Table 5. Significant SNPs associated with two traits in the A. thaliana population and one trait in the mouse population.

Population	Trait	Method	SNP	Chr.	Position (kb)	P-valuea	Varianceb	Candidate gene (kb)
A. thaliana	Bolt to flower	RANDOM-A	MN4_142943	4	143	0.011	0.437	FRIGIDA
		RANDOM-B	MN4_142943	4	143	0.005	0.517	Chr. 4: 269–272
			MN5_2707605	5	2,708	0.023	0.598
		IM	MASC02783	5	2,522	0.041	0.874
		MPWGAIM	MN4_142943	4	143	—c	0.527
			MN5_1931248	5	1,931	—c	0.629
	Growth rate	FIXED-B	GA1_3232	4	1,243	0.013	0.626	FRIGIDA
		RANDOM-B	GA1_8429	4	1,238	0.010	0.299	Chr. 4: 269–272
		MPWGAIM	GA1_8429	4	1,238	—c	0.253	AT4G02990 (RUG2)
		IM	FRI_1888	4	270	0.005	0.493	Chr. 4: 1322–1324
		CIM-10	GA1_7762	4	1,239	0.011	0.853	AT4G02780 (GA1)
								Chr. 4: 1238–1245
Mouse	PMN	FIXED-B	M2.887	2	87,583	0.040	0.471
		RANDOM-B	M2.887	2	87,583	0.030	0.292
		MPWGAIM	M2.887	2	87,583	—c	0.263
		IM	M2.887	2	87,583	0.013	0.450
		CIM-5	M2.824	2	80,663	0.028	0.496

^aP-value was obtained from a permutation test.

^bDenotes the variance of the effect of the detected marker combining the founder allele inheritance indicators.

^cOwing to the high computational cost, no permutation analysis was conducted.