| Gene |
Accessionnumber |
Functionalannotation |
Reference |
Controllingtrait |
P-value |
Haplotype |
688Coincidence |
Sequence |
| GmNF-YA02 |
Glyma.02G303800 |
adomainofthenucleartranscriptionfactorY |
Lu
et al.2016 |
Seed
quality(oilcontent) |
0.00497 |
freq |
hap |
Chr02__47899986 |
oil |
|
FAM |
AACAAGAGGATGAGGATAAAGGAAC |
| 362 |
Hap1 |
C |
HIGH |
270/324 |
83.33% |
HEX |
AACAAGAGGATGAGGATAAAGGAAT |
| 188 |
Hap2 |
T |
LOW |
120/179 |
67.04% |
R |
GCAAGGCAACACTGGACTAC |
| GmMPK1 |
Glyma.08G309500 |
mitogen-activated
protein kinase |
Wu
et al. 2020 |
Seed
quality |
0.02391 |
freq |
hap |
Chr08__42881055 |
oil |
|
FAM |
TCTCTTGGGTTCTTGTTATATTCCTCAA |
| 507 |
Hap1 |
T |
LOW |
343/369 |
92.95% |
HEX |
TCTCTTGGGTTCTTGTTATATTCCTCAG |
| 56 |
Hap2 |
C |
HIGH |
73/130 |
56.15% |
R |
GCAAACAAATAATGCTGCCAGC |
| GmSDP1-1 |
Glyma.02G190000 |
triacylglycerol
lipase SDP1 |
Kanai
et al. 2019 |
Seed
quality (oil content) |
0.02921 |
freq |
hap |
Chr02__35666459 |
oil |
|
FAM |
CCATTTCTAGCAAGTTTTGTCTATGATTG |
| 540 |
Hap1 |
C |
HIGH |
433/477 |
90.78% |
HEX |
CCATTTCTAGCAAGTTTTGTCTATGATTT |
| 37 |
Hap2 |
A |
LOW |
61/105 |
58.10% |
R |
ACCAAACTCAGGTGCATCAGG |
| GmMYB73 |
Glyma.06G303100 |
MYB
transcription factor MYB73 |
Liu
et al. 2014b |
Seed
quality (oil content) |
0.00705 |
freq |
hap |
Chr06__49257882 |
oil |
|
FAM |
GCGATCTATGTCAGCCATTGC |
| 554 |
Hap1 |
G |
HIGH |
492/507 |
97.04% |
HEX |
GCGATCTATGTCAGCCATTGG |
| 46 |
Hap4 |
C |
LOW |
46/65 |
70.77% |
R |
ACACACTTCTTTATCTGCATCTAATTC |
| GmZF351 |
Glyma.06G290100 |
Zinc
finger C-x8-C-x5-C-x3-H type family protein |
Li
et al. 2017b |
Seed
quality (oil content) |
2.38E-06 |
freq |
hap |
Chr06__47898749 |
oil |
|
FAM |
TGCGGAATTGGTCGGAGGCA |
| 89 |
Hap4 |
A |
LOW |
37/55 |
67.27% |
HEX |
TGCGGAATTGGTCGGAGGCG |
| 249 |
Hap2 |
G |
HIGH |
421/498 |
84.54% |
R |
AGTGGCTCCACTGACTCCTCCA |
| GmSWEET10b |
Glyma.08G183500 |
sugar
efflux transporter SWEET24 |
Wang
et al. 2020e |
Seed
quality (oil and protein contents) |
0.00428 |
freq |
hap |
Chr08__14722335 |
oil |
|
FAM |
TTGGCGAACACTCTACAACAGGT |
| 325 |
Hap1 |
T |
HIGH |
232/273 |
84.98% |
HEX |
TTGGCGAACACTCTACAACAGGG |
| 131 |
Hap6 |
G |
LOW |
188/276 |
68.12% |
R |
ACTGATAAGTGATAAGAGGAGTGATGATTGG |
| GmSWEET10b |
