Table 3.
eQTL pertaining to fruit quality pathway genes.
| Fruit Quality Genes | TPM (AA genotype) | TPM (AB genotype) | TPM (BB genotype) | Minor Allele | Minor Allele Frequency | p-value (FDR adjusted) | Estimated h2 | Single marker R2 | Single-marker p-value |
|---|---|---|---|---|---|---|---|---|---|
| L-Ascorbic Acid Metabolism | |||||||||
| (GALUR) D-galacturonate reductase | 597.5 ± 98.1 | 1218.4 ± 602.6 | 1969.4 ± 323.4 | A | 0.29 | 6.9E-04 | 0.71 | 0.10 | 2.2E-03 |
| (MDAR) Monodehydroascorbate reductase | 135.6 ± 37.4 | 78.9 ± 33.9 | 18.4 ± 40.2 | B | 0.24 | 2.8E-04 | 0.68 | 0.53 | 8.9E-10 |
| Carotenoid Metabolism | |||||||||
| (PSY) Phytoene chloroplastic | 36.9 ± 39.0 | 129.3 ± 36.2 | 222.9 ± NA | B | 0.33 | 1.8E-03 | 0.60 | 0.63 | 5.5E-13 |
| (ZDS) Zeta-carotene chloroplastic chromoplastic | 28.4 ± 12.4 | 16.4 ± 5.9 | 7.7 ± 4.2 | A | 0.42 | 3.5E-03 | 0.91 | 0.50 | 2.0E-09 |
| (BCH) Beta-carotene 3- chloroplastic | – | .6 ± .4 | .1 ± .1 | A | 0.30 | 4.02E-02 | 0.92 | 0.43 | 1.16E-08 |
| Monolignol Pathway | |||||||||
| (BAHD1) BAHD acyltransferase At5g47980 | 7.8 ± 50.3 | 587.5 ± 250.8 | – | B | 0.48 | 2.3E-05 | 1 | 0.79 | 2.2E-16 |
| (CCR1) Cinnamoyl- reductase 1 | 2864.5 ± 1483.0 | 1755.4 ± 425.8 | 455.3 ± 294.3 | A | 0.23 | 2.5E-02 | 0.51 | 0.69 | 2.6E-15 |
| (MTDH) Probable mannitol dehydrogenase | – | 1150 ± 325.9 | 197.2 ± 217.3 | B | 0.26 | 8.4E-04 | 0.37 | 0.72 | 2.2E-16 |
| Sugar/Carbohydrate Metabolism | |||||||||
| (ENO) Enolase | – | 124.8 ± 72.3 | 6.6 ± 21.6 | A | 0.29 | 3.8E-04 | 0.73 | 0.59 | 7.7E-13 |
| (E134) Endo-1,3 1,4-beta-D-glucanase | 20.1 ± 12.6 | 75.4 ± 27.3 | 167.3 ± 13.8 | B | 0.36 | 4.1E-04 | 0.95 | 0.71 | 3.7E-16 |
| (PGLR3) Probable polygalacturonase At3g15720 | 18.5 ± 30.3 | 90.5 ± 33.3 | 182.6 ± 49.9 | B | 0.31 | 5.2E-04 | 0.18 | 0.63 | 4.2E-13 |
| (MAN7) Mannan endo-1,4-beta-mannosidase 7 | 582.7 ± 170.1 | 322.6 ± 95.2 | 103.6 ± 100.3 | A | 0.46 | 5.8E-04 | 0.49 | 0.70 | 1.2E-15 |
| (AGP14) Arabinogalactan peptide 14 | – | 479.6 ± 139.0 | 78.5 ± 78.8 | A | 0.43 | 8.0E-04 | 0.99 | 0.78 | 2.2E-16 |
| (SWET1) Bidirectional sugar transporter SWEET1 | 9.0 ± 35.0 | 91.4 ± 61.2 | – | B | 0.19 | 8.1E-04 | 0.82 | 0.43 | 1.2E-08 |
