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Basic Information
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CGSNL Gene Symbol
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LCD1
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Gene Symbol Synonym
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NRAMP5, OsNRAMP5, OsNramp5, OsLCD1, NRAM5, OsNRAM5
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CGSNL Gene Name
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LOW CADMIUM ACCUMULATION 1
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Gene Name Synonym
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BACTERIOCIDE EFFECT 5, NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 5, low cadmium accumulation 1, low Cd-accumulation 1
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Protein Name
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NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 5
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Allele
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osnramp5, osnramp5-1, lcd-kmt1, osnramp5-2, lcd-kmt2, osnramp5-3, lcdkmt3, nramp5, OsNramp5-1, OsNramp5-2, OsNramp5-3, cr-OsNramp5, cr-OsNramp5-1, OsNRAMP5LAA, OsNRAMP5WSSM, lcd1, , osnramp5-L1, osnramp5-L2
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Chromosome No.
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7
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Explanation
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Q8H4H5. AB690551, AB690552, AB690553. AB698459. MH07t0175300. one of the two candidate genes for qSER-7 (QTL for stigma exsertion rate on chromosome 7). TO:0006059: cadmium concentration. TO:0006059: cadmium content trait. TO:1000056: shoot system cadmium content. TO:1000030: root system cadmium content. TO:1000039: root system manganese content. TO:1000064: shoot system manganese content. TO:0006048: manganese concentration. GO:0097054: L-glutamate biosynthetic process. TO:0020096: mineral and ion transport trait. TO:0020090: zinc content trait. GO:1900425: negative regulation of defense response to bacterium. GO:0140426: pathogen-associated molecular pattern receptor signaling pathway. GO:2000377: regulation of reactive oxygen species metabolic process. TO:0020089: iron content trait. TO:0001048: silicon content trait. TO:0001044: cobalt content trait. TO:0006051: nickel content. TO:0001045: chromium content trait. TO:0006054: arsenic content trait. GO:0097501: stress response to metal ion. GO:0098869: cellular oxidant detoxification. GO:0090551: response to manganese starvation.
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Trait Class
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Reproductive organ - Spikelet, flower, glume, awn
Biochemical character
Vegetative organ - Leaf
Vegetative organ - Culm
Coloration - Chlorophyll
Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK070788
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MSU ID
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LOC_Os07g15370.1
LOC_Os07g15370.2
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RAP ID
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Os07g0257200
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
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Build5
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RAP-DB
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IRGSP 1.0
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Build5
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Related IDs List (
IRGSP 1.0
/
Build5
)
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INSD Accession List
(Test version)
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Map
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Locate(cM)
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Link map
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Classical linkage map
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References
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Tang L., Wang J., Ji Z., Li X., Liu X., Lv Q., Wei P., Hu X., Li Y., Mao B., Shao Y., Peng Y., Wei Z., Bai L., Chen C., Zhao B.
Plant Commun 2026 7(4) 101690
Pyramiding elite alleles of the genetically linked OsNRAMP5 and OsHMA3 confers low Cd accumulation in rice grains without compromising stress tolerance.
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Xiao Q., Zhao B., Du C., Dun Z., Xiong D., Cui K., Peng S., Huang J.
Ecotoxicol. Environ. Saf. 2026 320 120370
Cadmium distribution in ratoon rice: OsNramp5 mutant reduces accumulation while physiological factors modulate node-specific partitioning.
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Fujii T., Yamaji N., Ma J.F.
J. Exp. Bot. 2025
Dual roles of suberin deposition at endodermal Casparian strip in manganese uptake of rice.
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Shao D., Yin L., Zhao J., Luo Z., Li W., Wang Y., Liu X., Tian B., Long X., Yin H., Zhou K.
Mol. Breed. 2025 45(8) 66
Navigating the genetic basis of cadmium accumulation: a comprehensive analysis of low-cadmium accumulation rice.
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Lu W.C., Zheng X.L., Xiao Y.T., Sun Z.F., Tang Z., Zhao F.J., Huang X.Y.
Int J Mol Sci 2025 26(19)
Spatiotemporal Transcriptome Profiling Reveals Nutrient Transport Dynamics in Rice Nodes and Roots During Reproductive Development.
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Wang X., Liu X., Su Y., Shen H.
Int J Mol Sci 2025 26(3)
Rice Responses to Abiotic Stress: Key Proteins and Molecular Mechanisms.
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Luo J.S., Yang Y., He Y., Xiao Y., He D., Shu T., Li X., Zhang K., Zhang Z.
