Table 3.
Phenotypic QTL co-localized with expression QTL
| Phenotype | SSC | Peak SNP | Position | Ea | VSb | h2 | qvaluec | Intervald | Ne |
|---|---|---|---|---|---|---|---|---|---|
| Carcass 10th-Rib Backfat | 1 | ALGA0010839 | 270.61 | + | 0.03 | 0.45 | 4.05e-03 | 270.39–274.20 | 1 |
| WBS | 2 | M1GA0002229 | 4.34 | – | 0.04 | 0.26 | 4.07e-04 | 4.34–7.32 | 1f |
| SP Tenderness | 2 | H3GA0005676 | 6.77 | + | 0.05 | 0.29 | 2.02e-04 | 4.34–7.32 | 1f |
| SP Overall Tenderness | 2 | H3GA0005676 | 6.77 | + | 0.05 | 0.28 | 4.80e-05 | 6.38–7.32 | 1f |
| Last Lumbar Backfat | 4 | ASGA0092651 | 88.28 | – | 0.04 | 0.41 | 4.53e-02 | 0 | 4 |
| Last-Rib Backfat 16-wk | 5 | ALGA0031990 | 55.01 | + | 0.03 | 0.47 | 4.62e-02 | 53.28–55.01 | 1 |
| Cook Yield | 5 | MARC0036560 | 66.10 | + | 0.03 | 0.31 | 3.30e-02 | 62.76–66.10 | 1 |
| Loin Muscle Area 16-wk | 6 | ASGA0105067 | 69.37 | + | 0.04 | 0.29 | 3.16e-02 | 69.37–69.91 | 4f |
| Last-Rib Backfat 13-wk | 6 | ALGA0104402 | 147.74 | – | 0.07 | 0.43 | 2.33e-05 | 108.75–151.35 | 6f |
| Carcass 10th-Rib Backfat | 6 | M1GA0008917 | 144.60 | – | 0.12 | 0.45 | 8.11e-08 | 108.75–153.26 | 6f |
| Last-Rib Backfat 10-wk | 6 | ALGA0104402 | 147.74 | – | 0.07 | 0.35 | 5.25e-05 | 114.92–153.13 | 6f |
| Loin Weight | 6 | ASGA0029651 | 144.64 | – | 0.06 | 0.30 | 2.24e-03 | 135.37–150.06 | 4f |
| Last-Rib Backfat 22-wk | 6 | ALGA0104402 | 147.74 | – | 0.07 | 0.49 | 8.80e-05 | 135.85–150.04 | 4f |
| 10th-Rib Backfat 13-wk | 6 | ALGA0104402 | 147.74 | – | 0.05 | 0.43 | 3.05e-03 | 142.22–150.04 | 4 |
| Last-Rib Backfat 16-wk | 6 | ALGA0104402 | 147.74 | – | 0.06 | 0.47 | 2.63e-04 | 142.75–153.05 | 5 |
| Last Lumbar Backfat | 6 | ALGA0104402 | 147.74 | – | 0.05 | 0.41 | 1.38e-02 | 142.75–153.13 | 5 |
| 10th-Rib Backfat 10-wk | 6 | ASGA0029651 | 144.64 | + | 0.06 | 0.41 | 1.56e-02 | 144.55–147.74 | 2 |
| 10th-Rib Backfat 22-wk | 6 | ALGA0104402 | 147.744 | – | 0.04 | 0.47 | 2.69e-02 | 144.60–147.74 | 2 |
| 10th-Rib Backfat 16-wk | 6 | ALGA0104402 | 147.74 | – | 0.06 | 0.49 | 2.14e-03 | 0 | 2 |
| 10th-Rib Backfat 19-wk | 6 | ALGA0104402 | 147.74 | – | 0.05 | 0.50 | 8.72e-03 | 147.74–147.74 | 2 |
| Last-Rib Backfat 19-wk | 6 | ALGA0104402 | 147.74 | – | 0.06 | 0.57 | 3.41e-04 | 147.74–150.04 | 2 |
| Number of Ribs | 7 | ALGA0043983 | 98.51 | + | 0.12 | 0.36 | 4.19e-09 | 59.41–111.38 | 10 |
| Cook Yield | 8 | DRGA0008986 | 134.93 | – | 0.03 | 0.31 | 2.01e-02 | 134.93–134.93 | 1 |
| Dressing Percent | 11 | M1GA0014839 | 6.88 | + | 0.03 | 0.24 | 4.33e-02 | 1.72–6.88 | 2 |
| Loin Weight | 11 | ALGA0060368 | 4.51 | – | 0.03 | 0.30 | 3.10e-02 | 4.51–4.51 | 2f |
| Last-Rib Backfat 10-wk | 12 | ASGA0054658 | 41.73 | – | 0.02 | 0.35 | 4.03e-02 | 41.73–41.73 | 2 |
| Protein Percent | 15 | MARC0093624 | 122.22 | + | 0.21 | 0.38 | 8.71e-20 | 48.78–131.28 | 21f |
| 24-h pH | 15 | MARC0093624 | 122.22 | + | 0.09 | 0.19 | 3.35e-07 | 110.22–131.45 | 16f |
| Cook Yield | 15 | MARC0093624 | 122.22 | + | 0.15 | 0.31 | 3.61e-13 | 113.26–132.44 | 16f |
| Drip Loss | 15 | MARC0093624 | 122.22 | – | 0.13 | 0.28 | 4.20e-11 | 113.26–137.87 | 17f |
| SP Overall Tenderness | 15 | H3GA0052416 | 121.81 | + | 0.07 | 0.28 | 3.59e-05 | 118.55–122.90 | 16f |
| WBS | 15 | MARC0093624 | 122.22 | + | 0.06 | 0.26 | 4.07e-04 | 120.03–122.90 | 16f |
| SP Juiciness | 15 | H3GA0052416 | 121.81 | + | 0.04 | 0.07 | 5.06e-03 | 120.03–122.22 | 16f |
| SP Tenderness | 15 | H3GA0052416 | 121.81 | + | 0.07 | 0.29 | 1.90e-05 | 120.03–122.90 | 16f |
SNP significantly associated with phenotype
aEffect of peak pQTL SNP on phenotype, positive indicates B allele increases phenotypic trait
bProportion of phenotypic variance explained by peak SNP
cGWAS qvalue for peak SNP
dInterval for pQTL: start and end position
eNumber of eQTL co-localized with the pQTL
fContains at least one eQTL significantly associated with the phenotype