| (XYL1) Alpha-xylosidase 1 | 45.5 ± 39.5 | 4.5 ± 6.8 | .5 ± NA | A | 0.31 | 8.3E-04 | 0.82 | 0.40 | 5.1E-06 |
| (XYL2) Beta-xylosidase alpha-L-arabinofuranosidase 2 | .2 ± .6 | 52.6 ± 49.5 | – | B | 0.33 | 2.4E-03 | 0.53 | 0.28 | 1.6E-05 |
| (MTDH) Probable mannitol dehydrogenase | – | 1150 ± 325.9 | 197.2 ± 217.3 | A | 0.20 | 8.4E-04 | 0.37 | 0.72 | 2.2E-16 |
| (BGL24) Beta-glucosidase 24 | 52.5 ± 23.2 | 21.9 ± 24.0 | 1.9 ± 1.5 | A | 0.45 | 1.3E-03 | 0.76 | 0.42 | 1.5E-07 |
| (GUN6) Endoglucanase 6 | 230.7 ± 88.6 | 711.9 ± 436.2 | 651.1 ± 237.6 | B | 0.40 | 2.2E-03 | 1 | 0.32 | 4.1E-05 |
| (GBA2) Non-lysosomal glucosylceramidase | – | 42.6 ± 26.3 | 11.2 ± 5.5 | A | 0.17 | 4.3E-03 | 0.29 | 0.48 | 9.4E-10 |
| (XYL1) Alpha-xylosidase 1 | 45.5 ± 39.5 | 4.5 ± 6.8 | .5 ± NA | A | 0.31 | 8.3E-04 | 0.82 | 0.40 | 5.1E-06 |
| (XYL2) Beta-xylosidase alpha-L-arabinofuranosidase 2 | .2 ± .6 | 52.6 ± 49.5 | – | B | 0.33 | 2.4E-03 | 0.53 | 0.28 | 1.6E-05 |
| (GPAT3) Probable glycerol-3-phosphate acyltransferase 3 | 13.5 ± 14.4 | 54.5 ± 34.0 | – | B | 0.28 | 5.4E-03 | 0.86 | 0.38 | 3.0E-07 |
| (BAM1) Beta-amylase chloroplastic | 89 ± 39.7 | 72.9 ± 25.8 | 29.7 ± 7.4 | B | 0.19 | 3.4E-02 | 0.77 | 0.19 | 2.8E-03 |
| (STC) Sugar carrier protein C | 73.1 ± 66.9 | 55.8 ± 43.5 | 13.5 ± 12.6 | A | 0.47 | 4.0E-02 | 0.75 | 0.23 | 6.5E-04 |
| (CSLG3) Cellulose synthase G3 | .6 ± 14.6 | 44.5 ± 20.6 | 76.7 ± 23.4 | A | 0.32 | 4.9E-02 | 0.82 | 0.38 | 9.9E-07 |
| (CSLC4) Cellulose synthase C4 | – | 165 ± 51.5 | 100.4 ± 48.8 | A | 0.25 | 6.6E-03 | 0.58 | 0.25 | 5.1E-05 |
| trans | – | 165.0 ± 51.5 | 100.4 ± 48.8 | A | 0.25 | 6.6E-03 | 0.25 | 5.1E-05 | |
| (DGAT) Diacylglycerol O-acyltransferase | .5 ± .6 | 559.5 ± 252.9 | – | B | 0.35 | 1.3E-05 | 1 | 0.64 | 2.3E-14 |
| (GLYK) D-glycerate 3-kinase, chloroplastic | 97.5 ± 40.1 | 53.0 ± 11.2 | 9.8 ± 1.7 | B | 0.31 | 9.6E-03 | 0.45 | 0.54 | 1.9E-10 |
| 84.3 ± 39.5 | 24.1 ± 20.6 | – | B | 0.12 | 9.6E-03 | 0.34 | 1.0E-06 | ||
| (PDC2) Pyruvate decarboxylase 2 | 71.1 ± 33.3 | 1019.2 ± 527.0 | 2012.6 ± 510.1 | A | 0.48 | 6.9E-04 | 0.97 | 0.69 | 7.2E-15 |