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Basic Information
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CGSNL Gene Symbol
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LSD3
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Gene Symbol Synonym
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HEMA1, OsHEMA1, HEMA, OsHEMA, GluTR, hemA, OsLSD3
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CGSNL Gene Name
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LEAF STARCH DEFICIENCY 3
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Gene Name Synonym
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glutamyl-tRNA reductase, Glutamyl-tRNA reductase 2, Leaf Starch Deficiency 3
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Protein Name
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GLUTAMYL-TRNA REDUCTASE
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Allele
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lsd3, lsd3-cr1, lsd3-cr2
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Chromosome No.
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10
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Explanation
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AB011416. A2Z928. P0C587. Glutamyl-tRNA reductase 2 in Jia et al. 2020. osa-miR2926 target gene. GO:0090549: response to carbon starvation. GO:0110126: phloem loading. GO:2000881: regulation of starch catabolic process. TO:0001167: starch gelatinization trait. TO:0000975: grain width.
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Trait Class
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Biochemical character
Coloration - Chlorophyll
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
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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AK099393
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MSU ID
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LOC_Os10g35840.1
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RAP ID
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Os10g0502400
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
/
Build5
)
RAP-DB
(
IRGSP 1.0
/
Build5
)
Related IDs List (
IRGSP 1.0
/
Build5
)
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INSD Accession List
(Test version)
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-
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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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Duan Y., Li X., Ma L., Jiao G., Cao R., Dong N., Li X., Wang Z., Wang P., Tang S., Wei X., Hu P.
Plant Commun 2025 6(11) 101527
A glutamyl-tRNA reductase and its binding protein promote transitory starch biosynthesis and enhance grain quality and yield in rice.
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Lim C., Kim Y., Shim Y., Cho S.H., Yang T.J., Song Y.H., Kang K., Paek N.C.
Plant J. 2023
Rice OsGATA16 is a positive regulator for chlorophyll biosynthesis and chloroplast development.
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Chen H., Wang Q., Fan M., Zhang X., Feng P., Zhu L., Wu J., Cheng X., Wang J.
Int J Mol Sci 2023 24(6)
A Single Nucleotide Variation of <i>CRS2</i> Affected the Establishment of Photosynthetic System in Rice.
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Qiu Z., Chen D., Teng L., Guan P., Yu G., Zhang P., Song J., Zeng Q., Zhu L.
Rice (N Y) 2022 15(1) 50
OsWHY1 Interacts with OsTRX z and is Essential for Early Chloroplast Development in Rice.
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Liu X., Deng X.J., Li C.Y., Xiao Y.K., Zhao K., Guo J., Yang X.R., Zhang H.S., Chen C.P., Luo Y.T., Tang Y.L., Yang B., Sun C.H., Wang P.R.
Int J Mol Sci 2022 23(10)
Mutation of Protoporphyrinogen IX Oxidase Gene Causes Spotted and rolled leaf and Its Overexpression Generates Herbicide Resistance in Rice.
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Li J., Zhao T., Chen L., Chen H., Luo D., Chen C., Miao Y., Liu D.
BMC Plant Biol. 2022 22(1) 368
Artemisia argyi allelopathy: a generalist compromises hormone balance, element absorption, and photosynthesis of receptor plants.
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Lin X., Huang Y., Rao Y., Ouyang L., Zhou D., Zhu C., Fu J., Chen C., Yin J., Bian J., He H., Zou G., Xu J.
BMC Plant Biol. 2022 22(1) 612
A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice.
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Xu T., Zhang J., Liu Y., Zhang Q., Li W., Zhang Y., Wu M., Chen T., Ding D., Wang W., Zhang Z.
Front Plant Sci 2022 13 986678
Exon skipping in <i>IspE</i> Gene is associated with abnormal chloroplast development in rice <i>albino leaf 4</i> mutant.
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Zhou K., Zhang C., Xia J., Yun P., Wang Y., Ma T., Li Z.
Rice (N Y) 2021 14(1) 47
Albino seedling lethality 4; Chloroplast 30S Ribosomal Protein S1 is Required for Chloroplast Ribosome Biogenesis and Early Chloroplast Development in Rice.
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Wang Q., Zhu B., Chen C., Yuan Z., Guo J., Yang X., Wang S., Lv Y., Liu Q., Yang B., Sun C., Wang P., Deng X.
