QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations

doi:10.1016/j.rsci.2018.06.003

Abstract

Abstract:

Identification of quantitative trait loci (QTLs) for grain mineral elements can assist in faster and more precise development of micronutrient dense rice varieties through marker-assisted breeding. In the present study, QTLs were mapped for Fe and Zn concentrations in two BC₂F₃ mapping populations derived from the crosses of O. sativa cv Swarna with two different accessions of O. nivara. In all, 10 and 8 QTLs were identified for grain Fe and Zn concentrations in population 1, and 7 and 5 QTLs were identified in population 2, respectively. Eighty percent of the QTLs detected in both populations were derived from O. nivara. Five QTLs for Fe and three QTLs for Zn explained more than 15% phenotypic variance either in interval or composite interval mapping. The locations of O. nivara derived QTLs such as qFe2.1, qFe3.1, qFe8.2 and qZn12.1 were consistently identified in both the populations. Epistatic interaction was observed only between RM106 and RM6 on chromosome 2 and between RM22 and RM7 on chromosome 3 for Fe concentration in population 1. Sixteen candidate genes for metal homeostasis were found to co-locate with 10 QTLs for Fe and Zn concentrations in both the populations. Most of the Fe and Zn QTLs were found to co-locate with QTLs for grain yield and grain quality traits. Some of the major effect QTLs identified can be used to improve rice grain Fe and Zn concentrations.

Key words: biofortification, micronutrient, Fe concentration, Zn concentration, rice, wild rice, quantitative trait locus, gene, marker assisted breeding

P. M. Swamy B., Kaladhar K., Anuradha K., K. Batchu Anil, Longvah T., Sarla N.. QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations[J]. Rice Science, 2018, 25(4): 197-207.

Figures/Tables 6

References 77

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Statistics	Population 1		Population 2
Statistics	Fe	Zn	Fe	Zn
Swarna (mg/kg)	10.3	25.4	11.8	23.5
IRGC81832 (mg/kg)	-	-	28.5	62.1
IRGC81848 (mg/kg)	26.2	65.2	-	-
Mean (mg/kg)	7.4	14.5	6.1	15.2
Range (mg/kg)	2.2-22.2	7.1-64.7	1.6-19.4	10.0-25.6
CV (%)	12.9	16.2	12.7	20.5
h² (%)	52.3	85.6	49.6	79.5
GA (%)	19.5	26.3	16.3	27.2
Correlation	0.685**		0.240**
CV, Coefficient of variation; h², Heritability; GA, Genetic advancement. ** means significant differences at the 0.01 level by the Pearson test.

Statistics	Population 1		Population 2
Statistics	Fe	Zn	Fe	Zn
Swarna (mg/kg)	10.3	25.4	11.8	23.5
IRGC81832 (mg/kg)	-	-	28.5	62.1
IRGC81848 (mg/kg)	26.2	65.2	-	-
Mean (mg/kg)	7.4	14.5	6.1	15.2
Range (mg/kg)	2.2-22.2	7.1-64.7	1.6-19.4	10.0-25.6
CV (%)	12.9	16.2	12.7	20.5
h² (%)	52.3	85.6	49.6	79.5
GA (%)	19.5	26.3	16.3	27.2
Correlation	0.685**		0.240**
CV, Coefficient of variation; h², Heritability; GA, Genetic advancement. ** means significant differences at the 0.01 level by the Pearson test.

