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Basic Information
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CGSNL Gene Symbol
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SBE3
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Gene Symbol Synonym
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SBEIII*, SBEIII, Sbe3, RBE3, QEIIa, QEIIA, BEIIb, BEIIB, SBEIIb, OsBEIIb, sbe3, SBE III, OsSBEIIb, SBEIIb
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CGSNL Gene Name
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STARCH BRANCHING ENZYME 3
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Gene Name Synonym
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starch branching enzyme3, starch branching enzyme 3, Starch branching enzyme III, Starch branching enzyme-3, starch branching enzyme IIb, branching enzyme-3, Q-enzyme IIa, starch Branching enzyme isoform Type B, Branching enzyme isoform Type B, BE isoform type B
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Protein Name
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STARCH BRANCHING ENZYME 3
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Allele
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sbe3-rs, be2b, sbeIIb, sbe3
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Chromosome No.
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2
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Explanation
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GRO:0007045; 09-mature grain stage. D16201, E08183. HQ712141, HQ712140, HQ712139, HQ712138, HQ712137, HQ712136, HQ712135, HQ712134. HQ679079-HQ679246 (O. sativa and other wild rice species). JQ937272 (SBE3-rs; resistant starch mutant). GBSEIIb (SBEIIb) in Ali et al. 2021, Jin et al. 2021. GO:1901698: response to nitrogen compound.
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Trait Class
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Character as QTL - Grain quality
Seed - Morphological traits - Endosperm
Seed - Physiological traits
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK108535
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MSU ID
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LOC_Os02g32660.1
LOC_Os02g32660.2
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RAP ID
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Os02g0528200
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
/
Build5
)
RAP-DB
(
IRGSP 1.0
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Build5
)
Related IDs List (
IRGSP 1.0
/
Build5
)
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INSD Accession List
(Test version)
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Link to INSD Accession List
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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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Chen J., Bian X., Chu R., Wang T., Yang R., Zhang C., Huang L., Fan X., Liu Q.
Plant Commun 2026 7(4) 101673
Three transcription factors, OsNF-YC8, OsNF-YC9, and OsNF-YC10, function redundantly to promote amylopectin synthesis by activating SBE3 expression in rice endosperm.
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Huang K., Chen L., Jiao G., Ruan Z., Li X., Tang S., Hu P., Wei X.
Life (Basel) 2025 15(6)
<i>OsMYBR1</i>, a 1R-MYB Family Transcription Factor Regulates Starch Biosynthesis in Rice Endosperm.
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Meng Y., Cui J., Zeng W., Li X., Du C., Wang P., Li G., Ge Q., Guo T., Kang G.
Nat Commun 2025 17(1) 511
The bHLH transcription factor PIL1 orchestrates starch synthesis in key cereal crops.
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Liu N., Li J., Wang C.C., Yang T., Li A., Zeng P., Peng H., Zhang Y., Huang D., Zheng X., Zhang X.Q.
Plants (Basel) 2025 14(17)
Extensin-like Protein OsPEX1 Modulates Grain Filling in Rice.
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Chen Y., Hui S., Li H., Jiao G., Cao R., Zhou L., Wang J., Mawia A.M., Yang L., Wu Y., Zhang Y., Sheng Z., Shao G., Zhao F., Wang L., Lyu Y., Tang S., Hu S., Hu P.
Plant Biotechnol. J. 2025 23(7) 2793-2808
A myb61-SWB9-KOs module regulates grain chalkiness via gibberellin biosynthesis in rice endosperm.
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Badoni S., Pasion-Uy EA., Kor S., Kim S.R., Tiozon R.N., Misra G., Buenafe R.J.Q., Labarga L.M., Ramos-Castrosanto AR., Pratap V., Slamet-Loedin I., Steimker J.V., Alseekh S., Fernie A.R., Kohli A., Khush G.S., Sreenivasulu N.
Proc. Natl. Acad. Sci. U.S.A. 2024 121(36) e2410598121
Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content.
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Sun C., Wang Y., Yang X., Tang L., Wan C., Liu J., Chen C., Zhang H., He C., Liu C., Wang Q., Zhang K., Zhang W., Yang B., Li S., Zhu J., Sun Y., Li W., Zhou Y., Wang P., Deng X.
