Gene - Detail

Detail of Gene

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Basic Information
CGSNL Gene Symbol ALK
Gene Symbol Synonym alk, SSII-3, OsSSIIa, OsSSII-3, SSIIa, SSS2A, OsSSIIaChr6, SS2a
Gene Name Synonym alkali degeneration, ALKALI DEGENERATION, "Soluble starch synthase 2-3, chloroplast precursor", "Soluble starch synthase 2-3, chloroplast", "Soluble starch synthase 2-3, chloroplastic/amyloplastic", Soluble starch synthase II-3, Starch synthase IIa, soluble starch synthase IIa, Starch synthase-IIa, Starch synthase IIa
Allele SSII-3-I, SSII-3-II, ss2a, ALKa, ALKb, ALKc/SSIIai
Chromosome No. 6
Explanation This gene causes the disintegration of endosperm starch granules in alkali solution. This gene is located on chromosome 6 flanked by RFLP markers R2147 and C1478 and to the same location with gel(t), acl(t) and SSIIa. This trait is used for identification. EC= P0C586(indica). Q0DDE3(japonica). AY423717, AF419099. GRO:0007045; 09-mature grain stage. HQ712150, HQ712151, HQ712152, HQ712153, HQ712154, HQ7121525, HQ712156, HQ712157. HQ679416-HQ679573 (O. sativa and other wild rice species).
Trait Class Seed - Morphological traits - Endosperm
Seed - Physiological traits
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
cDNA Accession No. AK101978
MSU ID LOC_Os06g12450.1
RAP ID Os06g0229800
Links Oryzabase Chromosome View ( IRGSP 1.0 / Build5 )
RAP-DB ( IRGSP 1.0 / Build5 )
Related IDs List ( IRGSP 1.0 / Build5 )
INSD Accession List
(Test version)
Link to INSD Accession List
Locate(cM) 56.0
Link map Classical linkage map
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.
Irshad F., Li C., Wu H.Y., Yan Y., Xu J.H.
Int J Mol Sci 2022  23(12) 
The Function of DNA Demethylase Gene ROS1a Null Mutant on Seed Development in Rice (<i>Oryza Sativa</i>) Using the CRISPR/Cas9 System.
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.
Zhang H., Jang S.G., Lar S.M., Lee A.R., Cao F.Y., Seo J., Kwon S.W.
Plants (Basel) 2021  10(6) 
Genome-Wide Identification and Genetic Variations of the starch synthase Gene Family in Rice.
Jiang L., Zhong H., Jiang X., Zhang J., Huang R., Liao F., Deng Y., Liu Q., Huang Y., Wang H., Tao Y., Zheng J.
Front Plant Sci 2021  12  814928
Identification and Pleiotropic Effect Analysis of <i>GSE5</i> on Rice Chalkiness and grain shape.
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.
Paul P., Dhatt B.K., Miller M., Folsom J.J., Wang Z., Krassovskaya I., Liu K., Sandhu J., Yu H., Zhang C., Obata T., Staswick P., Walia H.
Plant Physiol. 2020  182(2)  933-948
<i>MADS78</i> and <i>MADS79</i> Are Essential Regulators of Early Seed Development in Rice.
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.
Chen Z., Lu Y., Feng L., Hao W., Li C., Yang Y., Fan X., Li Q., Zhang C., Liu Q.
Rice (N Y) 2020  13(1)  39
Genetic Dissection and Functional Differentiation of ALKa and ALKb, Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low gelatinization temperature in Rice.
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.
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.
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.).
Lee H.S., Hwang W.H., Jeong J.H., Ahn S.H., Baek J.S., Jeong H.Y., Park H.K., Ku B.I., Yun J.T., Lee G.H., Choi K.J.
BMC Genomics 2019  20(1)  18
Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage.
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.
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.
Crofts N., Sugimoto K., Oitome N.F., Nakamura Y., Fujita N.
Plant Mol. Biol. 2017  94(4-5)  399-417
Differences in specificity and compensatory functions among three major starch synthases determine the structure of amylopectin in rice endosperm.
Yang J., Kim S.R., Lee S.K., Choi H., Jeon J.S., An G.