J. Agric. Food Chem. 2025 73(26) 16242-16250
Overexpression of Silicon Uptake Transporter <i>OsLsi1</i> and <i>OsLsi2</i> Decreased Cadmium Accumulation in Rice.
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Khan T.A., Su Q., Guoqin H., Du Z., Noor M.A., Asseri T.A.Y., Hassan M.U.
Front Plant Sci 2025 16 1609825
Integrative biochar and melatonin application mitigates lead toxicity in rice by modulating antioxidant activities and iron plaque formation and downregulating the expression of metal uptake genes.
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Zhang H., Sun B., Wu W., Li Y., Yin Z., Lu C., Zhao H., Kong L., Ding X.
Plant Commun 2024 5(6) 100859
The MYB transcription factor OsMYBxoc1 regulates resistance to Xoc by directly repressing transcription of the iron transport gene OsNRAMP5 in rice.
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Shahzad M., Peng D., Khan A., Ayyaz A., Askri S.M.H., Naz S., Huang B., Zhang G.
Ecotoxicol. Environ. Saf. 2024 288 117386
Sufficient manganese supply is necessary for OsNramp5 knockout rice plants to ensure normal growth and less Cd uptake.
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Hu S., Zhou L., Wang J., Mawia A.M., Hui S., Xu B., Jiao G., Sheng Z., Shao G., Wei X., Wang L., Xie L., Zhao F., Tang S., Hu P.
Plant Biotechnol. J. 2024
Production of grains with ultra-low heavy metal accumulation by pyramiding novel Alleles of OsNramp5 and OsLsi2 in two-line hybrid rice.
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Zhang W., Guan M., Chen M., Lin X., Xu P., Cao Z.
Environ. Pollut. 2024 341 122928
Mutation of OsNRAMP5 reduces cadmium xylem and phloem transport in rice plants and its physiological mechanism.
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Feng K., Li J., Yang Y., Li Z., Wu W.
Int J Mol Sci 2023 24(9)
Cadmium Absorption in Various Genotypes of Rice under Cadmium Stress.
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Qu Z., Nakanishi H.
Plants (Basel) 2023 12(24)
Amino Acid Residues of the Metal Transporter OsNRAMP5 Responsible for Cadmium Absorption in Rice.
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Wang X., Xu Q., Hu K., Wang G., Shi K.
Mol. Plant Microbe Interact. 2023 36(2) 95-108
A Coculture of <i>Enterobacter</i> and <i>Comamonas</i> Species Reduces Cadmium Accumulation in Rice.
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Syu C.H., Nieh T.I., Hsieh M.T., Lo Y.C., Du P.R., Lin Y.W., Wu D.H.
Plants (Basel) 2022 11(21)
Uncovering the Genetic of Cadmium Accumulation in the Rice 3K Panel.
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Zhang J., Zhu Y., Yu L., Yang M., Zou X., Yin C., Lin Y.
Cells 2022 11(3)
Research Advances in Cadmium Uptake, Transport and Resistance in Rice (<i>Oryza sativa</i> L.).
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Xue W., Wang P., Tang L., Zhang C., Wang C., Huang Y., Zhang X., Li Y., Zhao B., Liu Z.
Ecotoxicol. Environ. Saf. 2021 211 111921
Citric acid inhibits Cd uptake by improving the preferential transport of Mn and triggering the defense response of amino acids in grains.
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Wang K., Yan T.Z., Xu S.L., Yan X., Zhou Q.F., Zhao X.H., Li Y.F., Wu Z.X., Qin P., Fu C.J., Fu J., Zhou Y.B., Yang Y.Z.
Sci Rep 2021 11(1) 6053
Validating a segment on chromosome 7 of japonica for establishing low-cadmium accumulating indica rice variety.
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Ma C., Hao Y., Zhao J., Zuverza-Mena N., Meselhy A.G., Dhankher O.P., Rui Y., White J.C., Xing B.
Nanomaterials (Basel) 2021 11(4)
Graphitic Carbon Nitride (C3N4) Reduces Cadmium and Arsenic Phytotoxicity and Accumulation in Rice (<i>Oryza sativa</i> L.).
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Desai J.S., Lawas L.M.F., Valente A.M., Leman A.R., Grinevich D.O., Jagadish S.V.K., Doherty C.J.
Proc. Natl. Acad. Sci. U.S.A. 2021 118(25)
Warm nights disrupt transcriptome rhythms in field-grown rice panicles.
