Table 4 Effects of replacing B73 alleles by Mo17 alleles on the six traits for markers with significant marker main effects and/or marker by density interactions estimated by fitting the best multiple marker model in the B73 × Mo17 RIL population

Trait	Chromosome	Marker	Density	Effect	Epistatic with
Final height^a	1	umc133b	Low	−6.16^*	amp1(1), umc85(6)
			High	−3.62
	2	umc53a	Mean	4.75^*	amp1(1), umc85(6) nc134(9)
	3	phi036	Low	2.54	umc85(6)
			High	−0.55
	4	umc52	Low	−1.55	phi069(7), umc89(8)
			High	−3.81
	7	phi069	Mean	13.79^****	umc52(4)
	8	umc89	Mean	14.67^****	umc52(4)
	9	nc134	Mean	−17.62^****	umc53a(2)
	10	phi035	Mean	−7.74^**
Days to anthesis	2	npi254a	Low	−0.04
			High	0.29
	8	bngl666	Mean	0.78^*	phi070(6)
ASI		umc76	Mean	0.59^**
	1	amp1	Low	0.24	csu164b(5), umc21(6)
			High	0.65^**
	4	umc49d	Mean	−0.73^***	bngl180(2), bnl9.11(8)
	5	csu164b	Mean	0.76^**	amp1(1), bngl381(2)
		nrz5	Low	0.41
			High	0.82^***	bngl381(2), phi059(10)
	8	bnl9.11	Mean	−0.81^**	umc49d(4)
	10	phi059	Low	−0.55^*	bngl381(2), bngl180(2) nrz5(5), umc124(8)
			High	−1.27^****
Barrenness (%)	2	umc49a	Low	0.75
			High	2.36^**
	3	bngl197	Low	−0.60
			High	−2.69^**
	4	umc49d	Mean	−2.74^***	phi077(6), bngl210(10)
	5	umc156	Mean	2.19^*
	6	phi077	Low	−1.44	umc128(1), umc49d(4)
			High	−2.98^***
	10	bngl210	Low	−0.58	umc49d(4)
			High	−1.98^*
Ears per plant	4	umc49d	Low	0.043^**	phi091(7), csu093(9)
			High	0.066^****
	5	bnl5.40	Mean	−0.058^***	phi089(6), bngl210(10)
	6	phi089	Mean	−0.030^*	bnl5.40(5), phi091(7) bz1(9)
	7	php20581a	Low	0.027	bngl240(8)
			High	−0.001
		phi091	Low	0.002	umc49d(4), phi089(6)
			High	−0.024
	9	bz1	Mean	0.035^*	phi089(6)
	10	bngl210	Low	0.022	bnl5.40(5)
			High	0.042^**
Yield per plant	2	phi098	Mean	−4.90^*	bnl7.65(4)
	3	bnl6.16	Mean	8.55^***	umc70c(9)
	4	bnl7.65	Low	14.89^****	phi098(2)
			High	8.60^***

Abbreviations: ASI, anthesis-silking interval; RIL, recombinant inbred line.
If the 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.
^aThe final model includes these 8 main effects and 11 epistatic interactions.

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