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GWAS Report for Seed amino acids 1

Experimental Details

Number of germplasm analyzed	809
Number of loci tested	4M

Publication for This Experiment

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean
(Fang et al. 2017)

Genome Biology 2017, 18(161)
10.1186/s13059-017-1289-9

Controlled vocabulary terms associated with the QTL Family

SoyBase	SOY:0001757
GO	GO:0006520
PO	PO:0000003
TO	TO:0002673

Other traits reported in this paper

• First flower 5
• Interbranch length 1
• Branching 1
• Canopy width 1
• Leaflet chlorophyll 2
• Seed palmitic 2
• Seed long-chain fatty acid 1
• Seed stearic 1
• Seed alpha-linolenic acid 1
• Flower color 2
• Hilum color 2
• Leaflet area 1
• Leaflet length 1
• Leaflet shape 1
• Leaflet width 1
• Lodging 1
• Seed set 1
• Plant height 5
• R8 full maturity 5
• Pod shattering 1
• Pubescence color 2
• Reproductive stage length 1
• Seed coat luster 1
• Seed coat color 1
• Seed height 1
• Seed width to height ratio 1
• Seed length to thickness ratio 2
• Seed thickness 2
• Seed volume 1
• Stem termination type 1
• Internode length 1
• Node number 1
• Pod number 1
• Stem shape, main 1
• Seed oil to protein ratio 1
• Total seed number 3

GWAS QTL

The GWAS QTL can be shown in either the SoyBase CMap Genetic Map Viewer (where it can be compared to the other GWAS and biparental QTL) or in the SoyBase GBrowse Genome Viewer (where it can be compared to the genes in that chromosomal region). When a candidate gene has been identified clicking on the gene name ('Glyma') opens the SoyBase Gene Report page for that gene.

