Table 5 Epistatic interactions for plant height

Chromosome	Marker	Density	Marker effect estimate conditional on homozygous genotype at second marker (chromosome)
			amp1(1)		umc85(6)
			B73	Mo17	B73	Mo17
1	umc133b	Low	−0.37	−11.94^**	0.59	−10.36^**
		High	−1.27	−5.96
			umc133b(1)		umc53a(2)
			B73	Mo17	B73	Mo17
1	amp1	Low	1.86	−9.72^**	−9.61^**	0.32
		High	−3.02	−7.71^*
			umc85(6)
			B73	Mo17
		Low	−8.41^*	0.55
		High	−8.17^*	−2.56
			amp1(1)		umc85(6)
			B73	Mo17	B73	Mo17
2	umc53a	Low High	−0.22	9.71^**	12.67^****	−3.18
			nc134(9)
			B73	Mo17
		Low	3.27	5.40
		High	5.87	4.44
			umc85(6)
			B73	Mo17
3	phi036	Low High	−4.43	6.42
			phi069(7)		umc89(8)
			B73	Mo17	B73	Mo17
4	umc52	Low	5.43 4.79	−8.53^*	3.11	−8.48^**
		High		−12.42^***
			umc133b(1)		amp1(1)
			B73	Mo17	B73	Mo17
		Low	6.81	−4.14	−3.02	5.93
		High			−1.59	4.02
6	umc85		umc53a(2)		phi036(3)
			B73	Mo17	B73	Mo17
		Low High	9.26^**	−6.59	−4.09	6.76
			umc52(4)
			B73	Mo17
7	phi069	Low	21.02^****	7.07^*
		High	22.14^****	4.92
			umc52(4)
			B73	Mo17
8	umc89	Low High	20.46^****	8.87^**
			umc53a(2)
			B73	Mo17
9	nc134	Low	−18.96^****	−16.83^****
		High	−16.62^****	−18.05^****

Effects of replacing B73 alleles by Mo17 alleles estimated by fitting the best multiple marker model in the B73 × Mo17 recombinant inbred line (RIL) population. If the marker by marker by density interaction was significant, the effect of the marker is given for each density. Otherwise, an average effect across densities is reported.
^*, ^**, ^***, ^**** Significant at P⩽0.05, 0.01, 0.001, or 0.0001, respectively.

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