

6

3q/25p

  1. Salinity tolerance candidate genes included in comparisons were: Na+/K+-ATPase α1b isoform (ATP1α1b), calcium-sensing receptor (CaSR), cystic fibrosis transmembrane conductance regulator-like anion channel isoforms I and II (CFTRI/II), claudin isoform 10e (cldn10e), collagen type 1 alpha 1 (COL1A1) and alpha 2 (COL1A2), growth hormone 1 and 2 (GH1 & 2), growth hormone receptor (GHR), insulin-like growth factors 1 (IGF1) and 2 (IGF2), Na+/K+/2Cl- isoform 1 (NKCC1), and secreted protein, acidic, rich in cysteine (SPARC). Synteny blocks were defined from comparative genomics of Atlantic salmon (Salmo salar), Arctic charr (Salvelinus alpinus), and rainbow trout (Oncorhynchus mykiss) with the stickleback (Gasterosteus aculeatus) genome. Some genes have already been mapped in 4R genomes (a): ATP1α1b[37, 38]; GH[13, 14]; IGF1 and IGF2[12]; NKCC1[15]. Mapped genes are included where synteny between 3R and 4R genomes is not apparent (b). In certain cases gene homology was assigned based on close proximity with ATP1α1b (c) or IGF2 (d) in the stickleback genome.