Table 3.
Identified candidate genes for freshwater vs. marine adaptation in threespine stickleback
| SNP ID | Chr_position | F ST | Candidate gene | Related function | MG | SB | KF | OM | OF |
|---|---|---|---|---|---|---|---|---|---|
| 5812 | I_14574107 | 0,5 | Teneurin transmembrane protein 1 (ODZ1 ) | morphogenesis | × | ||||
| 5939 | I_16513837 | 0,57 | Claudin 4 (CLDN4) | internal organ development | × | ||||
| 28321 | I_21607623 | 0,27 | insulin-like growth factor binding protein 2 (IGFBP2)* | growth and developmental rates | × | ||||
| 28526 | I_4931967 | 0,89 | maltase-glucoamylase (alpha-glucosidase) (MGAM) | digestion | × | ||||
| 6844 | I_4932075 | 0,85 | maltase-glucoamylase (alpha-glucosidase) (MGAM) | digestion | × | ||||
| 1955 | II_22061028 | 0,81 | microfibrillar-associated protein 1 (MFAP1) | elastik fibres and collagen formation | × | ||||
| 2113 | II_3125972 | 0,8 | ADAM metallopeptidase with thrombospondin type 1 motif, 18 (ADAMTS18)* | tumor supressor, eye development | × | ||||
| 2114 | II_3182440 | 0,72 | testis-specific serine kinase 3 (TSSK3)* | germ cell development, protein kinase activity | × | ||||
| 276 | III_13446716 | 0,67 | RUN and SH3 domain containing 1 (RUSC1)* | neuronal differentiation, cytoplasmic development | × | × | |||
| 3231 | IV_20387384 | 0,71 | family with sequence similarity 19 (chemokine (C-C motif)-like) (FAM19A1) | regulators of immune and nervous cells | × | ||||
| 3644 | IV_29334535 | 0,7 | coiled-coil-helix-coiled-coil-helix domain containing 3 (CHCHD3) | crista integrity and mitochondrial function | × | ||||
| 27608 | IV_29334612 | 0,78 | coiled-coil-helix-coiled-coil-helix domain containing 3 (CHCHD3) | crista integrity and mitochondrial function | × | ||||
| 3851 | IV_3216905 | 0,7 | polycomb group ring finger 1 (PCGF1) | early embryonic development | × | ||||
| 4073 | IV_5292424 | 0,4 | vascular endothelial growth factor B (VEGFB) | vascular endothelial growth | × | ||||
| 27768 | IV_6660266 | 0,77 | family with sequence similarity 70, member A (FAM70A) | transmembrane protein | × | ||||
| 27791 | IV_8128962 | 0,7 | heparan sulfate (glucosamine) 3-O-sulfotransferase 1 (HS3ST1) | synthesis of anticoagulant | × | ||||
| 29903 | V_8795372 | 0,65 | retinol binding protein 4, plasma (RBP4)* | cardiac regulation, kidney filtration, retinal binding | × | × | |||
| 10131 | VI_12603660 | 0,68 | glutamate receptor, ionotropic, delta 1 (GRID1) | nervous system | × | ||||
| 8466 | VII_11202861 | 0,61 | lens intrinsic membrane protein 2 (LIM2) | eye development and cataractogenesis | × | ||||
| 9026 | VII_19985290 | 0,79 | SCC-112 | immune responses | × | ||||
| 9206 | VII_22946194 | 0,91 | RAD50 | cell growth and viability | × | ||||
| 7745 | VIII_17638021 | 0,82 | tumor protein p63 (TP73L) | regulation of epithelial morphogenesis | × | ||||
| 7807 | VIII_18320215 | 0,67 | WW and C2 domain containing 1 (Wwc2)* | memory performance, regulation of organ growth | × | × | |||
| 7808 | VIII_18320304 | 0,76 | WW and C2 domain containing 1 (Wwc2)* | memory performance, regulation of organ growth | × | × | |||
| 8351 | VIII_9101385 | 0,52 | nephrosis 2, idiopathic, steroid-resistant (NPHS2)* | renal regulation, cell development | × | × | |||
| 4521 | IX_13007542 | 0,4 | phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1)* | cell signaling and lipid metabolism | × | ||||
| 5200 | IX_5019009 | 0,78 | retinoblastoma binding protein 6 (RBBP6)* | suppresses cellular proliferation, embryonic development | × | ||||
| 5238 | IX_5337004 | 0,77 | KIAA0922 | immune responses | × | ||||
| 23341 | X_11668366 | 0,36 | protein kinase (cAMP-dependent, catalytic) inhibitor beta (PKIB) | urinary regulation | × | ||||
| 33387 | X_6967185 | 0,26 | Transcription factor EF1 (EF1) | regulates dendritic spine morphogenesis | × | ||||
| 16649 | XI_12761116 | 0,69 | ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 (ATP2A2)* | contraction/relaxation muscle cycle, heart regulation | × | ||||
| 16691 | XI_13340957 | 0,7 | transcription elongation factor B (SIII), polypeptide 2 (TCEB2) | renal regulation | × | ||||
