Synteny patterns between the Atlantic salmon ( Salmo salar ) mapping panel and chromosomes that contain salinity tolerance candidate genes in three-spined stickleback ( Gasterosteus aculeatus ). Synteny was established using the Atlantic salmon linkage map and the BROAD S1 stickleback genome sequence from ENSEMBL v59 - v61. Atlantic salmon linkage groups (grey) and stickleback chromosomes (red) are standardized to 100 units. Red synteny bands indicate linkage groups that contain salinity tolerance QTL. Chromosomes and linkage groups are arranged in a p-arm to q-arm clockwise orientation unless otherwise noted. The positions of centromeres (black bands) on metacentric linkage groups AS-4/11/12/17/24/28q are undefined, as is the orientation of AS-28q/33. Candidate genes include: Na+/K+-ATPase α-isoform (ATP1α1) and -α1b isoform (ATP1α1b), calcium-sensing receptor (CaSR), cystic fibrosis transmembrane conductance regulator-like anion channel (CFTR), claudin isoform 10e (cldn10e), collagen type 1 alpha 1 (COL1A1) and alpha 2 (COL1A2), growth hormone (GH), 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). The precise positions of candidate genes on stickleback chromosomes are denoted by connection lines (blue), as are genes mapped in Atlantic salmon[12, 38]. Predicted gene positions on Atlantic salmon linkage groups are represented by labels without connection lines. IGF1 and NKCC1 map to AS-24 and AS-17q, respectively, however their precise positions are unknown. Ideogram created using Circos.