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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.