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. 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
LOD Effect MAF r2 (%) LOD Effect MAF r2 (%) P-value Effect MAF r2 (%) P-value Effect MAF r2 (%)
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 10% were excluded. The critical value for significance was LOD3.0 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).