Table 4.

T values for which the lowest deviance or the lowest mean of squared differences between observed and expected P values were found for various association mapping methods in five plant species.

Mixed-model method	deviance	MSD	deviance	MSD	deviance	MSD
	Rapeseed
	TKW		OC		OY
KT	0.725	0.350 (0.0068)	0.800	0.475 (0.0006)	0.750	0.400 (0.0011)
Q1KT	0.775	0.700 (0.0039)	0.800	0.425 (0.0007)	0.775	0.700 (0.0011)
Q2KT	0.700	0.825 (0.0009)	0.800	0.850 (0.0007)	0.900	0.900 (0.0128)
PKT	0.725	0.700 (0.0006)	0.800	0.725 (0.0004)	0.750	0.750 (0.0019)
	Potato
	GPR		PIR		PM
KT	0.525	0.500 (0.0065)	0.625	0.550 (0.0034)	0.475	0.475 (0.0082)
Q1KT	0.600	0.600 (0.0054)	0.625	0.550 (0.0033)	0.475	0.525 (0.0086)
Q2KT	0.600	0.600 (0.0091)	0.625	0.500 (0.0010)	0.625	0.525 (0.0031)
PKT	0.575	0.550 (0.0121)	0.625	0.550 (0.0048)	0.475	0.475 (0.0153)
	Sugar beet
	AN		BY		CSY
KT	0.575	0.325 (0.0022)	0.475	0.300 (0.0022)	0.475	0.350 (0.0012)
Q1KT	0.575	0.325 (0.0023)	0.450	0.300 (0.0059)	0.475	0.375 (0.0006)
Q2KT	0.475	0.325 (0.0029)	0.475	0.275 (0.0021)	0.575	0.350 (0.0009)
PKT	0.475	0.300 (0.0019)	0.350	0.300 (0.0034)	0.475	0.350 (0.0009)
	Maize
	EH		ED		DPS
KT	0.575	0.450 (0.0002)	0.575	0.575 (0.0001)	0.600	0.575 (0.0002)
Q1KT	0.575	0.500 (0.0001)	0.725	0.575 (0.0003)	0.600	0.575 (0.0001)
Q2KT	0.875	0.475 (0.0003)	0.725	0.525 (0.0001)	0.600	0.525 (0.0001)
PKT	0.875	0.475 (0.0002)	0.725	0.525 (0.0001)	0.600	0.600 (0.0001)
	Arabidopsis
	FLC		FRI		LDV
KT	0.875	0.875 (0.0004)	0.825	0.975 (0.0007)	0.875	0.900 (0.0034)
Q1KT	0.875	0.975 (0.0023)	0.875	0.800 (0.0028)	0.875	0.900 (0.0020)
Q2KT	0.875	0.950 (0.0006)	0.875	0.800 (0.0018)	0.875	0.900 (0.0017)
PKT	0.875	0.775 (0.0015)	0.925	0.925 (0.0025)	0.900	0.900 (0.0011)

For the latter measure, the observed mean of squared differences are given in parentheses. For abbreviations of the analyzed traits see Table 2. For a detailed definition of the statistical models and description of the different methods see Materials and Methods.