Rice (N Y) 2021 14(1) 50
A Single Nucleotide Substitution of GSAM Gene Causes Massive Accumulation of Glutamate 1-Semialdehyde and Yellow Leaf Phenotype in Rice.
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Zhu X., Ze M., Yin J., Chern M., Wang M., Zhang X., Deng R., Li Y., Liao H., Wang L., Tu B., Song L., He M., Li S., Wang W.M., Chen X., Wang J., Li W.
Plant Sci. 2020 290 110295
A phosphofructokinase B-type carbohydrate kinase family protein, PFKB1, is essential for chloroplast development at early seedling stage in rice.
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Jia Y., Li C., Li Q., Liu P., Liu D., Liu Z., Wang Y., Jiang G., Zhai W.
Int J Mol Sci 2020 21(3)
Characteristic Dissection of <i>Xanthomonas oryzae</i> pv. o<i>ryzae</i> Responsive MicroRNAs in Rice.
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Kusano M., Fukushima A., Tabuchi-Kobayashi M., Funayama K., Kojima S., Maruyama K., Yamamoto Y.Y., Nishizawa T., Kobayashi M., Wakazaki M., Sato M., Toyooka K., Osanai-Kondo K., Utsumi Y., Seki M., Fukai C., Saito K., Yamaya T.
Plant Physiol. 2020 182(4) 1894-1909
Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots.
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Wang H., Shi Y., Zhang X., Xu X., Wu J.L.
Int J Mol Sci 2020 21(4)
Characterization of a Novel Rice Dynamic Narrow-rolled leaf Mutant with Deficiencies in Aromatic Amino Acids.
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Huang W., Zhang Y., Shen L., Fang Q., Liu Q., Gong C., Zhang C., Zhou Y., Mao C., Zhu Y., Zhang J., Chen H., Zhang Y., Lin Y., Bock R., Zhou F.
New Phytol. 2020
Accumulation of the RNA polymerase subunit RpoB depends on RNA editing by OsPPR16 and affects chloroplast development during early leaf development in rice.
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Zhu X., Mou C., Zhang F., Huang Y., Yang C., Ji J., Liu X., Cao P., Nguyen T., Lan J., Zhou C., Liu S., Jiang L., Wan J.
Rice (N Y) 2020 13(1) 45
WSL9 Encodes an HNH endonuclease domain-containing protein that Is Essential for Early Chloroplast Development in Rice.
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Zhang Q., Shen L., Wang Z., Hu G., Ren D., Hu J., Zhu L., Gao Z., Zhang G., Guo L., Zeng D., Qian Q.
Int J Mol Sci 2019 20(18)
OsCAF1, a CRM Domain Containing Protein, Influences Chloroplast Development.
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Atul Prakash Sathe, Su X., Chen Z., Chen T., Wei X., Tang S., Xiao-Bo Zhang, Jian-Li Wu
Rice (N Y) 2019 12(1) 68
Identification and characterization of a spotted-leaf mutant spl40 with enhanced bacterial blight resistance in rice.
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He Y., Li L., Zhang Z., Wu J.L.
Int J Mol Sci 2018 19(1)
Identification and Comparative Analysis of Premature Senescence Leaf Mutants in Rice (Oryza sativa L.).
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Lin D., Zheng K., Liu Z., Li Z., Teng S., Xu J., Dong Y.
Plant Genome 2018 11(1)
Rice <i>TCM1</i> Encoding a Component of the TAC Complex is Required for Chloroplast Development under Cold Stress.
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Liu Z., Wang Z., Gu H., You J., Hu M., Zhang Y., Zhu Z., Wang Y., Liu S., Chen L., Liu X., Tian Y., Zhou S., Jiang L., Liu L., Wan J.
Front Plant Sci 2018 9 782
Identification and Phenotypic Characterization of <i>ZEBRA LEAF16</i> Encoding a beta-hydroxyacyl-ACP dehydratase in Rice.
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Xiao H., Xu Y., Ni C., Zhang Q., Zhong F., Huang J., Liu W., Peng L., Zhu Y., Hu J.
J. Exp. Bot. 2018 69(12) 2923-2936
A rice dual-localized pentatricopeptide repeat protein is involved in organellar RNA editing together with OsMORFs.
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Tran L.H., Jung S.
Int J Mol Sci 2017 18(3)
Effects of Light-Emitting Diode Irradiation on Growth Characteristics and Regulation of Porphyrin Biosynthesis in Rice Seedlings.
