Research on Mechanism and QTL Mapping Associated with Cadmium Accumulation in Rice Leaves and Grains

doi:10.13560/j.cnki.biotech.bull.1985.2021-1192

Abstract

Abstract:

Rice is the most important staple food in China,thus mining the key genes controlling cadmium（Cd）accumulation in rice leaves and grains and clarifying the genetic mechanism of Cd accumulation and transport may provide the basis for breeding rice varieties with low cadmium accumulation and ensuring food security and human health. Inomics screening was performed to systemically profile ionic spectrum in the grains of 209 rice varieties from the Rice Core Germplasm cultivated in China. The accessions with differential cadmium and/or iron（Fe）/zinc（Zn）accumulations were identified,from which indicia cultivar HQ03 and japonica cultivar SKC were selected for further study. Results showed that there was no significant difference in cadmium tolerance and uptake between the two varieties,and Cd accumulations in the HQ03 shoots and grains were significantly higher than those in SKC,while no difference in Fe,Zn,etc. Using a doubled haploid（DH）population derived from HQ03 and SKC of 137 individuals,8 quantitative trait loci（QTL）controlling Cd accumulation in the leaves and grains were identified on chromosome 2,3,4,7,8,10 and 11,accounting for 10.6%-39.4% of the phenotypic variance detected. Among them,qGCd3,controlling Cd transport to grains,was delimited in the interval of RM6266-RM2334 on chromosome 3,with an LOD（limit of detection）value of 3.81 and a phenotypic contribution of 39.4%,indicating that an important gene controlling cadmium transport to grain may exist here.

Key words: rice, core germplasm, cadmium, QTL mapping

HUANG Jing, ZHU Liang, XUE Peng-bo, FU Qiang. Research on Mechanism and QTL Mapping Associated with Cadmium Accumulation in Rice Leaves and Grains[J]. Biotechnology Bulletin, 2022, 38(8): 118-126.

Figures/Tables 11

Fig. 1 Profiling of Cd accumulation in grains of rice core germplasm Z value =（individual value-population average）/population SD,and represents SD from the average value of the whole population. X axis refers to the serial number of rice cultivars

Fig. 2 Correlation among Cd2+, Fe2+, Zn2+ and Mn2+ elements in rice grains

Table 1 Contents of Cd and other metals in the soil of contaminated paddy field,contaminated sink and control sink （μg·g-1 DW）

土壤类型Soil type	镉Cd	铁Fe	锌Zn	铜Cu	锰Mn	砷As
对照水槽Control sink	0.14±0.02	19 047.64±232.07	157.34±8.26	23.51±9.55	318.16±3.63	9.69±2.69
污染水槽 Contaminated sink	1.09±0.11	20 495.83±270.84	271.98±9.51	45.39±8.31	322.02±9.58	12.99±1.28
污染大田土壤Contaminated paddy field	0.55±0.07	19 603.91±267.35	265.89±4.15	48.20±3.93	330.8±14.11	12.53±1.34

Fig.3 Cd accumulation in the grains and milled rice of HQ03 and SKC A：Cd accumulation in the grains of HQ03 and SKC from the rice grown in the contaminated paddy field,contaminated and control sink,respectively. B：Cd accumulation in the milled rice of HQ03 and SKC from the rice grown in the contaminated sink. **：P < 0.01. The same below

Fig.4 Elements accumulation in the leaves of HQ03 and SKC A：Cd accumulation in the leaves of HQ03 and SKC. B, C：Contents of metal elements such Fe（B）and major elements such as K（C）in the leaves of HQ03 and SKC

Fig.5 Cd accumulation in the leaves and roots of HQ03 and SKC from rice seedlings exposed to CdCl2 for indicated concentrations and days A：Cd levels in leaves from rice seedlings exposed to CdCl2 for 7 d at indicated concentrations;B：Cd levels in leaves from rice seedlings exposed to 10 μmol/L CdCl2 for indicated days;C：Cd levels in roots from rice seedlings exposed to CdCl2 for 7 d at indicated concentrations;D：Cd levels in roots from rice seedlings exposed to 10 μmol/L CdCl2 for indicated days

Fig. 6 Tolerance assay of HQ03 and SKC to Cd A：Fresh weight（FW）of shoots of HQ03 and SKC under different concentrations of Cd treatment. B：Fresh weight（FW）of roots of HQ03 and SKC under different concentrations of Cd treatment

Fig.7 Root uptake assay of HQ03 and SKC A：Normal culture condition（28℃）. B：Low temperature culture condition（4℃）

Table 2 Quantitative trait loci（QTLs）mapping for Cd accumulation in rice leaves

数量性状基因座位QTL	染色体Chr.	标记区间Marker interval	LOD值LOD value	贡献率 R²/%	加性效应Additive effect
qLCd2	2	RM450-RM5472	2.70	13.4	12.792
qLCd4	4	RM307-RM401	2.14	11.1	11.234
qLCd10	10	RM271-RM258	3.02	10.6	-0.081 8
qLCd11	11	RM167-RM220	2.07	11.0	7.576 1

Table 3 Quantitative trait loci（QTLs）mapping for Cd accumulation in rice grains

数量性状基因座位QTL	染色体Chr.	标记区间Marker interval	LOD值LOD value	贡献率R²/%	加性效应Additive effect
qGCd2	2	RM324-RM341	3.39	20.2	-0.187 4
qGCd3	3	RM6266-RM2334	3.81	39.4	0.125 4
qGCd7	7	RM6574-RM6449	2.51	13.2	-5.381 7
qGCd8	8	RM1235-RM1376	3.15	20.4	-0.278 1

