Table 2.

List of candidate genes identified for seed composition traits using GWAS from individual studies and meta-GWAS

Chromosome	Likely gene	Meta-GWAS	Individual studies GWAS	Trait(s)	Studies source
1	BCAT/MDH	*	*	Isoleucine, Leucine, Lysine, Methionine, Palmitic acid, Threonine, Tryptophan	aa op sugar fa 2009, il0102, meta, ms967
3	Glyma.03g173400		*	Methionine	aa op sugar fa 2009
5	fap3	*	*	Iodine number, Palmitic acid, Stearic acid	aa op sugar fa 2009, 1il64, 2il81.1, 2il81.2, 2ky81, 2mn81, 3il83.1, 3il84, 3il87, il0102, meta, ms1999.01, ms2000.02, ms923, ms967
	MTFL		*	Linoleic acid, Seed oil, Oleic acid, Tryptophan	aa op sugar fa 2009, 2il81.1, il0102, ms1999.01, ms967
6	Glyma.06G214800	*	*	Stearic acid	meta, ms1999.01, ms2000.02
	Glyma.06g275100		*	Cysteine	aa op sugar fa 2009
	T		*	Arginine, Cysteine, Isoleucine, Leucine	aa op sugar fa 2009
8	I/AK-HDSH	*	*	Cysteine, Isoleucine, Leucine, Linoleic acid, Lysine, Methionine, Seed oil, Palmitic acid, Stearic acid, Threonine, Valine	aa op sugar fa 2009, meta, ms967
9	Glyma.09g090600	*	*	Palmitic acid	il0102, meta
	R		*	Tryptophan	aa op sugar fa 2009
13	Glyma.13g149700	*	*	Oleic acid, Palmitic acid, Seed protein	meta, ms2000.02
14	fan1	*	*	Linolenic acid	2mn81, 3il83.1, il0102, meta, mn945, ms967
15	Glyma.15g049200 “GmSWEET15”	*	*	Linolenic acid, Seed oil, Seed protein, Threonine	aa op sugar fa 2009, 2ky81, 3il83.1, 3il84, il989, meta, ms1999.01, ms923
19	Dt1, Glyma.19g194300		*	Linoleic acid, Oleic acid, Valine	aa op sugar fa 2009, ms1999.01, ms2000.02
20	CHR20OP	*	*	Seed oil, Seed protein	aa op sugar fa 2009, 2il81.1, meta, ms1999.01, ms967
14 (3)	SACPD-C	*	*	Stearic acid	1il66, 2il81.1, 2mn81, 3il83.1, 4il87, 5il90, il0102, meta, mn945, ms923

* Bonferroni corrected P-value threshold [p-value 0.05 / number of markers].