Glyma.08G183500 |
sugar
efflux transporter SWEET24 |
Wang
et al. 2020e |
Seed
quality (oil and protein contents) |
0.00428 |
freq |
hap |
Chr08__14722343 |
oil |
|
FAM |
AAGAGGAGTGATGATTGGATTTGAACG |
| 325 |
Hap1 |
C |
HIGH |
341/398 |
85.68% |
HEX |
AAGAGGAGTGATGATTGGATTTGAACA |
| 131 |
Hap6 |
T |
LOW |
94/152 |
61.84% |
R |
ATATTGGCGAACACTCTACAACAGG |
| GmSDP1-2 |
Glyma.10G105200 |
triacylglycerol
lipase SDP1 |
Kanai
et al. 2019 |
Seed
quality (oil content) |
0.04929 |
freq |
hap |
Chr10__23337981 |
oil |
|
FAM |
CCATGAGAAGCAGCAGCAGT |
| 154 |
Hap1 |
C |
HIGH |
295/334 |
88.32% |
HEX |
CCATGAGAAGCAGCAGCAGC |
| 491 |
Hap2 |
T |
LOW |
101/167 |
60.48% |
R |
TCGGCCATGAAAGCAAATTGT |
| GmSWEET10a |
Glyma.15G049200 |
sugar
efflux transporter SWEET39 |
Wang
et al. 2020e |
Seed
quality (oil and protein contents) |
1.58E-10 |
freq |
hap |
Chr15__3875093 |
oil |
|
FAM |
TGACTTTGTCATCATCCACTTCCT |
| 653 |
Hap1 |
T |
HIGH |
488/504 |
96.83% |
HEX |
TGACTTTGTCATCATCCACTTCCA |
| 33 |
Hap2 |
A |
LOW |
10/27 |
37.04% |
R |
CGGTGAGAGTGAGAAGGAGC |
| GmPDAT |
Glyma.13G108100 |
REGULATOR
OF CHROMOSOME CONDENSATION |
Liu
et al. 2020a; Liu et al. 2020b |
Seed
quality (oil content) |
0.04737 |
freq |
hap |
Chr13__22247900 |
oil |
|
FAM |
TTGGCACCGCATCCAGAAACC |
| 160 |
Hap5 |
G |
LOW |
202/258 |
78.29% |
HEX |
TTGGCACCGCATCCAGAAACA |
| 198 |
Hap1 |
T |
HIGH |
203/311 |
65.27% |
R |
GAAAGGGATTTCAGATTCGGACACG |
| GmOLEO1 |
Glyma.20G196600 |
oleosin-encoding
gene |
Zhang
et al. 2019b |
Seed
quality (oil content) |
0.01788 |
freq |
hap |
Chr20__43441604 |
oil |
|
FAM |
TCGTTGTTAAGTGTTAACGCTGG |
| 577 |
Hap1 |
G |
HIGH |
490/508 |
96.46% |
HEX |
TCGTTGTTAAGTGTTAACGCTGC |
| 26 |
Hap2 |
C |
LOW |
34/62 |
54.84% |
R |
TGGTTGTTGTTTGTTGCATGTT |
| GmDGAT1B1 |
Glyma.17G053300 |
diacylglycerolacyltransferase-1b |
Roesler
et al. 2016 |
Seed
quality (oil content) |
0.03650 |
freq |
hap |
Chr17__4054733 |
oil |
|
FAM |
GACTCCATCAACAGCGACGA |
| 571 |
Hap1 |
A |
HIGH |
491/513 |
95.71% |
HEX |
GACTCCATCAACAGCGACGC |
| 25 |
Hap3 |
C |
LOW |
26/46 |
56.52% |
R |
TCCTTCACTTTGCGGTGAGC |
| GmSDP1-4 |
Glyma.03g130900 |
triacylglycerol
lipase SDP1 |
Kanai
et al. 2019 |
Seed
quality (oil content) |
9.98E-05 |
freq |
hap |
Chr03__34612476 |
oil |
|
FAM |
