Table II. Significant QTLs identified by composite interval analysis for each trait.

For each QTL detected, the following are listed: the logarithm of the odds (LOD), the parent donor allele, the IBM version 1 (centimorgan [cM]) interval distance at threshold α = 0.05, the location of the maximum LOD score (peak), the marker closest to the peak location, the chromosomal bin location, the r² value at the peak, and an ANOVA model summary including the adjusted r² for each trait, the F test score, and its associated P value. r² represents the proportion of phenotypic variation explained by a QTL, and adjusted r² represents the percentage of the phenotypic variation explained by all the significant QTLs detected for each trait.

Trait		LOD	Donor Allele	Interval	Peak Position	Marker at Peak	Bin	r2 at Peak	Model Summary
									r2 Adjusted	F	P
				cM				%	%
Mesocotyl	Control	4.29	B73	244–253	250.8	umc191	4.04	8.0	13.0	19.38	<0.001
		4.12	Mo17	582–589	584.3	mmp175	5.08	7.8
	EOD-FR	4.78	B73	12–34	28.0	php20568b	2.01	7.2	26.7	16.09	<0.001
		4.84	Mo17	473–496	485.4	umc1404	3.07	6.0
		4.39	Mo17	0–5	0.0	npi220a	8.01	6.1
		5.52	Mo17	226–236	233.5	umc1921	9.03	6.8
	EOD-FR response ratio	8.87	Mo17	222–236	233.1	umc20	9.03	14.0	5.1	12.94	<0.001
First leaf sheath	Control	5.74	B73	0–23	6.0	isu53a	2.01	15.9	23.9	20.99	<0.001
		4.68	Mo17	369–402	381.4	umc60	3.06	7.5
		4.69	Mo17	214–222	219.8	mmp2	9.03	6.4
	EOD-FR	4.70	B73	0–19	12.0	isu144a	2.01	15.2	30.2	16.94	<0.001
		7.47	Mo17	367–402	379.4	umc60	3.06	13.2
		5.92	Mo17	161–185	179.4	umc1902	4.03	8.7
		5.80	Mo17	498–523	511.6	umc2135	4.09	6.9
		5.55	B73	0–7	2.7	csu582	7.00	6.7
	EOD-FR response ratio	4.31	Mo17	534–552	545.3	umc1999	4.09	11.0	4.9	13.30	<0.001