Table 3.
Summary of the gill smoltification gene expression patterns for the four groups
| Gene name | Assay name | All groups | Coho salmon | Sockeye salmon | Chinook salmon (s-t) | Chinook salmon (o-t) | Seawater |
|---|---|---|---|---|---|---|---|
| Upregulated in smolt (predicted) | |||||||
| Beta actin | ACTB_v1 | + | − | ||||
| Carbonic anhydrase 4 | CA4_v1 | + | + | + | + | + | + |
| Cystic fibrosis transmembrane conductance regulator I | CFTR.I_v1 | + | + | + | + | + | + (t) |
| C-type lectin domain family 4 member M | CLEC4M_v1 | + | − | + | − | ||
| Cytochrome P450 2 K1 | CYP2K1_v2 | + | + | + | - (t) | − | |
| Elongation factor 2 | EEF2_v1 | + | + | − | + | - (t) | |
| FK506-binding protein 5 | FKBP5_v1 | + | + | + | + | + (t) | |
| Growth hormone receptor 1 | GHR1_v1 | + | + | + | − | ||
| Hemoglobin subunit α | HBA_v1 | + | + | + | + | + | |
| Hemoglobin subunit α (true) | HBAt_v1 | − | + | + | + | + | |
| Mitochondrial pyruvate carrier 1 | MPC1_v1 | + | + | + (t) | − | ||
| NADH dehydrogenase 1 beta subcomplex subunit 2 | NDUFB2_v1 | + | + | + | − | − | |
| NADH dehydrogenase 1 beta subcomplex subunit 4 | NDUFB4_v1 | + | + | + | + (t) | − | |
| Na+/K+-ATPase α-1b (seawater) | NKAa1.b_v2 | + | + | + | + | + | |
| Glucorticoid receptor 1 | NR3C1_v1 | − | + (t) | − | |||
| Rhesus blood group-associated glycoprotein | RHAG_v1 | + | + | + | − | − | |
| 60S ribosomal protein L31 | RPL31_v1 | + | − | − | |||
| Monocarboxylate transporter 10 | SLC16A10_v1 | + | + | + | − | ||
| Thyroid hormone receptor beta 1 | THRB1_v2 | − | + | + | - (t) | ||
| Translocator protein | TSPO_v2 | + | + | + | + | ||
| Downregulated in smolt (predicted) | |||||||
| C-C motif chemokine 19 | CCL19_v1 | − | − | − | − | + | − |
| C-C motif chemokine 4 | CCL4_v1 | − | − | − | − | + | − |
| Exonuclease 1 | EXO1_v1 | − | − | − | |||
| Formin-like protein 1 | FMNL1_v1 | − | − | − | − | ||
| Interferon-induced protein 44 | IFI44_v1 | − | − | − | − | + | − |
| Interleukin-12 beta | IL12B_v1 | − | − | − | − | + | - (t) |
| DNA replication licensing factor MCM4 | MCM4_v1 | − | − | − | |||
| Membrane-spanning 4-domains A-4A | MS4A4A_v1 | − | − | - (t) | |||
| Nicotinamide phosphoribosyltransferase | NAMPT_v1 | − | − | − | − | ||
| Na+/K+-ATPase α-1a (freshwater) | NKAa1.a_v2 | − | + | + (t) | − | ||
| Serine/threonine-protein kinase PLK2 | PLK2_v2 | − | + | ||||
| Prolactin receptor | PRLR_v1 | − | + | + | + | − | |
| Regulator of G-protein signalling 21 | RGS21_v1 | − | + | − | − | + | + |
| T-cell receptor alpha | TRA_v1 | − | − | − | + (t) | ||
| Tubulin, alpha 8 like 2 | TUBA8L2_v1 | − | - (t) | − | |||
| Ubiquitin-like modifier-activating enzyme 1 X | UBA1_v1 | − | − | + | − | ||
| Wiskott–Aldrich Syndrome protein | WAS_v1 | − | − | − | + | − | |
The expression values of the 37 candidate genes were subjected to PCA for all four groups and each group separately: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. Gene expression relationships with the main PC axis separating earlier and later months were examined. Student t-tests examined expression differences between freshwater and seawater Nitinat ocean-type Chinook salmon sampled at the same time in late April; estuary juveniles were exposed to seawater for about 2 weeks. Presented are the significant (P < 0.05) expression patterns: + for positive correlation with smoltification or higher in seawater and − for negative correlation with smoltification or lower in seawater. Trends (P < 0.1) are presented with a t in brackets. Pearson correlations and P-values, as well as freshwater and seawater mean differences and statistics, are displayed in the Supplementary Analysis.