GWAS QTL name	Original name	Associated locus	p-value	Chromosome	Linkage Group
Seed amino acids 1-g1.1	L_Glu(Gln) content	Chr01_53486467	3.16E-08	Gm01	D1a
Seed amino acids 1-g1.2	L_Glu(Gln) content	Chr01_53486650	3.16E-08	Gm01	D1a
Seed amino acids 1-g2.1	L_Glu(Gln) content	Chr08_35266140	2.19E-08	Gm08	A2
Seed amino acids 1-g2.2	L_Glu(Gln) content	Chr08_35266158	2.19E-08	Gm08	A2
Seed amino acids 1-g2.3	L_Glu(Gln) content	Chr08_35266324	2.19E-08	Gm08	A2
Seed amino acids 1-g3	L_Glu(Gln) content	Chr09_33309127	6.03E-08	Gm09	K
Seed amino acids 1-g4.1	L_Glu(Gln) content	Chr13_2546775	1.12E-08	Gm13	F
Seed amino acids 1-g4.2	L_Glu(Gln) content	Chr13_2546862	1.12E-08	Gm13	F
Seed amino acids 1-g5.1	L_Glu(Gln) content	Chr14_5055466	5.62E-08	Gm14	B2
Seed amino acids 1-g5.2	L_Glu(Gln) content	Chr14_5055474	5.62E-08	Gm14	B2
Seed amino acids 1-g6.1	L_Gly content	Chr10_2422267	1.05E-07	Gm10	O
Seed amino acids 1-g6.2	L_Gly content	Chr10_2428789	1.05E-07	Gm10	O
Seed amino acids 1-g6.3	L_Gly content	Chr10_2436611	1.05E-07	Gm10	O
Seed amino acids 1-g7	L_Phe content	Chr13_2546862	1.82E-07	Gm13	F
Seed amino acids 1-g8	L_Ser content	Chr01_989187	7.94E-10	Gm01	D1a
Seed amino acids 1-g9.1	L_Ser content	Chr01_53486467	1.82E-10	Gm01	D1a
Seed amino acids 1-g9.2	L_Ser content	Chr01_53486490	1.82E-10	Gm01	D1a
Seed amino acids 1-g9.3	L_Ser content	Chr01_53486686	1.82E-10	Gm01	D1a
Seed amino acids 1-g10.1	L_Ser content	Chr08_35266140	7.94E-11	Gm08	A2
Seed amino acids 1-g10.2	L_Ser content	Chr08_35266158	7.94E-11	Gm08	A2
Seed amino acids 1-g10.3	L_Ser content	Chr08_35266324	7.94E-11	Gm08	A2
Seed amino acids 1-g11	L_Ser content	Chr09_33309127	1.74E-09	Gm09	K
Seed amino acids 1-g12.1	L_Ser content	Chr13_2546775	1.02E-11	Gm13	F
Seed amino acids 1-g12.2	L_Ser content	Chr13_2546862	1.02E-11	Gm13	F
Seed amino acids 1-g13.1	L_Ser content	Chr14_5055466	9.77E-10	Gm14	B2
Seed amino acids 1-g13.2	L_Ser content	Chr14_5055474	9.77E-10	Gm14	B2
Seed amino acids 1-g14	L_Thr content	Chr01_53486490	1.91E-07	Gm01	D1a
Seed amino acids 1-g15	L_Thr content	Chr10_2436611	1.07E-07	Gm10	O
Seed amino acids 1-g16	L_Thr content	Chr13_2546862	4.57E-08	Gm13	F
Seed amino acids 1-g17	L_Thr content	Chr20_38215861	2.45E-07	Gm20	I
Seed amino acids 1-g18.1	L_Tyr content	Chr01_989187	1.66E-12	Gm01	D1a
Seed amino acids 1-g18.2	L_Tyr content	Chr01_989204	1.66E-12	Gm01	D1a
Seed amino acids 1-g19	L_Tyr content	Chr01_2181558	5.37E-08	Gm01	D1a
Seed amino acids 1-g20.1	L_Tyr content	Chr01_53486467	1.35E-16	Gm01	D1a
Seed amino acids 1-g20.2	L_Tyr content	Chr01_53486686	1.35E-16	Gm01	D1a
Seed amino acids 1-g21.1	L_Tyr content	Chr08_35266140	1.15E-16	Gm08	A2
Seed amino acids 1-g21.2	L_Tyr content	Chr08_35266324	1.15E-16	Gm08	A2
Seed amino acids 1-g22	L_Tyr content	Chr09_33309127	1.41E-16	Gm09	K
Seed amino acids 1-g23.1	L_Tyr content	Chr13_2546775	9.12E-17	Gm13	F
Seed amino acids 1-g23.2	L_Tyr content	Chr13_2546862	9.12E-17	Gm13	F
Seed amino acids 1-g24.1	L_Tyr content	Chr14_5055466	2.09E-15	Gm14	B2
Seed amino acids 1-g24.2	L_Tyr content	Chr14_5055474	2.09E-15	Gm14	B2
Seed amino acids 1-g25.1	L_Tyr content	Chr19_44806855	1.29E-07	Gm19	L
Seed amino acids 1-g25.2	L_Tyr content	Chr19_44912660	1.29E-07	Gm19	L
Seed amino acids 1-g25.3	L_Tyr content	Chr19_44922846	1.29E-07	Gm19	L
Seed amino acids 1-g26.1	Total AA subgroup 1 content	Chr10_2400625	1.17E-07	Gm10	O
Seed amino acids 1-g26.2	Total AA subgroup 1 content	Chr10_2415581	1.17E-07	Gm10	O
Seed amino acids 1-g27	Total AA subgroup 2 content	Chr01_989187	1.45E-08	Gm01	D1a
Seed amino acids 1-g28.1	Total AA subgroup 2 content	Chr01_53486467	7.76E-11	Gm01	D1a
Seed amino acids 1-g28.2	Total AA subgroup 2 content	Chr01_53486686	7.76E-11	Gm01	D1a
Seed amino acids 1-g29.1	Total AA subgroup 2 content	Chr08_35266140	7.94E-11	Gm08	A2
Seed amino acids 1-g29.2	Total AA subgroup 2 content	Chr08_35266324	7.94E-11	Gm08	A2
Seed amino acids 1-g30	Total AA subgroup 2 content	Chr09_33309127	1.10E-10	Gm09	K
Seed amino acids 1-g31.1	Total AA subgroup 2 content	Chr13_2546775	2.19E-11	Gm13	F
Seed amino acids 1-g31.2	Total AA subgroup 2 content	Chr13_2546862	2.19E-11	Gm13	F
Seed amino acids 1-g32.1	Total AA subgroup 2 content	Chr14_5055466	2.82E-10	Gm14	B2
Seed amino acids 1-g32.2	Total AA subgroup 2 content	Chr14_5055474	2.82E-10	Gm14	B2

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