. 2017 Feb 1;19(4):700–712. doi: 10.1093/bib/bbw145

Table 3.

GWAS for four flowering time traits in Arabidopsis using six GWAS methods

Trait	Gene	Chr	SNP (bp)	FASTmrEMMA				E-BAYES				SUPER				EMMA				References
Trait	Gene	Chr	SNP (bp)	LOD	Effect	MAF	r² (%)	LOD	Effect	MAF	r² (%)	P-value	Effect	MAF	r² (%)	P-value	Effect	MAF	r² (%)	References
LD	At1g22770	1	8045438	4.872	−0.112	0.395	0.549													[31]
	At1g23000	1	8128350	9.006	−0.197	0.461	1.767													[31]
	At2g22540	2	9588685	10.338	−0.330	0.281	4.034	10.753	−0.611	0.281	13.817					2.78E-09	−0.815	0.281	24.607	[31]
	At2g22610	2	9588685	10.338	−0.330	0.281	4.034	10.753	−0.611	0.281	13.817					2.78E-09	−0.815	0.281	24.607	[31]
	At3g61970	3	22949227	5.919	0.149	0.413	0.986													[31]
	At5g10140	5	3188328	12.759	−0.272	0.263	2.630													[31]
	At4g00310	4	153459									8.39E-08	−0.363	0.168	3.374					[31]
	At4g00335	4	167142									6.75E-08	−0.538	0.138	6.307					[31]
	At4g00450	4	196614									2.88E-08	−0.227	0.389	2.243					[31]
	At4g01280	4	516758									8.15E-08	−0.504	0.108	4.483					[31]
SDV	At1g05440	1	1595585	4.298	0.117	0.214	1.346													[31]
	At1g05470	1	1595585	4.298	0.117	0.214	1.346													[31]
	At1g77080	1	28965510	10.817	−0.177	0.484	4.576	4.020	−0.170	0.484	4.221									[31]
	At2g41890	2	17488070	4.339	0.099	0.302	1.208													[31]
	At3g20260	3	7084425	3.309	0.068	0.302	0.570													[31]
	At3g49600	3	18385143	4.529	0.118	0.321	1.774													[31]
	At4g05420	4	2748735	4.286	−0.091	0.459	1.203													[31]
	At5g04240	5	1164843	4.479	−0.137	0.220	1.884													[31]
	At5g09805	5	3055565	4.763	−0.105	0.233	1.151													[32]
	At5g57360	5	23249199	5.419	−0.141	0.321	2.533													[31]
	At5g57390	5	23249199	5.419	−0.141	0.321	2.533													[31]
	At5g46880	5	19044037													3.55E-08	0.408	0.107	9.296	[31]
	At5g67100	5	26794176													1.79E-07	−0.292	0.321	10.864	[31]
	At5g67200	5	26794176													1.79E-07	−0.292	0.321	10.864	[33]
8W GH LN	At1g77080	1	28965510	3.857	−0.109	0.497	2.610													[31]
	At2g27380	2	11703876	9.631	−0.153	0.325	4.514													[33]
	At4g32980	4	15918498	4.651	−0.147	0.147	2.384													[31]
	At5g15850	5	5196549	5.923	−0.106	0.319	2.145													[31]
	At5g45890	5	18600041	4.608	−0.107	0.423	2.456													[31]
8W GH FT	At1g03457	1	863771	5.055	0.040	0.460	1.199													[31]
	At2g27380	2	11703876	4.744	−0.043	0.323	1.122													[33]
	At2g47230	2	19396129	4.208	−0.038	0.298	0.911													[31]
	At3g56900	3	21079518	3.081	−0.032	0.311	0.661													[31]
	At3g57000	3	21079518	3.081	−0.032	0.311	0.661													[31]
	At5g06550	5	2002341	3.169	−0.070	0.186	2.241													[31]
	At5g06590	5	2002341	3.169	−0.070	0.186	2.241													[33]
	at5g67100	5	26781546					4.302	0.076	0.317	3.772									[31]

MAF: minor allele frequency. The individuals with missing phenotypes and the SNPs with MAF $\leq 10 %$ were excluded. The critical value for significance was $LOD \geq 3.0$ for FASTmrEMMA and E-BAYES, and approximately 2.8E-07 P-value for SUPER, EMMA, CMLM and ECMLM. The results from CMLM and ECMLM were not listed in this table because no genes were detected. The data set was derived from Atwell et al. (2010).