GCTAGCTCTGCATCTGAACAC |
| 264 |
Hap3 |
G |
HIGH |
512/533 |
96.06% |
HEX |
GCTAGCTCTGCATCTGAACAT |
| 45 |
Hap4 |
A |
LOW |
26/44 |
59.09% |
R |
ATCCATACCCGAATCTGTGCC |
| GmDof4 |
Glyma.17G081800 |
Downregulates
expression of seed storage protein gene CRA1（Increases fatty acid
content by activating the expression of genes encoding acetyl-CoA carboxylase
and long-chain acyl-CoA synthetase） |
Sun et al., 2018 |
Seed
quality (oil and protein contents) |
4.30E-04 |
Freq |
Hap |
Chr17__6349671 |
oil |
|
FAM |
GTTGATGTCAGTGAGTGCGTCGT |
| 471 |
Hap1 |
T |
HIGH |
370/416 |
88.94% |
HEX |
GTTGATGTCAGTGAGTGCGTCGA |
| 64 |
Hap3 |
A |
LOW |
88/159 |
55.35% |
R |
CGATAGAGAGAAGAAGTACGTTGTTGCAG |
| GmPLDγ |
Glyma.01G215100 |
Participates
in fatty acid remodeling |
Bai et al., 2020 |
Seed
quality (oil content) |
0.03866 |
Freq |
Hap |
Chr01__54580463 |
oil |
|
FAM |
CTTACATTACATGGCTCATTTGGTTTAT |
| 305 |
Hap1 |
T |
HIGH |
378/438 |
86.30% |
HEX |
CTTACATTACATGGCTCATTTGGTTTAC |
| 98 |
Hap3 |
C |
LOW |
95/141 |
67.38% |
R |
AGTGGTTTGAAATGGAACAATTTGC |
| GmFAD2-1A |
Glyma.10G278000 |
Catalyzes
formation of linoleic acid from oleic acid and linolenic acid |
Ustun et al., 2017; Combs et al., 2019 |
Seed
quality (oil content) |
2.09E-05 |
Freq |
Hap |
Chr10__50013104 |
oil |
|
FAM |
TGCGTAGAGAGTTTAATGGCAGGT |
| 652 |
Hap1 |
T |
HIGH |
551/566 |
97.35% |
HEX |
TGCGTAGAGAGTTTAATGGCAGGG |
| 36 |
Hap2 |
G |
LOW |
12/20 |
60.00% |
R |
CAGTGTAATTATGACTACAGGTCAATTTGC |
| GmLox3 |
Glyma.15G026300 |
Catalyzes
the oxidation of linoleic acid to produce lipid hydroperoxide |
González-Gordo et al., 2023 |
Seed
quality (oil content) |
4.10E-05 |
Freq |
Hap |
Chr15__2127717 |
oil |
|
FAM |
CAAATTGGACATCTGATACAAGAGCA |
| 578 |
Hap1 |
A |
HIGH |
454/484 |
93.80% |
HEX |
CAAATTGGACATCTGATACAAGAGCG |
| 35 |
Hap3 |
G |
LOW |
49/94 |
51.04% |
R |
CAGTTTCTCATCGTTGTTTCTCTCTGAG |
| GmLPAAT |
Glyma.15G034100 |
Catalyzes
formation of PA from LPA |
McNaughton et al., 2015 |
Seed
quality (oil content) |
1.06E-03 |
Freq |
Hap |
Chr15__2725475 |
oil |
|
FAM |
TCGGCCACTATCAAAGAACTGC |
| 345 |
Hap1 |
G |
HIGH |
239/300 |
79.67% |
HEX |
TCGGCCACTATCAAAGAACTGT |
| 125 |
Hap2 |
A |
LOW |
195/271 |
71.96% |
R |
CATGACACCTTGATGCCAGCC |
| GmDGAT3-2 |
Glyma.17G041600 |
