TABLE 4.

The list of detected QTLs for 730 nm using different GWAS methods in the tested soybean panel.

GWAS Method	Chromosome	Peak SNP position	Co-located QTL	Environmenta	References
MLM	1	41281098		NA
	2	17694706		NA
		17694726		NA
	5	1115689	Seed palmitic 4-g1	NA	Zhang et al., 2018
			Seed palmitic 2-g1.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g21.2	NA	Fang et al., 2017
		1153958	Seed long-chain fatty acid 1-g19.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g14.1	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g14.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g1.2	NA	Fang et al., 2017
			Seed stearic 3-g1	NA	Zhang et al., 2018
	14	2259506	Reproductive stage length 1-g3.1	NA	Fang et al., 2017
			Reproductive stage length 1-g3.2	NA	Fang et al., 2017
	15	9020829		NA
	17	31797213		NA
	18	6686269		NA
		6728432	Seed protein 7-g27	NA	Zhang et al., 2017
FarmCPU	1	16343505		NA
		41281098		NA
	2	17694706		NA
		17694726		NA
		42645195	WUE 2-g6	4	Kaler et al., 2017
			WUE 3-g4	4	Dhanapal et al., 2018
			WUE 3-g5	4	Dhanapal et al., 2018
			WUE 3-g6	4	Dhanapal et al., 2018
	5	1115619	Seed palmitic 4-g1	NA	Zhang et al., 2018
			Seed palmitic 2-g1.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g21.2	NA	Fang et al., 2017
		1115673	Seed long-chain fatty acid 1-g19.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g14.1	NA	Fang et al., 2017
		1115689	Seed long-chain fatty acid 1-g14.2	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g1.2	NA	Fang et al., 2017
		1153958	Seed stearic 3-g1	NA	Zhang et al., 2018
		1467115	Seed palmitic 5-g2	NA	Li et al., 2015
			Seed palmitic 5-g1	NA	Li et al., 2015
			Seed palmitic 2-g1.3	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g21.3	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g19.3	NA	Fang et al., 2017
			Seed long-chain fatty acid 1-g1.3	NA	Fang et al., 2017
			Seed width to height ratio 1-g2.1	NA	Fang et al., 2017
			Seed width to height ratio 1-g2.2	NA	Fang et al., 2017
			Seed width to height ratio 1-g2.3	NA	Fang et al., 2017
	14	2259506	Reproductive stage length 1-g3.1	NA	Fang et al., 2017
		2259506	Reproductive stage length 1-g3.2	NA	Fang et al., 2017
	15	9020829	Seed coat luster 1-g1.1	NA	Fang et al., 2017
			WUE 3-g26	NA	Dhanapal et al., 2018
			WUE 3-g27.1	NA	Dhanapal et al., 2018
	17	31797213		NA
	18	6686269	Seed protein 7-g27	NA	Zhang et al., 2017
		6728432	Seed protein 7-g27	NA	Zhang et al., 2017
SVR	1	47953926		1
	4	19007585		NA
		18643026		NA
	6	41477920		NA
	9	39659468	Seed Ser 2-g1	2	Li et al., 2018
			Seed Thr 2-g1	2	Li et al., 2018
		39664525	Seed Tyr 2-g2	NA	Li et al., 2018
			Seed Lys 2-g2	NA	Li et al., 2018
			Seed Leu 2-g2	NA	Li et al., 2018
			Seed Ala 2-g2	NA	Li et al., 2018
			Seed Gly 2-g2	NA	Li et al., 2018
		39366957	Pod number 1-g4.1	NA	Fang et al., 2017
			Pod number 1-g4.2	NA	Fang et al., 2017
		39372117	Pod number 1-g4.3	NA	Fang et al., 2017
			seed thickness 2-g4	2	Fang et al., 2017
		40355403		NA
	10	3054709		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.