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GWAS Report for Pubescence color 2

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:0001719
PO	PO:0000282
TO	TO:0000911

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
• Seed amino acids 1
• 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
• 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
Pubescence color 2-g1.1	Pubescence color	Chr03_45188204	1.32E-10	Gm03	N
Pubescence color 2-g1.2	Pubescence color	Chr03_45301350	1.32E-10	Gm03	N
Pubescence color 2-g1.3	Pubescence color	Chr03_45546666	1.32E-10	Gm03	N
Pubescence color 2-g2.1	Pubescence color	Chr06_16701822	1.38E-61	Gm06	C2
Pubescence color 2-g2.2	Pubescence color	Chr06_18734414	1.38E-61	Gm06	C2
Pubescence color 2-g2.3	Pubescence color	Chr06_19482848	1.38E-61	Gm06	C2
Pubescence color 2-g3.1	Pubescence color	Chr12_16899433	1.70E-15	Gm12	H
Pubescence color 2-g3.2	Pubescence color	Chr12_16906312	1.70E-15	Gm12	H
Pubescence color 2-g4.1	Pubescence color	Chr16_1439581	6.31E-23	Gm16	J
Pubescence color 2-g4.2	Pubescence color	Chr16_1440263	6.31E-23	Gm16	J
Pubescence color 2-g4.3	Pubescence color	Chr16_1445782	6.31E-23	Gm16	J

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