Table 4.
BLAST search results for pre-selected candidate genes for the single nucleotide polymorphism (SNP)-trait associations with P < 1.28e-05 (Bonferroni correction of α = 0.05) within a distance of 2.5 Mbp around the SNP-trait associations across the 184 inbreds of the spring trial.
| Trait | SNP abbrevation | Chr.a | SNP position (bp) | Candidate gene | NCBI gene ID | Locus tag | Identity (%) | Start position | End position | Gene position | Distance to SNP |
|---|---|---|---|---|---|---|---|---|---|---|---|
| AGRONOMIC TRAITS | |||||||||||
| BOF | BOF.A2.s.1 | A02 | 4055363 | GNC | 835788 | AT5G56860 | 79 | 4162702 | 4163847 | 4163275 | 107912 |
| VIN3 | 835844 | AT5G57380 | 80 | 3864072 | 3864747 | 3864410 | 190954 | ||||
| FT | 842859 | AT1G65480 | 87 | 6375965 | 6376243 | 6376104 | 2320741 | ||||
| BOF.A8.s.1 | A08 | 12587052 | FD | 829744 | AT4G35900 | 76 | 12446708 | 12448076 | 12447392 | 139660 | |
| AP1 | 843244 | AT1G69120 | 84 | 15078189 | 15078309 | 15078249 | 2491197 | ||||
| SOC1/AGL20 | 819174 | AT2G45660 | 78 | 15081763 | 15081902 | 15081833 | 2494781 | ||||
| BOF.C1.s.1 | C01 | 10885704 | SVP | 816787 | AT2G22540 | 78 | 11245513 | 11245696 | 11245605 | 359901 | |
| AGL24 | 828556 | AT4G24540 | 77 | 11245357 | 11246128 | 11245743 | 360039 | ||||
| SOC1/AGL20 | 819174 | AT2G45660 | 83 | 9682339 | 9682526 | 9682433 | 1203272 | ||||
| GNC | 835788 | AT5G56860 | 84 | 12641365 | 12641490 | 12641428 | 1755724 | ||||
| BOF.C2.s.1 | C02 | 22964625 | TPS1 | 844194 | AT1G78580 | 93 | 22384412 | 22384513 | 22384463 | 580163 | |
| LD | 827904 | AT4G02560 | 90 | 24966748 | 24966982 | 24966865 | 2002240 | ||||
| FT | 842859 | AT1G65480 | 93 | 20908311 | 20908383 | 20908347 | 2056278 | ||||
| EOF | EOF.A5.s.1 | A05 | 18017730 | SPA3 | 820767 | AT3G15354 | 77 | 18186337 | 18189758 | 18188048 | 170318 |
| AP1 | 843244 | AT1G69120 | 84 | 17789288 | 17789416 | 17789352 | 228378 | ||||
| VRN1 | 821432 | AT3G18990 | 82 | 16379258 | 16379735 | 16379497 | 1638234 | ||||
| SEED QUALITY TRAITS | |||||||||||
| ADF | ADF.A4.s.1 | A04 | 16611781 | GAUT7 | 818447 | AT2G38650 | 81 | 16723369 | 16725115 | 16724242 | 112461 |
| ADF.C7.s.1 | C07 | 986655 | GAUT10 | 816611 | AT2G20810 | 85 | 342567 | 342660 | 342614 | 644042 | |
| ADL | ADL.A7.s.1 | A07 | 5709631 | QUA1 | 822105 | AT3G25140 | 87 | 5464119 | 5465842 | 5464981 | 244651 |
| ADL.C7.s.1 | C07 | 986655 | GAUT10 | 816611 | AT2G20810 | 85 | 342567 | 342660 | 342614 | 644042 | |
| ERA | ERA.A8.s.3 | A08 | 7825612 | FAE1/KCS18 | 829603 | AT4G34520 | 84 | 10187612 | 10189220 | 10188416 | 2362804 |
