Table 1.
Comparative analysis of quantitative trait loci (QTLs) identified for protein, oil, and sucrose traits in the Williams 82 × PI483460B population using skim‐WGS and 3K SNP marker data sets
| Trait | Environment | Skim_WGS | 3K_Chip | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| QTL name | Marker interval (location) | Phy. interval (Kb) | Genetic interval (cM) | LOD | R 2 | Add. effect | PVE (%) | QTL name | Maker interval | LOD | R 2 | Phy. location (Mb) | ||
| Protein | BREC12 | qPro_06 | bin_6_21984752∼bin_6_22687378 | 702.62 | 0.31 | 3.9 | 9.7 | −0.70 | 30.4 | qPro_06 | SNP8573_PI516C∼BARC_054471_12085 | 5.3 | 8.9 | 20.2–23.1 |
| qPro_19 | bin_19_1024102∼bin_19_1420747 | 396.64 | 3.86 | 3.4 | 8.4 | 0.62 | qPro_19 | NCSB_004483∼NCSB_004480 | 4.2 | 7.6 | 18.4–20.3 | |||
| qPro_20 | bin_20_2558940 | 2.9 | 6.9 | 0.57 | qPro_20 | NCSB_004739∼SNP30392_PI516C | 4.1 | 6.5 | 2.50–3.2 | |||||
| qPro_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 2.9 | 5.4 | 0.50 | qPro_20 | BARC_027790_06672∼BARC_062091_17651 | 4.4 | 8 | 33.8–37.4 | |||
| BREC13 | qPro_19 | bin_19_1024102∼bin_19_1420747 | 396.64 | 3.86 | 5.2 | 10.7 | 0.70 | 24.7 | qPro_06 | BARC_047703_10385∼BARC_038923_07397 | 3.6 | 5 | 49.6–50.2 | |
| qPro_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 6.6 | 14 | 0.82 | qPro_15 | BARC_040373_07720∼SNP35548_Magellan | 4.2 | 5.4 | 45.2–52.0 | |||
| qPro_20 | NCSB_004738∼SNP30369_PI516C | 5.0 | 6.2 | 22.2–25.6 | ||||||||||
| qPro_20 | BARC_062091_17653∼BARC_027790_06672 | 6.9 | 15.8 | 33.8–37.4 | ||||||||||
| BREC14 | qPro_08 | bin_8_7951579∼bin_8_8602440 | 650.8 | 1.52 | 3.1 | 4.6 | −0.46 | 32.7 | qPro_06 | BARC_047703_10385∼BARC_038923_07397 | 4.3 | 6.1 | 49.6–50.2 | |
| qPro_13 | bin_13_33162248∼bin_13_33151214 | 11.03 | 4.61 | 4.5 | 7.4 | 0.59 | qPro_20 | NCSB_004739∼SNP30392_PI516C | 3.5 | 5 | 22.2–25.6 | |||
| qPro_19 | bin_19_1024102∼bin_19_1420747 | 396.64 | 0.3 | 3.9 | 6.4 | 0.55 | ||||||||
| qPro_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 8.3 | 14.3 | 0.83 | qPro_20 | BARC_062091_17652∼BARC_062091_17653 | 7.5 | 11.2 | 33.8–37.4 | |||
| CR13 | qPro_19 | bin_19_1147261∼bin_19_1420747 | 273.4 | 3.86 | 2.1 | 4.6 | 0.43 | 24.2 | qPro_05 | BARC_029787_06341∼BARC_029787_06360 | 4.3 | 6.3 | ||
| qPro_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 7.8 | 19.6 | 0.90 | qPro_15 | NCSB_003365∼NCSB_003366 | 6.3 | 9 | ||||
| qPro_20 | NCSB_004738∼SNP30369_PI516C | 4.5 | 5.6 | |||||||||||
| qPro_20 | BARC_064871_18952∼BARC_062091_17651 | 8.7 | 13.3 | |||||||||||
| Oil | BREC12 | qOil_02 | bin_2_45571767∼bin_2_45622096 | 50.32 | 0.61 | 3.1 | 7.1 | 0.17 | 23.7 | qOil_02 | BARC_028373_05856∼BARC_031227_07011 | 6.0 | 12.4 | 43.4–46.6 |
| qOil_17 | bin_17_2091529∼bin_17_2097727 | 6.19 | 0.21 | 3.0 | 7.6 | −0.17 | ||||||||
| qOil_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 3.5 | 9 | −0.19 | qOil_20 | BARC_027790_06672∼NCSB_004789 | 5.1 | 10.4 | 33.9–34.8 | |||
| BREC13 | qOil_02 | bin_2_45571767∼bin_2_45623045 | 51.27 | 0.31 | 5.1 | 10.1 | 0.27 | 35.9 | qOil_02 | SNP3239_PI516C∼SNP3244_PI516C | 3.6 | 5.3 | 43.4–46.6 | |
