Table 2. General linear models for the top scoring SNPs for circadian period and phase measured in July for the Arabidopsis thaliana Ws-2 × C24 (A), Ws-2 × Ler (B) and Ler × Ws-2 (C) RIL sets. Chromosome and nucleotide position for each SNP are provided. R² for each SNP as estimated from ANOVA models and phenotypic means and standard errors for genotypic classes are shown.

							Genotypic Mean ± SE.
	Trait	Chr.	Nucleotide	F-value	P-value	R2	Ws-2/Ws-2	C24/C24
A. Ws-2 × C24	Period	2	14,500,577	12.71	0.0006	0.14	23.40 ± 0.11	23.90 ± 0.08
		3	5,551,187	4.56	0.036	0.06	24.37 ± 0.30	23.70 ± 0.07
		3	9,377,864	4.00	0.0492	0.05	23.42 ± 0.17	23.80 ± 0.08
		5	669,813	6.58	0.0124	0.08	24.06 ± 0.14	23.65 ± 0.08
	Phase	1	27,046,266	9.27	0.0013	0.13	14.43 ± 0.16	15.13 ± 0.14
		3	5,551,187	4.91	0.0296	0.06	15.83 ± 0.48	14.74 ± 0.11
		3	9,377,864	7.45	0.0079	0.09	14.17 ± 0.26	14.95 ± 0.12
		3	18,651,928	12.97	0.0006	0.15	14.39 ± 0.15	15.14 ± 0.14
							Genotypic Mean ± SE.
	Trait	Chr.	Nucleotide	F-value	P-value	R2	Ws-2/Ws-2	Ler/Ler
B. Ws-2 × Ler	Period	3	849,706	18.71	0.0001	0.20	23.68 ± 0.13	22.92 ± 0.11
		3	8,816,904	4.98	0.0286	0.06	22.67 ± 0.27	23.31 ± 0.10
		5	1,335,242	26.06	0.0001	0.26	24.13 ± 0.19	23.03 ± 0.09
	Phase	1	5,689,169	3.15	0.08	0.04	11.67 ± 0.38	10.95 ± 0.14
		2	17,179,798	8.47	0.0047	0.10	10.12 ± 0.34	11.18 ± 0.14
		3	849,706	5.23	0.0250	0.07	10.78 ± 0.17	11.38 ± 0.20
							Genotypic Mean ± SE.
	Trait	Chr.	Nucleotide	F-value	P-value	R2	Ler/Ler	Ws-2/Ws-2
C. Ler × Ws-2	Period	3	849,706	14.10	0.0004	0.18	23.31 ± 0.42	20.45 ± 0.64
		5	9,524,947	8.22	0.0056	0.11	22.96 ± 0.40	20.34 ± 0.82
		5	24,941,285	17.48	0.0001	0.22	21.66 ± 0.39	24.99 ± 0.70
	Phase	1	18,082,872	11.55	0.0012	0.15	19.08 ± 0.22	14.88 ± 1.22
		5	24,941,285	6.91	0.0107	0.10	18.57 ± 0.25	19.94 ± 0.45