TABLE 1.

The list of detected QTLs for 390 nm using different GWAS methods in the tested soybean panel.

GWAS Method	Chromosome	Peak SNP position	Co-located QTL	Environmenta	References
MLM	3	44121448	Ureide content 1-g13.1	NA	Ray et al., 2015
			Ureide content 1-g13.2	NA	Ray et al., 2015
			Ureide content 1-g13.3	NA	Ray et al., 2015
			Ureide content 1-g13.4	NA	Ray et al., 2015
			Ureide content 1-g13.5	NA	Ray et al., 2015
		44198005		NA
		44326068		NA
		44328629		NA
		45039908		NA
	6	11953156		NA
		11953223		NA
	10	2906452		NA
		2906459		NA
		2906496		NA
FarmCPU	3	44121448	Ureide content 1-g13.1	NA	Ray et al., 2015
			Ureide content 1-g13.2	NA	Ray et al., 2015
			Ureide content 1-g13.3	NA	Ray et al., 2015
		44198005	Ureide content 1-g13.4	NA	Ray et al., 2015
			Ureide content 1-g13.5	NA	Ray et al., 2015
		44326068		NA
		44328629		NA
		45039908	Internode length 1-g3	NA	Fang et al., 2017
			Pubescence color 2-g1.1	NA	Fang et al., 2017
	6	11953223		NA
		11953223		NA
	10	2906452		NA
		2906459		NA
		2906496		NA
		50548092		NA
	13	30231980	Seed Yield 3-g5	NA	Contreras-Soto et al., 2017
		30232000	seed weight 6-g2	2	Sonah et al., 2015
			Phytoph 3-g22	2	Chang et al., 2016
			Phytoph 2-g4	2	Qin et al., 2017
			Phytoph 2-g5	2	Qin et al., 2017
			Phytoph 3-g23	2	Chang et al., 2016
			Leaflet width 1-g1	2	Fang et al., 2017
SVR	2	858431		NA
		858458		NA
	3	3729245	Phytoph 3-g1	NA	Chang et al., 2016
			Phytoph 3-g2	NA	Chang et al., 2016
			Phytoph 3-g3	NA	Chang et al., 2016
			Phytoph 3-g4	NA	Chang et al., 2016
			Phytoph 3-g5	NA	Chang et al., 2016
			Phytoph 3-g6	NA	Chang et al., 2016
	6	38679976		NA
		38787915		NA
		36746367		NA
	9	39344365	pod number 1-g4.1	NA	Fang et al., 2017
			pod number 1-g4.2	NA	Fang et al., 2017
		39344439	pod number 1-g4.3	NA	Fang et al., 2017
			seed thickness 2-g4	NA	Fang et al., 2017
	15	22232022		NA
		22231908		NA
	16	7313753	Sclero 3-g60	NA	Moellers et al., 2017
			ureide content 1-g43	NA	Ray et al., 2015
	20	22656999		NA

^aDetected in separate environments in addition to the combined environment. (1) 2018Ridgetown, (2) 2019Ridgetwon, (3) 2018Palmyra, (4) 2019Palmyra, (NA) Not found in any separate environment.

MLM, mixed linear model; FarmCPU, fixed and random model circulating probability unification; RF, random forest; SVR, support vector regression.