| 31479 | XI_9810247 | 0,5 | ATP-binding cassette, sub-family A (ABC1), member 3 (ABCA3)* | programmed cell death, membrane regulation | × | × | |||
| 13340 | XII_12843029 | 0,78 | COMM domain containing 7 (COMMD7) | hepato cellular growth | × | ||||
| 13682 | XII_18204005 | 0,68 | TPX2, microtubule-associated (TPX2) | cell development | × | ||||
| 13744 | XII_3061560 | 0,6 | keratin 18 (KRT18) | internal organ development | × | ||||
| 30542 | XII_8981405 | 0,39 | erythrocyte membrane protein band 4.1-like 1 (EPB41L1)* | neuronal plasma regulation, cytoskeleton regulation | × | × | |||
| 14188 | XII_9924630 | 0,54 | suppression of tumorigenicity 5 (ST5) | immune responses | × | ||||
| 11996 | XIII_11719547 | 0,47 | transient receptor potential cation channel, subfamily M, member 3 (TRPM3) | mediates calcium entry | × | ||||
| 19976 | XVI_18491 | 0,47 | MMADHC (uc010fnu.1) (CR595331) | vitamine B12 metabolism | × | ||||
| 20063 | XVI_3012006 | 0,24 | sodium leak channel, non-selective (VGCNL1) | neuronal background sodium leak conductance, cell death | × | ||||
| 35236 | XVI_5021761 | 0,54 | retinoid X receptor, alpha (RXRA)* | retinoid development, heart development and morphogenesis | × | × | |||
| 20222 | XVI_565127 | 0,54 | FLJ10154 | hormonal expression | × | ||||
| 20238 | XVI_593641 | 0,89 | FLJ10154 | hormonal expression | × | ||||
| 18651 | XVII_11584572 | 0,68 | EPH receptor A8 (EPHA8) | nervous system development | × | ||||
| 18814 | XVII_13715805 | 0,7 | PDZ domain containing ring finger 3 (PDZRN3) | myogenic differentiation | × | ||||
| 32060 | XVII_7058248 | 0,49 | vitamin D (1,25- dihydroxyvitamin D3) receptor (VDR) | hormone receptor for vitamine D3, related to bone density | × | ||||
| 17506 | XVIII_10340214 | 0,63 | FBJ osteosarcoma oncogene (FOS) | cell proliferation, differentiation, transformation | × | ||||
| 17577 | XVIII_11202384 | 0,49 | iodotyrosine deiodinase (C6orf71) | thyroid hormone production | × | ||||
| 17787 | XVIII_14143185 | 0,76 | phospholipase C, beta 1 (PLCB1) | intracellular transduction | × | ||||
| 18047 | XVIII_3081169 | 0,26 | regulatory factor X, 6 (RFXDC1) | Production of insulin | × | ||||
| 18262 | XVIII_6321841 | 0,77 | estrogen receptor 2 (ER beta) (ESR2) | hormonal receptor, gametogenesis | × | ||||
| 15358 | XIX_11929930 | 0,62 | death-associated protein kinase (DAPK2) | programmed cell death | × | ||||
| 30997 | XIX_16674218 | 0,69 | lipase maturation factor 2 (LMF2) | maturation of the endoplasmic reticulum | × | ||||
| 30997b | XIX_16674221 | 0,68 | lipase maturation factor 2 (LMF2) | maturation of the endoplasmic reticulum | × | ||||
| 15971 | XIX_3850285 | 0,48 | Fc receptor-like A (FCRLM1) | immune responses | × | ||||
| 31101 | XIX_5560633 | 0,72 | AK130540 | salivary gland | × | ||||
| 22229 | XX_10890902 | 0,5 | cornifelin (CNFN) | ion transport across squamous epithelia, keratinization | × | ||||
| 32994 | XX_15998772 | 0,53 | ubiquilin 4 (UBQLN4) | proteasomal protein degradation | × | ||||
| 22693 | XX_17936432 | 0,93 | TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor (TAF12) | transcriptional activators | × | ||||
| 23102 | XX_7553459 | 0,56 | metastasis suppressor 1 (MTSS1) | metastases supressor | × | ||||
| 21688 | XXI_11538922 | 0,65 | AK095260 | osmoregulation | × | ||||
| 21693 | XXI_11580802 | 0,69 | cadherin 20 (CDH20) | tumor suppressor | × |
Candidate genes are identified for 63 SNPs under putative directional selection. Note that 7 out of the 70 putative outliers SNPs were not found near to a coding gene and are not reported in the table. This concerns the six SNPs identified in diverse scaffold and one SNP (22037) in chromosome XX (see Table 2). Genes are assigned to one of the following categories: MG = Morphogenesis and Growth, OM = Osmoregulation, SB = skeletal Biology, KF = Kidney Function, OF = Other Function. These putative functions have been assessed using both the GeneCard database (http://www.genecards.org/) and AmiGO 2 GO browser. In cases of multiple functions assigned to a single gene, this is denoted by “*”. For genes with multiple functions, only main functions previously documented in vertebrate species are reported.