Table 3.
A list of differentially transcribed candidate genes within two QTL credible intervals on chromosome 14 from the V. rupestris B38 × ‘Horizon’ F1 family ordered by significance
| Gene ID | UniProt ID | Protein name | Heterozygous parent | Fold changea | q Value | Transcript range (bp)b |
|---|---|---|---|---|---|---|
| VIT_14s0108g01130 | F6H5V6 | Putative uncharacterized protein | V. rupestris B38 | 0.33|2.97 | 1 × 10−11 | 29,767,850–29,771,739 |
| VIT_14s0068g00980 | D7SVG4 | Putative uncharacterized protein | Horizon | 1.50|0.67 | 0.000004 | 24,740,077–24,753,861 |
| VIT_14s0068g01970 | F6H3X5 | Putative uncharacterized protein | Horizon | 0.57|1.76 | 0.000005 | 25,633,234–25,634,255 |
| VIT_14s0108g00040 | D7SX63 | FACT complex subunit SSRP1 | V. rupestris B38 | 0.85|1.17 | 0.000044 | 28,871,463–28,878,208 |
| VIT_14s0066g02550 | D7TX08 | Plasma membrane ATPase | V. rupestris B38 | 1.50|0.66 | 0.000229 | 28,745,606–28,754,974 |
| VIT_14s0068g01730 | D7SVM8 | Putative uncharacterized protein | Horizon | 1.51|0.66 | 0.000245 | 25,424,955–25,439,887 |
| VIT_14s0068g00800 | D7SVE8 | Putative uncharacterized protein | Horizon | 0.81|1.23 | 0.000316 | 24,574,253–24,580,946 |
| VIT_14s0108g00150 | F6H5P3 | Putative uncharacterized protein | V. rupestris B38 | 1.51|0.66 | 0.000628 | 28,944,177–28,951,278 |
| VIT_14s0068g01720 | F6H465 | Putative uncharacterized protein | Horizon | 0.65|1.53 | 0.002021 | 25,424,822–25,425,652 |
| VIT_14s0068g01100 | F6H429 | Putative uncharacterized protein | Horizon | 1.19|0.84 | 0.002182 | 24,882,721-24,885,537 |
| VIT_14s0068g02110 | A5BE40 | Putative uncharacterized protein | Horizon | 1.43|0.70 | 0.002228 | 25,707,772–25,712,673 |
| VIT_14s0068g01940 | A5BCW2 | Putative uncharacterized protein | Horizon | 0.81|1.24 | 0.002607 | 25,605,002–25,609,466 |
| VIT_14s0066g02560 | A5BD80 | Thioredoxin h4 | V. rupestris B38 | 0.83|1.20 | 0.008721 | 28,755,934–28,756,776 |
| VIT_14s0068g00660 | Q19N38 | WD repeat 2 | Horizon | 1.30|0.77 | 0.010981 | 24,473,597–24,477,950 |
| VIT_14s0108g01100 | F6H5V3 | Putative uncharacterized protein | V. rupestris B38 | 1.37|0.73 | 0.012521 | 29,753,062–29,756,587 |
| VIT_14s0108g00070 | D7SX65 | Putative uncharacterized protein | V. rupestris B38 | 0.71|1.40 | 0.013738 | 28,889,440–28,894,772 |
| VIT_14s0066g00830 | D7TWK7 | Putative uncharacterized protein | V. rupestris B38 | 0.75|1.33 | 0.017500 | 27,308,643–27,313,582 |
| VIT_14s0068g01310 | F6H442 | Putative uncharacterized protein | Horizon | 0.82|1.22 | 0.021602 | 25,043,826–25,044,557 |
| VIT_14s0068g01710 | D7SVM6 | Putative uncharacterized protein | Horizon | 0.75|1.33 | 0.021602 | 25,408,934–25,417,805 |
| VIT_14s0066g02380 | A5AEQ 0 | Putative uncharacterized protein | V. rupestris B38 | 1.16|0.86 | 0.022765 | 28,580,980–28,583,873 |
| VIT_14s0068g01840 | A5BFT4 | Putative uncharacterized protein | Horizon | 0.72|1.39 | 0.024415 | 25,554,099–25,554,809 |
| VIT_14s0068g01260 | F6H440 | Putative uncharacterized protein | Horizon | 0.58|1.71 | 0.027264 | 25,012,954–25,022,155 |
| VIT_14s0068g01990 | D7SVP7 | Putative uncharacterized protein | Horizon | 0.72|1.39 | 0.028077 | 25,641,499–25,645,266 |
| VIT_14s0068g01270 | F6H441 | Putative uncharacterized protein | Horizon | 1.84|0.54 | 0.029598 | 25,022,156–25,022,479 |
| VIT_14s0068g01160 | D7SVI1 | Putative uncharacterized protein | Horizon | 2.20|0.45 | 0.048404 | 24,943,888–24,944,747 |
GO terms for these genes are given in Supplementary Table 2
aCalculated as two raised to a power equal to that of the effect size of the grouping covariate for a given gene. Two fold change values are given due to the uncertainty of which phase the effect is coming from for a given QTL. Each column left or right of the vertical bar represents one phase
bThe range was calculated by finding the start and end locations of all transcripts for a gene and finding the most proximal start location and the most distal end location