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Liu J., Zhan J., Chen J., Lu X., Zhi S., Ye G.
Front Genet 2021 12 701658
Validation of Genes Affecting Rice Grain Zinc Content Through Candidate Gene-Based Association Analysis.
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Liu A., Zhou Z., Yi Y., Chen G.
BMC Genomics 2020 21(1) 127
Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain.
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Zhang S., Li Q., Nazir M.M., Ali S., Ouyang Y., Ye S., Zeng F.
Int J Mol Sci 2020 21(21)
Calcium Plays a Double-Edged Role in Modulating Cadmium Uptake and Translocation in Rice.
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Chang J.D., Huang S., Konishi N., Wang P., Chen J., Huang X.Y., Ma J.F., Zhao F.J.
J. Exp. Bot. 2020
Overexpression of the manganese/cadmium transporter OsNRAMP5 reduces cadmium accumulation in rice grain.
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Chang J.D., Huang S., Yamaji N., Zhang W., Ma J.F., Zhao F.J.
Plant Cell Environ. 2020 43(10) 2476-2491
OsNRAMP1 transporter contributes to cadmium and manganese uptake in rice.
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Treesubsuntorn C., Thiravetyan P.
Plant Biol (Stuttg) 2019 21(5) 862-872
Calcium acetate-induced reduction of cadmium accumulation in Oryza sativa: Expression of auto-inhibited calcium-ATPase and cadmium transporters.
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Himeno S., Sumi D., Fujishiro H.
Toxicol Res 2019 35(4) 311-317
Toxicometallomics of Cadmium, Manganese and Arsenic with Special Reference to the Roles of Metal Transporters.
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Liu Y., Zhang A., Wang F., Kong D., Li M., Bi J., Zhang F., Wang J., Luo X., Pan Z., Yu X., Liu G., Luo L.
Rice (N Y) 2019 12(1) 46
Fine mapping a quantitative trait locus, qSER-7, that controls stigma exsertion rate in rice (Oryza sativa L.).
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Cao Z.Z., Lin X.Y., Yang Y.J., Guan M.Y., Xu P., Chen M.X.
BMC Plant Biol. 2019 19(1) 250
Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq.
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Mani A., Sankaranarayanan K.
Protein J. 2018 37(3) 237-247
In Silico Analysis of Natural Resistance-Associated Macrophage Protein (NRAMP) Family of Transporters in Rice.
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Tanaka N., Uraguchi S., Kajikawa M., Saito A., Ohmori Y., Fujiwara T.
Plant J. 2018 96(5) 997-1006
A rice PHD-finger protein OsTITANIA, is a growth regulator that functions through elevating expression of transporter genes for multiple metals.
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Chen X., Ouyang Y., Fan Y., Qiu B., Zhang G., Zeng F.
J. Exp. Bot. 2018 69(21) 5279-5291
The pathway of transmembrane cadmium influx via calcium-permeable channels and its spatial characteristics along rice root.
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Luo B., Chen J., Zhu L., Liu S., Li B., Lu H., Ye G., Xu G., Fan X.
Front Plant Sci 2018 9 1192
Overexpression of a High-Affinity Nitrate Transporter <i>OsNRT2.1</i> Increases Yield and Manganese Accumulation in Rice Under Alternating Wet and Dry Condition.
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Tsunemitsu Y., Yamaji N., Ma J.F., Kato S.I., Iwasaki K., Ueno D.
Plant Signal Behav 2018 13(1) e1422466
Rice reduces Mn uptake in response to Mn stress.
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Ding Y., Ye Y., Jiang Z., Wang Y., Zhu C.
Front Plant Sci 2016 7 235
MicroRNA390 Is Involved in Cadmium Tolerance and Accumulation in Rice.
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Takahashi R., Ishimaru Y., Shimo H., Bashir K., Senoura T., Sugimoto K., Ono K., Suzui N., Kawachi N., Ishii S., Yin Y.G., Fujimaki S., Yano M., Nishizawa N.K., Nakanishi H.
PLoS ONE 2014 9(6) e98816
From laboratory to field: OsNRAMP5-knockdown rice is a promising candidate for Cd phytoremediation in paddy fields.
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Sasaki,A., Yamaji,N., Yokosho,K. and Ma,J.F.
Plant Cell 2012 24(5) 2155-2167
Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice
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Ishimaru Y., Bashir K., Nakanishi H., Nishizawa N.K.