Fig.8 QTLs mapping of Cd accumulation in the rice leaves and grains

References 23

[1]	Haider FU, Liqun C, Coulter JA, et al. Cadmium toxicity in plants:Impacts and remediation strategies[J]. Ecotoxicol Environ Saf, 2021, 211:111887. doi: 10.1016/j.ecoenv.2020.111887 URL
[2]	Chen HM, Chen WC, Chen YX, et al. Pollution of heavy metals in soil-plant system[M]. Beijing: Science Press, 1996.
[3]	Song Y, Wang Y, Mao WF, et al. Dietary cadmium exposure assessment among the Chinese population[J]. PLoS One, 2017, 12(5):e0177978. doi: 10.1371/journal.pone.0177978 URL
[4]	Nawrot TS, Staessen JA, Roels HA, et al. Cadmium exposure in the population:from health risks to strategies of prevention[J]. Biometals, 2010, 23(5):769-782. doi: 10.1007/s10534-010-9343-z pmid: 20517707
[5]	Meng L, Huang TH, Shi JC, et al. Decreasing cadmium uptake of rice(Oryza sativa L.)in the cadmium-contaminated paddy field through different cultivars coupling with appropriate soil amendments[J]. J Soils Sediments, 2019, 19(4):1788-1798. doi: 10.1007/s11368-018-2186-x URL
[6]	Mendoza-Cózatl DG, Jobe TO, Hauser F, et al. Long-distance transport, vacuolar sequestration, tolerance, and transcriptional responses induced by cadmium and arsenic[J]. Curr Opin Plant Biol, 2011, 14(5):554-562. doi: 10.1016/j.pbi.2011.07.004 pmid: 21820943
[7]	Zhao JL, Yang W, Zhang SH, et al. Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection[J]. Rice:N Y, 2018, 11(1):61.
[8]	Xue DW, Chen MC, Zhang GP. Mapping of QTLs associated with cadmium tolerance and accumulation during seedling stage in rice(Oryza sativa L.)[J]. Euphytica, 2008, 165(3):587-596. doi: 10.1007/s10681-008-9785-3 URL
[9]	Ueno D, Kono I, Yokosho K, et al. A major quantitative trait locus controlling cadmium translocation in rice(Oryza sativa)[J]. New Phytol, 2009, 182(3):644-653. doi: 10.1111/j.1469-8137.2009.02784.x pmid: 19309445
[10]	Ishikawa S, Abe T, Kuramata M, et al. A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7[J]. J Exp Bot, 2010, 61(3):923-934. doi: 10.1093/jxb/erp360 pmid: 20022924
[11]	Ueno D, Yamaji N, Kono I, et al. Gene limiting cadmium accumulation in rice[J]. Proc Natl Acad Sci USA, 2010, 107(38):16500-16505. doi: 10.1073/pnas.1005396107 URL
[12]	Miyadate H, Adachi S, Hiraizumi A, et al. OsHMA3, a P1B-type of ATPase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles[J]. New Phytol, 2011, 189(1):190-199. doi: 10.1111/j.1469-8137.2010.03459.x URL
[13]	Huang Y, Sun CX, Min J, et al. Association mapping of quantitative trait loci for mineral element contents in whole grain rice(Oryza sativa L.)[J]. J Agric Food Chem, 2015, 63(50):10885-10892. doi: 10.1021/acs.jafc.5b04932 URL
[14]	Wang FJ, Wang M, Liu ZB, et al. Different responses of low grain-Cd-accumulating and high grain-Cd-accumulating rice cultivars to Cd stress[J]. Plant Physiol Biochem, 2015, 96:261-269. doi: 10.1016/j.plaphy.2015.08.001 URL
[15]	Luo JS, Huang J, Zeng DL, et al. A defensin-like protein drives cadmium efflux and allocation in rice[J]. Nat Commun, 2018, 9(1):645. doi: 10.1038/s41467-018-03088-0 URL
[16]	Hu DW, Sheng ZH, Li QL, et al. Identification of QTLs associated with cadmium concentration in rice grains[J]. J Integr Agric, 2018, 17(7):1563-1573. doi: 10.1016/S2095-3119(17)61847-1 URL
[17]	Liu WQ, Pan XW, Li YC, et al. Identification of QTLs and validation of qCd-2 associated with grain cadmium concentrations in rice[J]. Rice Sci, 2019, 26(1):42-49. doi: 10.1016/j.rsci.2018.12.003 URL
[18]	Yan HL, Xu WX, Xie JY, et al. Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies[J]. Nat Commun, 2019, 10(1):2562. doi: 10.1038/s41467-019-10544-y URL
[19]	Pan XW, Li YC, Liu WQ, et al. QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study[J]. Sci Rep, 2020, 10(1):11791. doi: 10.1038/s41598-020-68742-4 URL
[20]	Lincoln SE, Daly MJ, Lander ES. Constructing genetic linkage maps with mapmaker/Exp version 3.0: A tutorial and reference manual[M]. 3rd ed. Cambridge: Whitehead Institute for Biometrical Research, 1993.
[21]	Lincoln SE, Daly MJ, Lander ES. Mapping genes controlling quantitative traits using MAPMAKER/QTL version 1.1: A tutorial and reference manual[M]. 2nd ed. Cambridge: Whitehead Institute for Biometrical Research, 1993.
[22]	Uraguchi S, Mori S, Kuramata M, et al. Root-to-shoot Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice[J]. J Exp Bot, 2009, 60(9):2677-2688. doi: 10.1093/jxb/erp119 pmid: 19401409
[23]	Takahashi A, Agrawal GK, Yamazaki M, et al. Rice Pti1a negatively regulates RAR1-dependent defense responses[J]. Plant Cell, 2007, 19(9):2940-2951. pmid: 17890377