Involved
in the distribution of 18:3 to TAG |
Hernández et al., 2012 |
Seed
quality (oil content) |
0.04631 |
Freq |
Hap |
Chr17__3095917 |
oil |
|
FAM |
CCATCTCTACCTCTCACCGTTGT |
| 460 |
Hap1 |
A |
HIGH |
341/381 |
89.50% |
HEX |
CCATCTCTACCTCTCACCGTTGA |
| 73 |
Hap2 |
T |
LOW |
118/196 |
60.20% |
R |
AGGTTGTGATGTAGACGGAAGTCG |
| GmLEC2b |
Glyma.20G035700 |
Promotes
TAG accumulation |
Manan et al., 2017b |
Seed
quality (oil content) |
0.01288 |
Freq |
Hap |
Chr20__5007737 |
oil |
|
FAM |
TCAACATTGACGGGTGCTGC |
| 526 |
Hap1 |
C |
LOW |
350/395 |
88.61% |
HEX |
TCAACATTGACGGGTGCTGT |
| 162 |
Hap2 |
T |
HIGH |
98/180 |
54.44% |
R |
CAATATTGTGGGGGAGGGGG |
| GmFAD2-1B |
Glyma.20G111000 |
Catalyzes
formation of linoleic acid from oleic acid and linolenic acid |
Ustun et al., 2017; Combs et al., 2019 |
Seed
quality (oil content) |
0.01410 |
Freq |
Hap |
Chr20__35315397 |
oil |
|
FAM |
GTGCCAAAGGATTTTCGACCATC |
| 109 |
Hap2 |
G |
LOW |
326/364 |
89.56% |
HEX |
GTGCCAAAGGATTTTCGACCATA |
| 40 |
Hap3 |
T |
HIGH |
111/206 |
53.88% |
R |
GCTTACTCACAAAGCAGTCTTACACT |
| GmFATB1A |
Glyma.05G012300 |
Maintains
the saturated/unsaturated balance of membrane fatty acids |
Zhou
et al. , 2021;
Carrero-Colon et al., 2022 |
Seed
quality (oil content) |
6.71E-05 |
Freq |
Hap |
Chr05__1129082 |
oil |
|
FAM |
TCACGTAAAAGCCAATCACGG |
| 524 |
Hap1 |
G |
HIGH |
399/447 |
89.26% |
HEX |
TCACGTAAAAGCCAATCACGA |
| 55 |
Hap2 |
A |
LOW |
81/132 |
61.36% |
R |
TGGACACTTGGGTTTCTGGATC |
| GmSEIPIN1A |
Glyma.09G250400 |
Regulates
the number and size of lipid droplets |
Qi
et al., 2024 |
Seed
quality (oil content) |
0.01970 |
Freq |
Hap |
Chr09__47112910 |
oil |
|
FAM |
CACTTAGCGAGGAGAAGGAGC |
| 370 |
Hap1 |
C |
LOW |
249/307 |
81.11% |
HEX |
CACTTAGCGAGGAGAAGGAGT |
| 148 |
Hap2 |
T |
HIGH |
176/246 |
71.54% |
R |
GCCATTAACTAGCGTATCCCATTG |
| GmDGAT3-1 |
Glyma.13G118300 |
Involved
in the distribution of 18:3 to TAG |
Hernández et al., 2012 |
Seed
quality (oil content) |
0.00927 |
Freq |
Hap |
Chr13__23112925 |
oil |
|
FAM |
CGCGCACTTTCGTTCGGT |
| 506 |
Hap1 |
T |
HIGH |
364/404 |
90.10% |
HEX |
CGCGCACTTTCGTTCGGC |
| 149 |
Hap2 |
C |
LOW |
100/167 |
59.88% |
R |
GTCTCCACCGTAGGATGCTGG |
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