QTL	Chr	Marker interval	Allelic effect	IM			CIM			Population	Reference
QTL	Chr	Marker interval	Allelic effect	LOD	R² (%)	A ^a (mg/kg)	LOD	R² (%)	A^a (mg/kg)	Population	Reference
qFe1.1	1	RM499-RM428	O. nivara	5.5	10	-6.55	5.0	8	-0.76	P2	Lu et al, 2008
qFe1.2	1	RM243-RM81A	O. nivara	4.2	14	-3.17	5.6	17	-3.80	P1
qFe1.3	1	RM24-RM595	O. nivara	3.1	12	-2.20				P1
qFe2.1	2	RM324-RM475	O. nivara	3.1	12	-3.04				P1
qFe2.1	2	RM324-RM475	O. nivara	4.1	8	-0.16	3.7	12	-0.12	P2
qFe2.2	2	RM6-RM250	Swarna	3.1	8	2.39	2.7	5	2.00	P1
qFe3.1	3	RM517-RM156	O. nivara	3.1	12	-2.70				P1	Anuradha et al, 2012b
qFe3.1	3	RM517-RM7	O. nivara	5.7	5	-0.62	4.9	4	-1.07	P2	Anuradha et al, 2012b; Kumar et al, 2014
qFe3.2	3	RM520-RM514	O. nivara	4.2	16	-1.64	4.4	19	-2.86	P2
qFe4.1	4	RM241-RM348	O. nivara	5.2	12	-5.57	9.0	15	-5.10	P2	Norton et al, 2010
qFe6.1	6	RM204-RM314	O. nivara	3.9	10	-1.72				P1	Norton et al, 2010; Zhang et al, 2014
qFe8.1	8	RM337-RM152	O. nivara	3.2	6	-1.60				P2	Garcia-Oliviera et al, 2009
qFe8.2	8	RM152-RM38	O. nivara	3.6	4	-1.28				P1	Garcia-Oliviera et al, 2009
qFe8.2	8	RM38-RM223	Swarna	5.1	6	0.24	4.0	3	0.81	P2	Garcia-Oliviera et al, 2009
qFe11.1	11	RM332-RM287	O. nivara	3.6	18	-6.60	3.2	19	-6.50	P1
qFe11.2	11	RM209-RM21	O. nivara	5.1	25	-4.68	2.5	9	-2.90	P1
qFe11.3	11	RM254-RM224	O. nivara	3.1	7	-1.70	2.7	6	-1.70	P1	Nawaz et al, 2015
qFe12.1	12	RM19-RM247	O. nivara	5.3	5	-0.75	5.0	4	-0.39	P2	Nawaz et al, 2015
qZn1.1	1	RM488-RM431	Swarna	2.6	4	0.56				P1	Nawaz et al, 2015
qZn2.1	2	RM250-RM535	O. nivara	4.3	13	-2.10	3.4	8	-1.83	P1
qZn3.1	3	RM517-RM16	O. nivara	3.2	23	-2.36	2.9	15	-1.34	P2
qZn3.2	3	RM55-RM520	O. nivara	3.5	10	-1.56	2.9	7	-1.54	P1	Anuradha et al, 2012
qZn5.1	5	RM153-RM413	O. nivara	8.6	16	-1.82	12.4	36	-2.07	P2
qZn6.1	6	RM30-RM439	O. nivara	2.7	10	-0.77				P2
qZn8.1	8	RM152-RM223	Swarna	2.8	13	1.87				P2
qZn8.2	8	RM256-RM264	O. nivara	5.1	3	-6.60	4.8	3	-0.26	P1	Garcia-Oliviera et al, 2009
qZn9.1	9	RM215-RM189	O. nivara	2.5	4	-0.79				P1	Lu et al, 2008
qZn10.1	10	RM216-RM467	O. nivara	6.8	6	-1.34	5.1	3	-0.21	P1
qZn12.1	12	RM415-RM19	Swarna				7.1	7	1.13	P1
qZn12.1	12	RM415-RM19	O. nivara	8.5	14	-1.38	8.9	21	-2.28	P2
Chr, Chromosome; IM, Interval mapping; CIM, Composite interval mapping; A, Additive effect; P1, Population 1; P2, Population 2. ^a The negative values indicate trait increasing allele from O. nivara.

