Identification of QTLs and Validation of qCd-2 Associated with Grain Cadmium Concentrations in Rice

doi:10.1016/j.rsci.2018.12.003

Abstract

Abstract:

Cadmium (Cd) is one of heavy metals harmful to human health. As rice is the main staple food in Asia and Cd is easily contaminated in rice, the molecular regulation of Cd accumulation should be explored. In this study, a recombinant inbred population derived from Xiang 743/Katy was grown in Cd-polluted fields and used to map the quantitative trait loci (QTLs) for Cd accumulation in rice grains. We identified seven QTLs distributed on chromosomes 2, 3, 6, 7, 8 and 10. These QTLs displayed phenotypic variances of 58.50% and 40.59% in 2014 and 2015, respectively. Two QTLs, qCd-2 and qCd-7, were identified in both the two years. qCd-2 was detected on the interval of RM250-RM207 on chromosome 2, with an LOD of 2.51 and a phenotypic contribution of 13.75% in 2014, and an LOD of 3.35 and a phenotypic contribution of 14.16% in 2015. qCd-7 co-localized with the cloned qCdT7 on chromosome 7 and may represent the correct candidate. The other five QTLs were detected only in one year. To further confirm the effects of qCd-2, a residual heterozygous line designated as RHL945, with a heterozygous interval of RM263-RM207 on chromosome 2, was selected from the recombinant inbred population and used to develop an F₂ population consisting of 155 individual plants. By incorporating further simple sequence repeat markers into the segmental linkage map of the target region, qCd-2 was delimited in the interval of RM5404-RM3774, with an LOD value of 4.38 and a phenotypic contribution of 15.52%. These results reflected the genetic regulation of grain Cd in rice and paved the way for the future cloning of qCd-2.

Key words: cadmium, recombinant inbred line, quantitative trait locus, rice, simple sequence repeat

Wenqiang Liu, Xiaowu Pan, Yongchao Li, Yonghong Duan, Jun Min, Sanxiong Liu, Licheng Liu, Xinnian Sheng, Xiaoxiang Li. Identification of QTLs and Validation of qCd-2 Associated with Grain Cadmium Concentrations in Rice[J]. Rice Science, 2019, 26(1): 42-49.

Figures/Tables 5

Fig. 1. Frequency distributions of Cd concentration in Xiang 743/Katy recombinant inbred lines in 2014 (A) and 2015 (B). Cd concentrations in the parental lines are indicated by arrows.

Table 1 QTL analysis for grain Cd concentration in Xiang 743/Katy recombinant inbred lines in 2014 and 2015.

Year	Chromosome	Name	Interval	LOD	Additive ^a	R² (%)	DPE
2014	2	qCd-2	RM250-RM207	2.51	0.14	13.75	Katy
	6	qCd-6.1	RM225-RM276	3.31	0.15	16.98	Katy
	7	qCd-7	RM6872-RM3718	2.89	0.1	8.9	Katy
	8	qCd-8	RM152-RM310	2.61	0.03	8.96	Katy
	10	qCd-10	RM7492-RM474	2.76	-0.11	9.91	Xiang 743
2015	2	qCd-2	RM250-RM207	3.35	0.19	14.16	Katy
	3	qCd-3	RM6301-RM175	2.87	-0.12	6.3	Xiang 743
	6	qCd-6.2	RM5371-RM340	2.82	0.13	6.1	Katy
	7	qCd-7	RM6872-RM3718	6.66	0.2	14.03	Katy

Fig. 2. Chromosomal location of QTLs for Cd concentration in a genetic linkage map of Xiang 743/Katy recombinant inbred lines. The intervals where QTLs located were determined on the basis of LOD peak flanking markers.

Fig. 3. Schematic diagram depicting the genotype of 12 chromosomes of RHL945 genome. The positions of DNA markers used to determine genotypes are indicated by thin lines.

Fig. 4. Frequency distribution (A) and QTL likelihood cure of LOD score (B) of Cd concentration in the F2 population derived from RHL945.a, Additive effect. The genetic effect of the putative QTL when Xiang 743 allele was replaced by Katy allele. R2, Percentage of phenotypic variance explained by each QTL

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