| ERA.A8.s.4 | A08 | 10337576 | FAE1/KCS18 | 829603 | AT4G34520 | 84 | 10187612 | 10189220 | 10188416 | 149160 | |
| ERA.C3.s.3 | C03 | 55545323 | FAE1/KCS18 | 829603 | AT4G34520 | 84 | 55684172 | 55685778 | 55684975 | 139652 | |
| GSL | GSL.A6.s.1 | A06 | 18128799 | SUR1-like | 103837982 | LOC103837982 | 79 | 17341006 | 17341137 | 17341072 | 787728 |
| OBP2 | 837277 | AT1G07640 | 84 | 17014601 | 17014756 | 17014679 | 1114121 | ||||
| GSL.A9.s.1 | A09 | 3084578 | ATR1/MYB34 | 836210 | AT5G60890 | 77 | 2698822 | 2699466 | 2699144 | 385434 | |
| OBP2 | 837277 | AT1G07640 | 80 | 2683543 | 2683694 | 2683619 | 400960 | ||||
| SUR1-like | 103837982 | LOC103837982 | 99 | 5083167 | 5085820 | 5084494 | 1999916 | ||||
| SUR1 | 816585 | AT2G20610 | 86 | 5085356 | 5085820 | 5085588 | 2001010 | ||||
| AOP1 | 828100 | AT4G03070 | 82 | 697138 | 697534 | 697336 | 2387242 | ||||
| AOP2 | 828102 | AT4G03060 | 79 | 692952 | 693321 | 693137 | 2391442 | ||||
| AOP3 | 828104 | AT4G03050 | 79 | 692952 | 693321 | 693137 | 2391442 | ||||
| HCL | HCL.A1.s.1 | A01 | 18784468 | GAUT1 | 825285 | AT3G61130 | 91 | 20219967 | 20220082 | 20220025 | 1435557 |
| NDF | NDF.A7.s.1 | A07 | 5709631 | QUA1 | 822105 | AT3G25140 | 87 | 5464119 | 5465842 | 5464981 | 244651 |
| GAUT10 | 816611 | AT2G20810 | 83 | 4127749 | 4129555 | 4128652 | 1580979 | ||||
| OLA | OLA.A1.s.1 | A01 | 18784468 | FAR7 | 832303 | AT5G22420 | 78 | 21097835 | 21098001 | 21097918 | 2313450 |
| OLA.A6.s.1 | A06 | 18059898 | FAR7 | 832303 | AT5G22420 | 76 | 15755098 | 15755262 | 15755180 | 2304718 | |
| OLA.A8.s.1 | A08 | 10337576 | CER4 | 829521 | AT4G33790 | 92 | 10388255 | 10388380 | 10388318 | 50742 | |
| FAR1 | 832311 | AT5G22500 | 79 | 10389865 | 10390018 | 10389942 | 52366 | ||||
| FAR7 | 832303 | AT5G22420 | 79 | 11667520 | 11667667 | 11667594 | 1330018 | ||||
| OLA.C3.s.1 | C03 | 17808711 | FAR7 | 832303 | AT5G22420 | 78 | 16964614 | 16964759 | 16964687 | 844025 | |
| SUL | SUL.A6.s.1 | A06 | 18128799 | ATSERAT3;1 | 816271 | AT2G17640 | 76 | 17771333 | 17772947 | 17772140 | 356659 |
| APK3 | 821077 | AT3G03900 | 76 | 17301192 | 17301351 | 17301272 | 827528 | ||||
| APK4 | 836888 | AT5G67520 | 76 | 17300756 | 17301552 | 17301154 | 827645 | ||||
| SUL.A9.s.1 | A09 | 3084578 | APK4 | 836888 | AT5G67520 | 80 | 3615223 | 3615740 | 3615482 | 530904 | |
| APK3 | 821077 | AT3G03900 | 78 | 3615562 | 3615705 | 3615634 | 531056 | ||||
| ATSERAT3;1 | 816271 | AT2G17640 | 75 | 4588363 | 4588772 | 4588568 | 1503990 | ||||