QTL	Chr	Marker interval	Allelic effect	IM			CIM			Population	Reference
QTL	Chr	Marker interval	Allelic effect	LOD	R² (%)	A ^a (mg/kg)	LOD	R² (%)	A^a (mg/kg)	Population	Reference
qFe1.1	1	RM499-RM428	O. nivara	5.5	10	-6.55	5.0	8	-0.76	P2	Lu et al, 2008
qFe1.2	1	RM243-RM81A	O. nivara	4.2	14	-3.17	5.6	17	-3.80	P1
qFe1.3	1	RM24-RM595	O. nivara	3.1	12	-2.20				P1
qFe2.1	2	RM324-RM475	O. nivara	3.1	12	-3.04				P1
qFe2.1	2	RM324-RM475	O. nivara	4.1	8	-0.16	3.7	12	-0.12	P2
qFe2.2	2	RM6-RM250	Swarna	3.1	8	2.39	2.7	5	2.00	P1
qFe3.1	3	RM517-RM156	O. nivara	3.1	12	-2.70				P1	Anuradha et al, 2012b
qFe3.1	3	RM517-RM7	O. nivara	5.7	5	-0.62	4.9	4	-1.07	P2	Anuradha et al, 2012b; Kumar et al, 2014
qFe3.2	3	RM520-RM514	O. nivara	4.2	16	-1.64	4.4	19	-2.86	P2
qFe4.1	4	RM241-RM348	O. nivara	5.2	12	-5.57	9.0	15	-5.10	P2	Norton et al, 2010
qFe6.1	6	RM204-RM314	O. nivara	3.9	10	-1.72				P1	Norton et al, 2010; Zhang et al, 2014
qFe8.1	8	RM337-RM152	O. nivara	3.2	6	-1.60				P2	Garcia-Oliviera et al, 2009
qFe8.2	8	RM152-RM38	O. nivara	3.6	4	-1.28				P1	Garcia-Oliviera et al, 2009
qFe8.2	8	RM38-RM223	Swarna	5.1	6	0.24	4.0	3	0.81	P2	Garcia-Oliviera et al, 2009
qFe11.1	11	RM332-RM287	O. nivara	3.6	18	-6.60	3.2	19	-6.50	P1
qFe11.2	11	RM209-RM21	O. nivara	5.1	25	-4.68	2.5	9	-2.90	P1
qFe11.3	11	RM254-RM224	O. nivara	3.1	7	-1.70	2.7	6	-1.70	P1	Nawaz et al, 2015
qFe12.1	12	RM19-RM247	O. nivara	5.3	5	-0.75	5.0	4	-0.39	P2	Nawaz et al, 2015
qZn1.1	1	RM488-RM431	Swarna	2.6	4	0.56				P1	Nawaz et al, 2015
qZn2.1	2	RM250-RM535	O. nivara	4.3	13	-2.10	3.4	8	-1.83	P1
qZn3.1	3	RM517-RM16	O. nivara	3.2	23	-2.36	2.9	15	-1.34	P2
qZn3.2	3	RM55-RM520	O. nivara	3.5	10	-1.56	2.9	7	-1.54	P1	Anuradha et al, 2012
qZn5.1	5	RM153-RM413	O. nivara	8.6	16	-1.82	12.4	36	-2.07	P2
qZn6.1	6	RM30-RM439	O. nivara	2.7	10	-0.77				P2
qZn8.1	8	RM152-RM223	Swarna	2.8	13	1.87				P2
qZn8.2	8	RM256-RM264	O. nivara	5.1	3	-6.60	4.8	3	-0.26	P1	Garcia-Oliviera et al, 2009
qZn9.1	9	RM215-RM189	O. nivara	2.5	4	-0.79				P1	Lu et al, 2008
qZn10.1	10	RM216-RM467	O. nivara	6.8	6	-1.34	5.1	3	-0.21	P1
qZn12.1	12	RM415-RM19	Swarna				7.1	7	1.13	P1
qZn12.1	12	RM415-RM19	O. nivara	8.5	14	-1.38	8.9	21	-2.28	P2
Chr, Chromosome; IM, Interval mapping; CIM, Composite interval mapping; A, Additive effect; P1, Population 1; P2, Population 2. ^a The negative values indicate trait increasing allele from O. nivara.

Chromosome	Marker interval	Co-located QTLs
2	RM6-RM535	qFe2.2 and qZn2.1
3	RM517-RM16	qFe3.2 and qZn3.1
8	RM337-RM223	qFe8.1, qFe8.2 and qZn8.1
12	RM415-RM247	qFe12.1 and qZn12.1