Plant Biotechnol. J. 2023 21(3) 621-634
MATE transporter GFD1 cooperates with sugar transporters, mediates carbohydrate partitioning and controls grain-filling duration, grain size and number in rice.
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Jin S.K., Zhang M.Q., Leng Y.J., Xu L.N., Jia S.W., Wang S.L., Song T., Wang R.A., Yang Q.Q., Tao T., Cai X.L., Gao J.P.
Front Plant Sci 2022 13 905148
<i>OsNAC129</i> Regulates Seed Development and Plant Growth and Participates in the Brassinosteroid Signaling Pathway.
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Gavgani H.N., Fawaz R., Ehyaei N., Walls D., Pawlowski K., Fulgos R., Park S., Assar Z., Ghanbarpour A., Geiger J.H.
J. Biol. Chem. 2022 298(1) 101395
A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb.
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Liu M., Fan F., He S., Guo Y., Chen G., Li N., Li N., Yuan H., Si F., Yang F., Li S.
Rice (N Y) 2022 15(1) 17
Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design.
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Liu X., Luo J., Li T., Yang H., Wang P., Su L., Zheng Y., Bao C., Zhou C.
Rice (N Y) 2021 14(1) 25
SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications.
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Niu B., Zhang Z., Zhang J., Zhou Y., Chen C.
Plant J. 2021 106(5) 1233-1246
The rice LEC1-like transcription factor OsNF-YB9 interacts with SPK, an endosperm-specific sucrose synthase protein kinase, and functions in seed development.
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Ali I., Ullah S., Iqbal A., Quan Z., Liang H., Ahmad S., Muhammad I., Amanullah, Imran, Guo Z., Wei S., Jiang L.
BMC Plant Biol. 2021 21(1) 600
Combined application of biochar and nitrogen fertilizer promotes the activity of starch metabolism enzymes and the expression of related genes in rice in a dual cropping system.
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Pasion E.A., Badoni S., Misra G., Anacleto R., Parween S., Kohli A., Sreenivasulu N.
Plant Biotechnol. J. 2021
OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty.
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Baysal C., He W., Drapal M., Villorbina G., Medina V., Capell T., Khush G.S., Zhu C., Fraser P.D., Christou P.
Proc. Natl. Acad. Sci. U.S.A. 2020 117(42) 26503-26512
Inactivation of rice starch branching enzyme IIb triggers broad and unexpected changes in metabolism by transcriptional reprogramming.
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Chen L., Yuan Y., Wu J., Chen Z., Wang L., Shahid M.Q., Liu X.
Rice (N Y) 2019 12(1) 34
Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes.
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Sera Y., Hanamata S., Sakamoto S., Ono S., Kaneko K., Mitsui Y., Koyano T., Fujita N., Sasou A., Masumura T., Saji H., Nonomura K.I., Mitsuda N., Mitsui T., Kurusu T., Kuchitsu K.
Sci Rep 2019 9(1) 18544
Essential roles of autophagy in metabolic regulation in endosperm development during rice seed maturation.
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Xue M., Liu L., Yu Y., Zhu J., Gao H., Wang Y., Wan J.
Rice (N Y) 2019 12(1) 100
Lose-of-Function of a Rice Nucleolus-Localized Pentatricopeptide Repeat Protein Is Responsible for the floury endosperm14 Mutant Phenotypes.
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Chen C., He B., Liu X., Ma X., Liu Y., Yao H.Y., Zhang P., Yin J., Wei X., Koh H.J., Yang C., Xue H.W., Fang Z., Qiao Y.
Plant Biotechnol. J. 2019
Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.).
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Long W., Wang Y., Zhu S., Jing W., Wang Y., Ren Y., Tian Y., Liu S., Liu X., Chen L., Wang D., Zhong M., Zhang Y., Hu T., Zhu J., Hao Y., Zhu X., Zhang W., Wang C., Zhang W., Wan J.
Plant Physiol. 2018 177(2) 698-712
FLOURY shrunken endosperm1 Connects Phospholipid Metabolism and Amyloplast Development in Rice.
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Jiang S., Sun S., Bai L., Ding G., Wang T., Xia T., Jiang H., Zhang X., Zhang F.
PLoS ONE 2017 12(7) e0181037
Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield.
