Table 1  Candidate genes with either common or rare variants showing associations to flowering time with the composite resequencing-based association study analysis
AssumptionGene (Gene ID)Single SNP TestMultiple CommonCombined Multivariate PooledA Priori Candidate GeneConnected in AraNetSupporting Evidence
CDCVAP1 (AT1G69120)JIC0W (2.91) FLC (2.85)JIC0W (3.17) FLC (3.35) JIC4W (3.37) JIC8W (3.09)JIC0W (3.28) FLC (3.72) JIC4W (3.48) VERN (3.77)YesYesGustafson-Brown et al. (1994) [Brachi et al. (2010)] Mouradov et al. 2002
CR88 (AT2G04030)JIC/USC (1.75)JIC/USC (2.59)JIC/USC (2.72)YesNoCao et al. 2000
TIC (AT3G22380)JIC4W (5.31)JIC4W (1.87)JIC4W (3.27)YesNoDing et al. 2007
DCL2 (AT3G03300)SDV (3.08)SDV (3.55)SDV (3.94)NoYesHenderson et al. 2006
FCA (AT4G16280)±V(SD) (4.19)±V(SD) (3.34)±V(SD) (3.62)YesYesMacknight et al. 1997 [Atwell et al. (2010)] [Brachi et al. (2010)] [Zhao et al. (2007)]
FRI (AT4G00650)FRI (14.78) FLC (4.13)FRI (12.34) FLC (4.77)FRI (9.43)
FLC (3.68) JIC4W (4.23)YesYesJohanson et al. 2000Shindo et al. 2005 [Atwell et al. (2010)] [Zhao et al. (2007)]
FLC (AT5G10140)SD/LD(V) (3.81)SD/LD(V) (3.14) SDV (3.59)SD/LD(V) (4.34) SDV (4.81)YesYesRatcliffe et al. 2001 [Atwell et al. (2010)] [Zhao et al. (2007)]
AssumptionGene (Gene ID)Sum TestWeighted SumFunction-Aided SumA Priori Candidate GeneConnected in AraNetSupporting Evidence
CDRVFLM (AT1G77080)LD (3.32) JIC2W (4.78) JIC4W (3.23)JIC2W (1.45)JIC2W (3.12)YesYesScortecci et al. 2001Werner et al. 2005
BAS1 (AT2G26710)LD (4.19) SD (2.91) JIC2W (3.52)LD (4.55) SD (3.47) JIC2W (3.69)LD (4.33) SD (3.12) JIC2W (2.23)YesYesTurk et al. 2005
SPL5 (AT3G15270)JIC/USC (3.22)JIC/USC (3.47)JIC/USC (3.57)YesYesWu et al. 2009Wu and Poethig 2006
FY (AT5G13480)JIC2W (3.55) JIC8W (2.24)JIC2W (4.05) JIC8W (2.31)JIC2W (3.67)YesYesSimpson et al. 2003 [Brachi et al. (2010)]
  • Numbers in parentheses indicate the permutation-derived-log10 (P-value). References in brackets are genome-wide association studies. CDCV, common disease–common variant; CDRV, common disease–rare variant; SNP, single-nucleotide polymorphism.