| qOil_08 | bin_8_7542280∼bin_8_7564536 | 22.25 | 0.3 | 3.4 | 6.6 | −0.22 | ||||||||
| qOil_15 | bin_15_5286513∼bin_15_5384732 | 98.21 | 0.3 | 3.2 | 6.2 | −0.21 | qOil_15 | BARC_040373_07720∼SNP35548_Magellan | 3.6 | 5.2 | 4.56–5.20 | |||
| qOil_19 | bin_19_1024102∼bin_19_930385 | 93.71 | 0.91 | 4.0 | 7.7 | −0.24 | ||||||||
| qOil_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.63 | 3.0 | 5.3 | −0.20 | qOil_20 | BARC_062091_17653∼BARC_027790_06672 | 4.8 | 7.2 | 45.1–46.3 | |||
| BREC14 | qOil_02 | bin_2_45571767∼bin_2_45623045 | 51.27 | 0.31 | 7.3 | 13.5 | 0.25 | 41.4 | qOil_02 | SNP3244_PI516C∼NCSB_000498 | 7.2 | 10.5 | 43.4–46.6 | |
| qOil_08 | bin_8_7951579∼bin_8_8095904 | 144.32 | 0.3 | 7.2 | 13.3 | −0.24 | qOil_08 | NCSB_001712∼SNP16086 | 8.3 | 12.3 | 7.99–8.10 | |||
| qOil_09 | bin_9_5819186∼bin_9_5896549 | 77.36 | 0.31 | 4.6 | 8.1 | 0.19 | qOil_09 | BARC_060871_16939∼NCSB_002034 | 3.5 | 4.9 | 5.60–6.21 | |||
| qOil_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 3.7 | 6.5 | −0.17 | qOil_15 | BARC_039433_07497∼BARC_054257_12402 | 3.9 | 5.5 | 4.52–5.21 | |||
| qOil_20 | BARC_062091_17651∼BARC_062091_17652 | 6.3 | 9.1 | 45.1–46.3 | ||||||||||
| CR13 | 32.4 | qOil_05 | NCSB_001051∼NCSB_001052 | 11.7 | 16.2 | 38.3–38.6 | ||||||||
| qOil_07 | bin_7_42136084∼bin_7_42040256 | 95.82 | 0.62 | 3.7 | 6.7 | −0.30 | qOil_07 | SNP10717_PI516C∼BARC_028517_05936 | 4.5 | 5.8 | 43.5–43.7 | |||
| qOil_08 | bin_8_11422070∼bin_8_11703885 | 281 | 0.92 | 4.5 | 8.1 | −0.33 | qOil_08 | SNP15995–NCSB_001726 | 3.5 | 4.6 | 7.99–8.10 | |||
| qOil_14 | bin_14_8471719∼bin_14_7775075 | 697 | 0.62 | 3.2 | 5.7 | −0.28 | qOil_15 | NCSB_003365∼NCSB_003366 | 5.2 | 6.4 | 4.52–5.21 | |||
| qOil_20 | bin_20_33975596∼bin_20_34027051 | 51.41 | 0.32 | 6.4 | 11.9 | −0.40 | qOil_20 | BARC_062091_17653∼BARC_027790_06672 | 5.2 | 6.9 | 45.1–46.3 | |||
| Sucrose | BREC12 | qSuc_06 | bin_6_37707727∼bin_6_38033477 | 325.75 | 2.43 | 3.3 | 7.4 | 0.22 | 31.8 | qOil_06 | NCSB_001275∼NCSB_001285 | 4.6 | 9.2 | 36.8–38.0 |
| qSuc_08 | bin_8_9130096∼bin_8_9319041 | 188.94 | 0.3 | 9.7 | 24 | 0.38 | qSuc_08 | NCSB_001722∼BARC_035233_07151 | 9.8 | 22.6 | 9.04–9.39 | |||
| BREC13 | qSuc_06 | bin_6_40104066∼bin_6_41202830 | 1470 | 2.43 | 7.1 | 13 | 0.36 | 35.9 | qSuc_06 | BARC_061709_17355∼SNP30079 | 7.5 | 12.4 | 36.7–38.0 | |
| qSuc_08 | bin_8_8561674∼bin_8_8602440 | 40.76 | 0.3 | 8.3 | 16 | 0.38 | qSuc_08 | SNP16067∼BARC_010947_01738 | 11.9 | 20.4 | 9.04–9.39 | |||
| qSuc_20 | bin_20_2558940∼bin_20_2386021 | 172.91 | 0.95 | 3.8 | 6.5 | −0.25 | ||||||||
| BREC14 | qSuc_06 | bin_6_18870607∼bin_6_19091375 | 220.76 | 3 | 5.4 | 10 | 0.31 | 42.4 | qSuc_06 | SNP35899∼BARC_014203_02694 | 6.3 | 8.5 | 18.6–19.1 | |
| CR13 | qSuc_08 | bin_8_7951579∼bin_8_8095904 | 144.32 | 0.3 | 13 | 27 | 0.49 | qSuc_08 | SNP16067∼BARC_010947_01738 | 17.4 | 27.5 | 9.04–9.39 | ||
| qSuc_08 | bin_8_8561674∼bin_8_8602440 | 40.76 | 0.3 | 12 | 29 | 0.44 | 28.7 | qSuc_08 | SNP16086∼BARC_016683_03318 | 17.0 | 35.4 | 8.51–8.72 | ||
The physical location for bin markers is designated within the marker id.