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GWAS Report for Seed coat color 3

Experimental Details

Number of germplasm analyzed	553
Number of loci tested	35,270
Platform name	SoySNP50K
Platform details	SoySNP50K iSelect BeadChip

Publication for This Experiment

Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean
(Vuong et al. 2015a)

BMC Genomics 2015, 16:593
10.1186/s12864-015-1811-y

Controlled vocabulary terms associated with the QTL Family

SoyBase	SOY:0001414
PO	PO:0009088
TO	TO:0000190

Other traits reported in this paper

• SCN 4
• Flower color 4
• Pubescence color 4
• Stem termination type 2
• Pod shattering 2
• Lodging 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	R2	Chromosome	Linkage Group
Seed coat color 3-g1	Black	ss715602762	0.62	Gm08	A2
Seed coat color 3-g2	Green	ss715580343	0.31	Gm01	D1a
Seed coat color 3-g3	Yellow	ss715620481	0.41	Gm15	E
Seed coat color 3-g4	Yellow	ss715580343	0.58	Gm01	D1a
Seed coat color 3-g5	Yellow	ss715602763	0.56	Gm08	A2
Seed coat color 3-g6	Yellow	ss715593807	0.55	Gm06	C2

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Click Here to View Full List of GWAS QTL