Table 1 Marker trait association for the tuber quality traits detected by the generalized linear model
Trait | SNP_ID | Chr | Allele | Consequence Type | Genomic Location | Effect (%) | Gene Model | Predicted Annotation | Pathway | QTN | |
|---|---|---|---|---|---|---|---|---|---|---|---|
Major | Minor | ||||||||||
Springiness | S1_10223458** | 1 | C | T | Stop gain | p.Trp287 > STOP | 0.38 | Dioal.01G024400.1 | Leucine-rich repeat | Pectin | qSp1.1 |
S1_10224508** | 1 | G | A | Stop gain | p.Gln104 > STOP | 0.36 | Dioal.01G024400.1 | Leucine-rich repeat | Pectin | qSp1.2 | |
S2_19082482** | 2 | C | T | Stop gain | p.Gln1032 > STOP | -0.05 | Dioal.02G062700.1 | Protein kinase | Pectin | qSp2.1 | |
S2_19095245 | 2 | C | G | Stop gain | p.Tyr578 > STOP | -0.04 | Dioal.02G062800.1 | Protein kinase | Pectin | qSp2.2 | |
S13_11781422 | 13 | A | G | splice_acceptor_variantintron_variant | c.63-2A > G | -0.37 | Dioal.13G053400.1 | Glucose isomerase | Pectin | qSp13.1 | |
S20_14416887** | 20 | G | T | Stop gain | p.Gly381 > STOP | -0.46 | Dioal.20G055400.1 | Malectin-like | Pectin | qS20.1 | |
Gumminess | S4_20715506 | 4 | C | T | Start Loss | p.Met1? | -3.97 | Dioal.04G130600.1 | Pectin methylesterase | Pectin | qG4.1 |
S7_6378890 | 7 | G | A | splice_donor_variant intron_variant | c.-109 + 1G > A | -9.23 | Dioal.07G051400.1 | Alpha amylase | Starch | qG7.1 | |
S13_11783621 | 13 | G | T | Stop gain | p.Glu208 > STOP | -2.61 | Dioal.13G053400.1 | Glucose isomerase | Pectin | qG13.1 | |
S13_11784207 | 13 | A | G | splice_acceptor_variant intron_variant | c.723-1G > A | 23.60 | Dioal.13G053400.1 | Glucose isomerase | Pectin | qG13.2 | |
S19_24800556 | 19 | G | A | splice_donor_variant intron_variant | c.537 + 2C > T | 4.87 | Dioal.19G187400.1 | Pectinesterase | Pectin | qG19.2 | |
Total area | S2_18814720** | 2 | T | A | Stop gain | p.Tyr289 > STOP | 21.88 | Dioal.02G061200.1 | Protein kinase | Pectin | qTa2.1 |
S4_20715506 | 4 | C | T | Start Loss | p.Met1? | -27.90 | Dioal.04G130600.1 | Pectin methylesterase | Pectin | qTa4.1 | |
S7_16450864 | 7 | G | T | Stop gain | p.Tyr228 > STOP | -29.42 | Dioal.07G067100.1 | 4-Alpha-glucanotransferase | Starch | qTa7.1 | |
Hardness | S13_28669451 | 13 | C | G | splice_donor_variant intron_variant | c.-837 + 1G > C | 62.22 | Dioal.13G093500.1 | Beta-glucosidase | Starch | qH13.2 |
S20_14334067** | 20 | G | T | Stop gain | p.Gly6 > STOP | -12.80 | Dioal.20G055000.1 | Malectin-like | Pectin | qH20.1 | |
S20_14364743** | 20 | A | C | Stop loss | p.Ter592Serext*? | 10.75 | Dioal.20G055100.1 | Malectin-like | Pectin | qH20.2 | |
Starch Content | S10_2314181 | 10 | G | T | Stop gain | p.Gly35 > STOP | -14.75 | Dioal.10G014800.1 | 1,3-beta-Glucan synthase | Starch | qSC10.1 |
S15_23348104 | 15 | T | C | splice_donor_variant intron_variant | c.1029 + 2C > T | 4.99 | Dioal.15G119500.1 | beta-Amylase | Starch | qSC15.2 | |
S17_19982533 | 17 | T | C | splice_acceptor_variant intron_variant | c.811-2A > G | -9.70 | Dioal.17G112400.1 | Glucose-1-phosphate adenylyltransferase | Starch | qSC17.1 | |
Brown Index | S19_17029453 | 19 | G | C | Stop gain | p.Tyr339 > STOP | 34.69 | Dioal.19G083800.1 | Flavanone 3-dioxygenase | Flavonoid | qYI19.1 |
HUE Index | S4_16031453 | 4 | C | T | Stop gain | p.Trp272 > STOP | 50.28 | Dioal.04G073400.1 | UDP-glucosyltransferase protein | Flavonoid | qHI4.1 |