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Yang R., Bai J., Fang J., Wang Y., Lee G., Piao Z.
Breed. Sci. 2016 66(4) 481-489
A single amino acid mutation of OsSBEIIb contributes to resistant starch accumulation in rice.
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Su J., Hu C., Yan X., Jin Y., Chen Z., Guan Q., Wang Y., Zhong D., Jansson C., Wang F., Schnürer A., Sun C.
Nature 2015 523(7562) 602-6
Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice.
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Wu Y.P., Pu C.H., Lin H.Y., Huang H.Y., Huang Y.C., Hong C.Y., Chang M.C., Lin Y.R.
Plant Sci. 2015 233 44-52
Three novel alleles of FLOURY ENDOSPERM2 (flo2) confer dull grains with low amylose content in rice.
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Sawada T., Nakamura Y., Ohdan T., Saitoh A., Francisco P.B., Suzuki E., Fujita N., Shimonaga T., Fujiwara S., Tsuzuki M., Colleoni C., Ball S.
Arch. Biochem. Biophys. 2014 562 9-21
Diversity of reaction characteristics of glucan branching enzymes and the fine structure of alpha-glucan from various sources.
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Abe N., Asai H., Yago H., Oitome N.F., Itoh R., Crofts N., Nakamura Y., Fujita N.
BMC Plant Biol. 2014 14(1) 80
Relationships between starch synthase I and branching enzyme isozymes determined using double mutant rice lines.
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Asai H., Abe N., Matsushima R., Crofts N., Oitome N.F., Nakamura Y., Fujita N.
J. Exp. Bot. 2014 65(18) 5497-507
Deficiencies in both Starch synthase IIIa and branching enzyme IIb lead to a significant increase in amylose in SSIIa-inactive japonica rice seeds.
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Wang J.C., Xu H., Zhu Y., Liu Q.Q., Cai X.L.
J. Exp. Bot. 2013 64(11) 3453-66
OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm.
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Yang,R., Sun,C., Bai,J., Luo,Z., Shi,B., Zhang,J., Yan,W. and Piao,Z.
PLoS ONE 2012 7 (8) E43026
A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.)
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Lu F.H., Park Y.J.
J. Cereal Sci. 2012 56 706-712
An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)
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Nakamura Y., Ono M., Utsumi C., Steup M.
Plant Cell Physiol. 2012 53(5) 869-78
Functional Interaction between Plastidial Starch Phosphorylase and Starch Branching Enzymes from Rice during the Synthesis of Branched Maltodextrins.
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Sun,M.M., Abdula,S.E., Lee,H.J., Cho,Y.C., Han,L.Z., Koh,H.J. and Cho,Y.G.
PLoS One 2011 6 (4) e18385
Molecular aspect of good eating quality formation in japonica rice
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Yan CJ,Tian ZX,Fang YW,Yang YC,Li J,Zeng SY,Gu SL,Xu CW,Tang SZ,Gu MH
Theor. Appl. Genet. 2011 122(1) 63-76
Genetic analysis of starch paste viscosity parameters in glutinous rice (Oryza sativa L.).
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Yu,G., Olsen,K.M. and Schaal,B.A.
Mol. Biol. Evol. 2011 28(1) 659-671
Molecular Evolution of the Endosperm Starch Synthesis Pathway Genes in Rice (Oryza sativa L.) and Its Wild Ancestor, O. rufipogon L
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Butardo V.M., Fitzgerald M.A., Bird A.R., Gidley M.J., Flanagan B.M., Larroque O., Resurreccion A.P., Laidlaw H.K., Jobling S.A., Morell M.K., Rahman S.
J. Exp. Bot. 2011 62(14) 4927-41
Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing.
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Tian,Z., Qian,Q., Liu,Q., Yan,M., Liu,X., Yan,C., Liu,G., Gao,Z., Tang,S., Zeng,D., Wang,Y., Yu,J., Gu,M. and Li,J.
Proc. Natl. Acad. Sci. U.S.A. 2009 106(51) 21760-5
Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities
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Satoh,H., Shibahara,K., Tokunaga,T., Nishi,A., Tasaki,M., Hwang,S.K., Okita,T.W., Kaneko,N., Fujita,N., Yoshida,M., Hosaka,Y., Sato,A., Utsumi,Y., Ohdan,T. and Nakamura,Y.
