QTL Mapping of Candidate Genes Involved in Cd Accumulation in Rice Grain

doi:10.11983/CBB20148

Abstract

Abstract: Rice is one of the world’s most important crops, but cadmium (Cd) pollution and Cd accumulation in rice fields pose a serious threat to its yield and quality as well as to human health. How to reduce Cd accumulation in rice has become a major concern. In this study, a japonica rice variety Nekken2 was used as the maternal parent, and an indica rice variety HZ was used as the paternal parent. After F₁ generation was obtained by cross-breeding, successive selfings were performed for 120 recombinant inbred lines (RILs) population as the QTL mapping populations. We measured the Cd content in rice grains of each line at the maturity stage. Meanwhile, QTL mapping was performed using genetic map. As a result, a total of 7 QTLs were detected, which were located on chromosome 2, 3, 9, and 12 of rice, with the highest LOD score of 4.97. The qRT-PCR analysis on the candidate genes involved in metal ion stress resistance in these QTL regions showed that the expression level of LOC_Os02g50240, LOC_Os02g52780, LOC_Os09g31200, LOC_Os09g35030 and LOC_Os09g37949 was significantly different from the parents. Combined with the data of concentration of different metal ions in the parents, we speculated that the high expression of LOC_Os02g50240, LOC_Os09g31200 and LOC_Os09g35030 might greatly improve the absorption and tolerance of rice to Cd ion stress. And these genes may be related to the accumulation of Cd in rice grains, and may affect the ability of rice to tolerate Cd stress, which could help for further breeding and screening for rice varieties to tolerate Cd stress, and exploring the molecular regulation mechanism of Cd accumulation in rice.

Key words: rice, cadmium accumulation, QTL mapping, candidate genes, ion stress, genetic map

Chenyang Pan, Hanfei Ye, Weiyong Zhou, Sheng Wang, Mengjia Li, Mei Lu, Sanfeng Li, Xudong Zhu, Yuexing Wang, Yuchun Rao, Gaoxing Dai. QTL Mapping of Candidate Genes Involved in Cd Accumulation in Rice Grain[J]. Chinese Bulletin of Botany, 2021, 56(1): 25-32.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB20148

https://www.chinbullbotany.com/EN/Y2021/V56/I1/25

Figures/Tables 7

References 30

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Primer name	Sequence (5'-3')	Tm (°C)	Length (bp)
LOC_Os02g50240-F-qrt	CTTCAAGGACCCATTCAGGA	60.04	113
LOC_Os02g50240-R-qrt	TGAAGATCTTGGCAGCATTG	59.95
LOC_Os02g52780-F-qrt	GTTTTCAAAGGTGGGCTGAG	59.71	148
LOC_Os02g52780-R-qrt	CCTCAGCTTCCAATTCCATC	59.68
LOC_Os09g31200-F-qrt	GCGACAAGAAGGATCAGGAG	59.95	117
LOC_Os09g31200-R-qrt	AGAAGCAGTTCTGGCAGAGG	59.75	117
LOC_Os09g35030-F-qrt	GGATCAAGCAGGAGATGAGC	59.92	135
LOC_Os09g35030-R-qrt	GCCTCGTCTCCCTGAACTT	59.39
LOC_Os09g37949-F-qrt	GGAAATCTGCCGATCAGTGT	60.08	123
LOC_Os09g37949-R-qrt	GGGTCCTTCGATGGGTTTAT	60.02

Primer name	Sequence (5'-3')	Tm (°C)	Length (bp)
LOC_Os02g50240-F-qrt	CTTCAAGGACCCATTCAGGA	60.04	113
LOC_Os02g50240-R-qrt	TGAAGATCTTGGCAGCATTG	59.95
LOC_Os02g52780-F-qrt	GTTTTCAAAGGTGGGCTGAG	59.71	148
LOC_Os02g52780-R-qrt	CCTCAGCTTCCAATTCCATC	59.68
LOC_Os09g31200-F-qrt	GCGACAAGAAGGATCAGGAG	59.95	117
LOC_Os09g31200-R-qrt	AGAAGCAGTTCTGGCAGAGG	59.75	117
LOC_Os09g35030-F-qrt	GGATCAAGCAGGAGATGAGC	59.92	135
LOC_Os09g35030-R-qrt	GCCTCGTCTCCCTGAACTT	59.39
LOC_Os09g37949-F-qrt	GGAAATCTGCCGATCAGTGT	60.08	123
LOC_Os09g37949-R-qrt	GGGTCCTTCGATGGGTTTAT	60.02

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Limit of detection
qRCd-1	2	30302111-35902152	129.90-153.90	4.48
qRCd-2	3	5112031-5335542	21.91-22.87	2.51
qRCd-3	3	6338887-6654517	27.17-28.53	2.61
qRCd-4	9	13883217-15424344	59.51-66.12	4.32
qRCd-5	9	16779765-22230863	71.93-95.30	4.97
qRCd-6	9	22748818-22938953	97.52-98.33	2.60
qRCd-7	12	21976412-22336740	94.21-95.75	2.66

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Limit of detection
qRCd-1	2	30302111-35902152	129.90-153.90	4.48
qRCd-2	3	5112031-5335542	21.91-22.87	2.51
qRCd-3	3	6338887-6654517	27.17-28.53	2.61
qRCd-4	9	13883217-15424344	59.51-66.12	4.32
qRCd-5	9	16779765-22230863	71.93-95.30	4.97
qRCd-6	9	22748818-22938953	97.52-98.33	2.60
qRCd-7	12	21976412-22336740	94.21-95.75	2.66

Chromosome	Gene	Function	Object
2	LOC_Os02g50240	It participates in the regulation of various biological processes and stress response	Cytoplasmic glutamine synthetase
2	LOC_Os02g52780	It regulates ABA-dependent stress-related gene expression to enhance the plant tolerance of drought and salt	Transcription factors bZIP
9	LOC_Os09g31200	A major determinant of plant response to stress	Zinc finger protein
9	LOC_Os09g35030	It specifically combines with drought response elements and controls many stress-induced genes	Transcription factors AP2/EREBP
9	LOC_Os09g37949	It plays an important role in salt stress response	Receptor protein kinase