Plant Sci. 2015  240  79-89
Alanine aminotransferase 1 (OsAlaAT1) plays an essential role in the regulation of starch storage in rice endosperm.
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.
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.
Huang X., Zhao Y., Wei X., Li C., Wang A., Zhao Q., Li W., Guo Y., Deng L., Zhu C., Fan D., Lu Y., Weng Q., Liu K., Zhou T., Jing Y., Si L., Dong G., Huang T., Lu T., Feng Q., Qian Q., Li J., Han B.
Nat. Genet. 2012  44(1)  32-9
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm.
Lu F.H., Park Y.J.
Genet Res (Camb) 2012  94  179-189
Sequence variations in OsAGPase significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)
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.).
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
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
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
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
Wang LQ,Liu WJ,Xu Y,He YQ,Luo LJ,Xing YZ,Xu CG,Zhang Q
Theor. Appl. Genet. 2007  115  463-76
Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain.
Ryoo N, Yu C, Park CS, Baik MY, Park IM, Cho MH, Bhoo SH, An G, Hahn TR, Jeon JS.
Plant Cell Rep. 2007  26(7)  1083-95
Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.).
Fujita N, Yoshida M, Asakura N, Ohdan T, Miyao A, Hirochika H, Nakamura Y.
Plant Physiol. 2006  140(3)  1070-84
Function and characterization of starch synthase I using mutants in rice.
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.).
Nakamura,Y., Francisco,P.B.,Jr., Hosaka,Y., Sato,A., Sawada,T., Kubo,A. and Fujita,N.
Plant Mol. Biol. 2005  58(2)  213-227
Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties.
Hirose T, Terao T.
Planta. 2004  220(1)  9-16
A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.).
Gao,Z., Zeng,D., Cui,X., Zhou,Y., Yan,M., Huang,D., Li,J. and Qian,Q.
Sci. China, C, Life Sciences 2003  46  661-668
Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice
Umemoto, T., M. Yano, H. Satoh, A. Shomura, Y. Nakamura
Theor. Appl. Genet. 2002  104  1-8
Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties.
He, P., S.G. Li, Q. Qian, Y.Q. Ma, J.Z. Li, W.M. Wang, Y. Chen and L.H. Zhu
Theor. Appl. Genet. 1999  98  502-508
Genetic analysis of rice grain quality.
Yanagihara, S., S.R. McCouch, K. Ishikawa, Y. Ogi, K. Maruyama and H. Ikehashi
Theor. Appl. Genet. 1995  90  182-188.
Molecular analysis of the inheritance of the S-5 locus, conferring wide compatibility in Indica/Japonica hybrids of rice (O.sativa L.).
Lin, S.Y., Y. Nagamura, N. Kurata, M. Yano, Y. Minobe and T. Sasaki
RGN 1994  11  108-109.
DNA markers tightly linked to genes, Ph, alk and Rc.
Kinoshita, T.
In Biology of Rice. S. Tsunoda and N. Takahashi eds. JSSP/Elsevier, Tokyo. 1984    187-274.
Gene analysis and linkage map.
Kudo, M.
Bull. Natl. Inst. Agric. Sci., Ser.D 1968  19  1-84.
Genetical and breeding studies on physiological and ecological characters in hybrids between ecological groups of rice.
Little, P.R., G.B. Hilder, and E.H. Dawson
Cereal Chem. 1958  35  111-126
Differential effect of dilute alkali on 25 varieties of milled white rice.
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DB Reference
Gramene ID GR:0060034,GR:0061112
Gene Ontology starch biosynthetic process( GO:0019252 )
starch synthase activity( GO:0009011 )
chloroplast( GO:0009507 )
plastid( GO:0009536 )
amyloplast( GO:0009501 )
response to flooding( GO:0009413 )
Trait Ontology alkali digestion( TO:0000134 )
seed composition based quality trait( TO:0000488 )
submergence sensitivity( TO:0000286 )
gelatinization temperature( TO:0000462 )
cool paste viscosity( TO:0000379 )
amylopectin content( TO:0000097 )
Plant Ontology endosperm( PO:0009089 )
Related Strains
Phenotype images
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Photo from A. Yoshimura
Last updated
Oct 21, 2022