Table 3. QTLs detected for controlling leaf phenotype following low temperature exposure in the IBM Syn4 population.

QTL	Trait	Bina	Peak position (cM)	Nearest marker	Left border (cM); 95% SI; flanking marker	Right border (cM); 95% SI; flanking marker	LOD Scoreb	P-valuec	Additive Effectd	R2 (%)e
QTL-1	Visual tolerance score	1.02	181.7	cdo860a	174.7	186.7	5.7	3.1*10−6	-3.8	14.8
					gpm536c	uaz1
	Proportion of green tissue	1.02	184.7	umc1711	174.7	238.7	3.4	3.3*10−5	-2.3	14.2
					gpm536c	IDP3914
	Absorbance at 663 nm	1.02	182.7	IDP4750	172.7	190.7	6.8	4.9*10−5	-3.1	16.2
					sfp1
	Absorbance at 645 nm	1.02	181.7	cdo860a	171.7	191.7	3.5	1.8*10−4	-2.8	7.8
					IDP7945	pco064372
QTL-2	Visual tolerance score	5.05	445	gpm912a	442	448	10.3	8.7*10−9	5.2	23.3
					gpm912a	TIDP5693
	Proportion of green tissue	5.05	449	umc1722	444	455	6.8	8.8*10−8	4.3	23.9
					myb86	lw3
	Absorbance at 663 nm	5.05	448	IDP8645	443	454	9.6	3.7*10−8	5.0	27.9
					myb86	csu550
	Absorbance at 645 nm	5.05	446	v12	441	453	5.2	2.8*10−6	4.1	14.8
					IDP8187	csu550

^aChromosome bins, qtl and nearest marker positions are shown based on IBM 2008 Neighbors Map;

^bLOD: Log10-likelihood value;

^cp-value of the QTL fit is estimated for one QTL at a time and for the model (Q1 + Q2 + Q1*Q2);

^dAdditive effect: The negative value of additive effect indicates the allele from B73 is positive;

^eR2: coefficient of determination, which represents the percentage of phenotypic variance explained by a putative QTL.