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GWAS Report for SCN 3

Experimental Details

Number of germplasm analyzed	200
Number of loci tested	33,194
Platform name	SLAF-seq
Platform details	Specific Locus Amplified Fragment Sequencing

Publication for This Experiment

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean
(Wen et al. 2014a)

BMC Genomics 2014, 15:809
10.1186/1471-2164-15-809

Controlled vocabulary terms associated with the QTL Family

SoyBase	SOY:0001335
GO	GO:0009624
TO	TO:0000384

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	Associated locus	p-value	Candidate gene	Chromosome	Linkage Group
SCN 3-g1	RS:7631207	7.7x10^(11)	Glyma.08G099400	Gm07	M
SCN 3-g2	RS:7640250	7.7x10^(11)	Glyma.08G099700	Gm07	M
SCN 3-g3	RS:7671170	7.7x10^(11)	Glyma.08G100100, Glyma.08G100700, Glyma.08G100800	Gm08	A2
SCN 3-g4	RS:7662003	3.2x10^(10)		Gm08	A2
SCN 3-g5	RS:7664479	3.2x10^(10)		Gm08	A2
SCN 3-g6	RS:7622492	1.5x10^(10)	Glyma.08G097300	Gm08	A2
SCN 3-g7	RS:7661660	6.6x10^(9)		Gm08	A2
SCN 3-g8	RS:46625879	1.3x10^(7)	Glyma.18G193200, Glyma.18G193300, Glyma.18G193400	Gm08	A2
SCN 3-g9	RS:36423980	5.4x10^(5)	Glyma.07G195400, Glyma.07G195500, Glyma.07G196000, Glyma.07G193900, Glyma.07G196500, Glyma.07G196800	Gm08	A2
SCN 3-g10	RS:3853672	3.3x10^(5)	Glyma.14G048600, Glyma.14G049500, Glyma.14G047900, Glyma.14G051600	Gm08	A2
SCN 3-g11	RS:35898587	1.0x10^(19)	Glyma.07G190900, Glyma.07G191000, Glyma.07G191100, Glyma.07G191200, Glyma.07G191500	Gm14	B2
SCN 3-g12	RS:16268025	3.0x10^(11)	Glyma.08G200800, Glyma.08G201000, Glyma.08G201100, Glyma.08G200100, Glyma.08G200200, Glyma.08G202300	Gm15	E
SCN 3-g13	RS:38522986	1.3x10^(6)		Gm18	G

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