Plant Signal Behav 2012 7(7) 1-4
OsNRAMP5, a major player for constitutive iron and manganese uptake in rice.
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Ishimaru Y., Takahashi R., Bashir K., Shimo H., Senoura T., Sugimoto K., Ono K., Yano M., Ishikawa S., Arao T., Nakanishi H., Nishizawa N.K.
Sci Rep 2012 2 286
Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport.
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Ishikawa S., Ishimaru Y., Igura M., Kuramata M., Abe T., Senoura T., Hase Y., Arao T., Nishizawa N.K., Nakanishi H.
Proc. Natl. Acad. Sci. U.S.A. 2012 109(47) 19166-71
Ion-beam irradiation, gene identification, and marker-assisted breeding in the development of low-cadmium rice.
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Takahashi R. , Ishimaru Y. , Senoura T. , Shimo H. , Ishikawa S. , Arao T. , Nakanishi H. , Nishizawa N.K.
J. Exp. Bot. 2011 -
The OsNRAMP1 iron transporter is involved in Cd accumulation in rice.
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Narayanan NN, Vasconcelos MW, Grusak MA.
Plant Physiol. Biochem. 2007 45(5) 277-86.
Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray.
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DB Reference
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Gramene ID
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-
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Ontologies
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Gene Ontology
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cadmium ion transport( GO:0015691 )
response to cadmium ion( GO:0046686 )
metal ion transport( GO:0030001 )
integral to membrane( GO:0016021 )
ion transport( GO:0006811 )
response to temperature stimulus( GO:0009266 )
temperature compensation of the circadian clock( GO:0010378 )
circadian rhythm( GO:0007623 )
glutamate biosynthetic process( GO:0006537 )
plasma membrane( GO:0005886 )
manganese ion transport( GO:0006828 )
response to organic substance( GO:0010033 )
L-phenylalanine biosynthetic process( GO:0009094 )
threonine biosynthetic process( GO:0009088 )
cadmium ion transmembrane transport( GO:0070574 )
response to phenylalanine( GO:0080053 )
response to symbiotic bacterium( GO:0009609 )
response to lead ion( GO:0010288 )
response to manganese ion( GO:0010042 )
response to oxidative stress( GO:0006979 )
alanine biosynthetic process( GO:0006523 )
endoplasmic reticulum( GO:0005783 )
response to heat( GO:0009408 )
vascular transport( GO:0010232 )
iron ion homeostasis( GO:0055072 )
response to calcium ion( GO:0051592 )
iron ion transport( GO:0006826 )
respiratory burst during defense response( GO:0002679 )
response to molecule of bacterial origin( GO:0002237 )
defense response to bacterium( GO:0042742 )
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Trait Ontology
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shoot dry weight( TO:0000552 )
shoot fresh weight( TO:0000571 )
root dry weight( TO:0000078 )
root fresh weight( TO:0000578 )
relative root dry weight( TO:0000644 )
relative shoot dry weight( TO:0000636 )
relative plant height( TO:0001034 )
root length( TO:0000227 )
leaf color( TO:0000326 )
plant height( TO:0000207 )
hydrogen peroxide content( TO:0000605 )
grain yield per plant( TO:0000449 )
tiller number( TO:0000346 )
seed set percent( TO:0000455 )
relative yield( TO:0000153 )
heat tolerance( TO:0000259 )
leaf rolling tolerance( TO:0002662 )
manganese sensitivity( TO:0000073 )
oxidative stress( TO:0002657 )
photosynthetic ability( TO:0000316 )
relative chlorophyll content( TO:0001016 )
relative root length( TO:0000516 )
micronutrient sensitivity( TO:0000080 )
sugar content( TO:0000333 )
chlorophyll-b content( TO:0000295 )
chlorophyll-a content( TO:0000293 )
chlorophyll content( TO:0000495 )
bacterial leaf streak disease resistance( TO:0000203 )
manganese content( TO:0020091 )
forage yield( TO:0000388 )
grain size( TO:0000397 )
amino acid content( TO:0002673 )
temperature response trait( TO:0000432 )
stigma exsertion( TO:0000044 )
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Plant Ontology
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seed development stage( PO:0001170 )
seed maturation stage( PO:0007632 )
root endodermis( PO:0005059 )
endosperm development stage( PO:0007633 )
exodermis( PO:0005772 )
root tip( PO:0000025 )
lateral root primordium( PO:0000016 )
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Related Strains
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Phenotype images
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Last updated
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Aug 29, 2026
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Update info.