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Sheng Z., Lv Y., Li W., Luo R., Wei X., Xie L., Jiao G., Shao G., Wang J., Tang S., Hu P.
PLoS ONE 2017 12(5) e0177989
Yellow-Leaf 1 encodes a magnesium-protoporphyrin IX monomethyl ester cyclase, involved in chlorophyll biosynthesis in rice (Oryza sativa L.).
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Lu G., Casaretto J.A., Ying S., Mahmood K., Liu F., Bi Y.M., Rothstein S.J.
Plant Mol. Biol. 2017
Overexpression of OsGATA12 regulates chlorophyll content, delays plant senescence and improves rice yield under high density planting.
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Li Y.Y., Shen A., Xiong W., Sun Q.L., Luo Q., Song T., Li Z.L., Luan W.J.
Rice (N Y) 2016 9(1) 46
Overexpression of OsHox32 Results in Pleiotropic Effects on Plant Type Architecture and Leaf Development in Rice.
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Wang Y., Zhang J., Shi X., Peng Y., Li P., Lin D., Dong Y., Teng S.
J. Exp. Bot. 2016
Temperature-sensitive albino gene tcd5, encoding a monooxygenase, affects chloroplast development at low temperatures.
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Inagaki N., Kinoshita K., Kagawa T., Tanaka A., Ueno O., Shimada H., Takano M.
PLoS ONE 2015 10(8) e0135408
Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings.
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Yang Y., Xu J., Huang L., Leng Y., Dai L., Rao Y., Chen L., Wang Y., Tu Z., Hu J., Ren D., Zhang G., Zhu L., Guo L., Qian Q., Zeng D.
J. Exp. Bot. 2015
PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice.
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Wang Y.a, Jiang X.a, Li K.a, Wu M.a b, Zhang R.a, Zhang L.a, Chen G.a
Biometals 2014 27 389-401
Photosynthetic responses of Oryza sativa L. seedlings to cadmium stress: Physiological, biochemical and ultrastructural analyses
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Zhou K., Ren Y., Lv J., Wang Y., Liu F., Zhou F., Zhao S., Chen S., Peng C., Zhang X., Guo X., Cheng Z., Wang J., Wu F., Jiang L., Wan J.
Planta 2013 237(1) 279-92
Young leaf chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice.
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Nakayashiki,T. and Inokuchi,H.
Plant Physiol. 1998 117 332
Nuceotide sequence of a cDNA clone encoding glutamyl-tRNA reductase from rice (accession No. AB011416) (PGR 98-080)
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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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sucrose metabolic process( GO:0005985 )
starch metabolic process( GO:0005982 )
phloem loading( GO:0009915 )
plastid( GO:0009536 )
circadian rhythm( GO:0007623 )
regulation of starch biosynthetic process( GO:0010581 )
response to other organism( GO:0051707 )
response to cadmium ion( GO:0046686 )
response to oxidative stress( GO:0006979 )
response to blue light( GO:0009637 )
chlorophyll biosynthetic process( GO:0015995 )
NADP or NADPH binding( GO:0050661 )
glutamyl-tRNA reductase activity( GO:0008883 )
chloroplast( GO:0009507 )
response to red light( GO:0010114 )
protoporphyrinogen IX biosynthetic process( GO:0006782 )
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Trait Ontology
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red light sensitivity( TO:0000158 )
blue light sensitivity( TO:0000159 )
seed quality( TO:0000162 )
grain yield( TO:0000396 )
carbon sensitivity( TO:0000001 )
starch content( TO:0000696 )
starch grain size( TO:0002655 )
starch grain synthesis( TO:0002658 )
amylose content( TO:0000196 )
leaf color( TO:0000326 )
chlorophyll content( TO:0000495 )
chalky endosperm( TO:0000266 )
floury endosperm( TO:0000104 )
endosperm storage protein content( TO:0002653 )
total soluble sugar content( TO:0000340 )
starch grain shape( TO:0002656 )
plant height( TO:0000207 )
grain width( TO:0000402 )
1000-seed weight( TO:0000382 )
grain yield per plant( TO:0000449 )
sucrose content( TO:0000328 )
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Plant Ontology
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root( PO:0009005 )
stem( PO:0009047 )
leaf( PO:0025034 )
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Related Strains
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Phenotype images
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Last updated
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Jan 8, 2026
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Update info.