Plant Cell 2008 20(7) 1833-1849
Mutation of the Plastidial {alpha}-Glucan Phosphorylase Gene in Rice Affects the Synthesis and Structure of Starch in the Endosperm
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Yamaguchi, Takeshi
Plant Physiol. 2007 144(1) 258-277
Comprehensive Expression Profiling of Rice Grain Filling-Related Genes under High Temperature Using DNA Microarray.
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Bao JS, Corke H, Sun M.
Theor. Appl. Genet. 2006 113(7) 1171-83
Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.).
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Bao JS, Corke H, Sun M.
Theor. Appl. Genet. 2006 113(7) 1185-96
Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.).
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Chen,X.H., Liu,Q.Q., Wu,H.K., Wang,Z.Y. and Gu,M.H.
Zhongguo Shuidao Kexue 2003 17 109-112
cDNA Cloning and Sequence Analysis of Rice Sbe1 and Sbe3 Genes
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Nishi A, Nakamura Y, Tanaka N, Satoh H
Plant Physiol. 2001 127(2) 459-72
Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm
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Harrington, S.E., H.F.J. Bligh, W.D. Park, C.A. Jones and S.R. McCouch
Theor. Appl. Genet. 1997 94 564-568.
Linkage mapping of starch branching enzyme III in rice (Oryza sativa L.) and prediction of location of orthologous genes in other grasses.
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Nakamura Y., Umemoto T., Takahata Y., Komae K., Amano E., Satoh H.
Physiol Plant 1996 97(3) 491-498
Changes in structure of starch and enzyme activities affected by sugary mutations in developing rice endosperm. Possible role of starch debranching enzyme (R-enzyme) in amylopectin biosynthesis
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Nakamura-Y
Plant Science 1996 121 1-18
Some properties of starch debranching enzymes and their possible role in amylopectin biosynthesis
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Mizuno,K., Kawasaki,T., Shimada,H., Satoh,H., Kobayashi,E., Okumura,S., Arai,Y. and Baba,T.
J. Biol. Chem. 1993 268(25) 19084-19091
Alteration of the structural properties of starch components by the lack of an isoform of starch branching enzyme in rice seeds.
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Nakamura,Y. and Yamanouchi,H.
Plant Physiol. 1992 99(3) 1265-1266
Nucleotide sequence of a cDNA encoding starch-branching enzyme, or Q-enzyme I, from rice endosperm
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Nakamura Y., Takeichi T., Kawaguchi K., Yamanouchi H.
Physiol Plant 1992 84(3) 329-335
Purification of two forms of starch branching enzyme (Q-enzyme) from developing rice endosperm
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Nakamura Y, Umemoto T, Takahata Y, Amano E
Gamma Field Symp. 1992 31 25-44
Characteristics and roles of key enzymes associated with starch biosynthesis in rice endosperm
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DB Reference
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Gramene ID
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GR:0060839
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Ontologies
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Gene Ontology
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amyloplast( GO:0009501 )
amyloplast starch grain( GO:0009568 )
starch biosynthetic process( GO:0019252 )
1,4-alpha-glucan branching enzyme activity( GO:0003844 )
hydrolase activity, hydrolyzing O-glycosyl compounds( GO:0004553 )
starch metabolic process( GO:0005982 )
polysaccharide metabolic process( GO:0005976 )
amylopectin biosynthetic process( GO:0010021 )
response to heat( GO:0009408 )
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Trait Ontology
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amylopectin content( TO:0000097 )
amylose content( TO:0000196 )
gelatinization temperature( TO:0000462 )
peak viscosity( TO:0000409 )
setback viscosity( TO:0000412 )
breakdown viscosity( TO:0000374 )
starch content( TO:0000696 )
sugar content( TO:0000333 )
fat and essential oil content( TO:0000604 )
amino acid content( TO:0002673 )
nitrogen sensitivity( TO:0000011 )
heat tolerance( TO:0000259 )
carbohydrate content( TO:0000291 )
carbohydrate composition related trait( TO:0000489 )
starch grain shape( TO:0002656 )
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Plant Ontology
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endosperm( PO:0009089 )
seed maturation stage( PO:0007632 )
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Related Strains
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Phenotype images
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Last updated
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Jul 30, 2026
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Update info.