Table 5.
Description of 26 significant QTL for 4 phenotypes in 3 diploid families. QTL peak marker is the marker with the highest LOD score for each QTL, cM is the position of the QTL peak marker, 95% CI is the approximate 95% confidence interval for the position of the QTL, PVE is the percentage of variation in the phenotype explained by the QTL, p(F) is the P value of the F statistic in the multiple-QTL model, and Sig denotes whether the QTL was significant at the LG or experiment-wide level (Exp). Gene abbreviations are provided for loci that were annotated directly (bold) or annotated based on flanking sequence from the Atlantic salmon genome (italics). See Supplementary Table S3 for more information on QTL annotations. Marker RAG3 is the 5′-nuclease assay One_RAG-93. Instances where the QTL peak marker location is not included in the 95% CI indicate a lack of confidence in the true QTL location and should be interpreted with caution
| Phenotype | Family | QTL Peak Marker | LG | cM | 95% CI | LOD | PVE | p(F) | Sig | Annotation(s) |
|---|---|---|---|---|---|---|---|---|---|---|
| Thermotolerance | D3 | 63 844 | 2 | 171.57 | 0.00–192.07 | 3.35 | 16.75 | 5.10E−04 | LG | KLD7A, MLVCB |
| Thermotolerance | D3 | 36 045 | 11 | 129.89 | 126.7–133.03 | 3.32 | 9.88 | 9.50E−03 | LG | |
| Thermotolerance | D4 | 70 808 | 25 | 48 | 41.28–50.74 | 3.57 | 12.37 | 4.00E−03 | LG | PABP |
| Thermotolerance | D5 | 7896 | 6 | 31.28 | 17.53–90.35 | 3.45 | 7.58 | 8.22E−03 | LG | SMHD3 |
| Thermotolerance | D5 | 87 489 | 13 | 51.86 | 6.13–138.3 | 4.01 | 16.35 | 5.68E−05 | LG | PANTR |
| Thermotolerance | D5 | 85 651 | 19 | 86.91 | 1.71–93.68 | 3.29 | 7.89 | 6.85E−03 | LG | |
| Length | D4 | RAG3 | 9 | 54.19 | 37.36–57.78 | 3.07 | 7.56 | 1.80E−02 | LG | RAG |
| Length | D4 | 76 581 | 26 | 68.59 | 14.44–158.81 | 3.49 | 8.49 | 1.10E−02 | LG | |
| Length | D4 | 767 479 | 28 | 21.56 | 19.73–23.02 | 3.59 | 10.63 | 4.00E−03 | LG | |
| Length | D5 | 44 010 | 7 | 63.04 | 3.61–111.8 | 3.40 | 6.97 | 1.53E−03 | LG | |
| Length | D5 | 84 879 | 11 | 164.78 | 164.48–164.9 | 4.13 | 13.06 | 1.03E−05 | LG | |
| Weight | D3 | 82 443 | 11 | 117.29 | 0.83–167.61 | 3.41 | 11.41 | 1.00E−02 | LG | |
| Weight | D4 | 70 636 | 15 | 116.61 | 112.53–117.01 | 3.67 | 10.85 | 2.20E−03 | LG | |
| Weight | D4 | 2639 | 25 | 78.49 | 54.16–78.92 | 3.09 | 6.18 | 2.70E−02 | LG | |
| Weight | D4 | 76 581 | 26 | 68.59 | 21.35–158.81 | 3.28 | 8.34 | 8.00E−03 | LG | SIA7B |
| Weight | D4 | 767 479 | 28 | 21.56 | 19.73–23.02 | 4.64 | 13.90 | 4.60E−04 | Exp | |
| Weight | D5 | 7896 | 6 | 31.28 | 3.60–126.87 | 3.60 | 6.67 | 4.70E−03 | LG | SMHD3 |
| Weight | D5 | 66 074 | 7 | 94.75 | 3.56–111.8 | 3.11 | 13.99 | 2.53E−05 | LG | BSN |
| Weight | D5 | 84 879 | 11 | 164.78 | 164.48–164.9 | 4.60 | 19.75 | 6.22E−07 | Exp | |
| Weight | D5 | 30 636 | 19 | 11.35 | 7.24–58.94 | 3.40 | 9.96 | 4.13E−04 | LG | |
| Condition factor | D3 | 86 442 | 6 | 53.86 | 50.26–58.87 | 5.56 | 34.08 | 1.33E−07 | LG | |
| Condition factor | D4 | 765 637 | 6 | 4.82 | 1.52–97.22 | 3.45 | 13.72 | 1.60E−03 | LG | |
| Condition factor | D4 | 5975 | 28 | 145.33 | 3.70–68.97 | 3.47 | 6.92 | 3.50E−02 | LG | FAS |
| Condition factor | D5 | 53 011 | 4 | 64.01 | 139.87–145.86 | 3.16 | 15.16 | 5.61E−06 | LG | |
| Condition factor | D5 | 15 419 | 10 | 27.56 | 9.69–82.72 | 4.92 | 33.89 | 5.86E−11 | LG | |
| Condition factor | D5 | 7448 | 20 | 0 | 0.00–144.99 | 3.49 | 9.74 | 2.93E−04 | LG |