Gene - Detail

Detail of Gene

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Basic Information
CGSNL Gene Symbol S5
Gene Symbol Synonym S5-3, S5-4
Gene Name Synonym Hybrid sterility5, Hybrid sterility 5, Hybrid sterility-5
Protein Name
Allele S5-n, S5-j, S5-i, S5-p, S5i, S5j, S5n
Chromosome No. 6
Explanation wide compatibility. EU889293 (S5-n), EU889294 (S5-j), EU889295 (S5-i). PO:0006465; integument (sensu Poaceae) ; PO:0006464; megaspore (sensu Poaceae) ; PO:0006462; nucellus (sensu Poaceae) ; PO:0006457; ovule (sensu Poaceae) ; PO:0006015; female archesporial cell ; PO:0006463; megasporocyte (sensu Poaceae) ; PO:0009046; flower. GRO:0007019; 4.02-embryo sac development. A killer-protector system at the S5 locus encoded by three tightly linked genes [Open Reading Frame 3 (ORF3) to ORF5] regulates fertility in indica-japonica hybrids (Yang et al. 2012). S5-4: JX138502, JX138503, JX138504, JX138505, S5-3: JX138498, JX138499, JX138500, JX138501. HQ846206 to HQ846327 (from O.sativa, O. rufipogon and O. nirvara), JF298922 (from O. barthii). KF892971-KF893059.
Trait Class Reproductive organ - Pollination, fertilization, fertility - Hybrid sterility
cDNA Accession No. -
MSU ID LOC_Os06g11010.1
RAP ID Os06g0213100
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) 49.0
Link map Classical linkage map
Zhou H., Xia D., Zeng J., Jiang G., He Y.
Rice (N Y) 2017  10(1)  39
Dissecting combining ability effect in a rice NCII-III population provides insights into heterosis in indica-japonica cross.
Craig S.M., Reagon M., Resnick L.E., Caicedo A.L.
PLoS ONE 2014  9(1)  e86647
Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.
Yang J., Zhao X., Cheng K., Du H., Ouyang Y., Chen J., Qiu S., Huang J., Jiang Y., Jiang L., Ding J., Wang J., Xu C., Li X., Zhang Q.
Science 2012  337(6100)  1336-40
A killer-protector system regulates both hybrid sterility and segregation distortion in rice.
Du H. , Ouyang Y. , Zhang C. , Zhang Q.
New Phytol. 2011  191(1)  275-87
Complex evolution of S5, a major reproductive barrier regulator, in the cultivated rice Oryza sativa and its wild relatives.
Chen,J., Ding,J., Ouyang,Y., Du,H., Yang,J., Cheng,K., Zhao,J., Qiu,S., Zhang,X., Yao,J., Liu,K., Wang,L., Xu,C., Li,X., Xue,Y., Xia,M., Ji,Q., Lu,J., Xu,M. and Zhang,Q.
Proc. Natl. Acad. Sci. U.S.A. 2008  105(32)  11436-11441
A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice
Singh SP, Sundaram RM, Biradar SK, Ahmed MI, Viraktamath BC, Siddiq EA.
Theor. Appl. Genet. 2006  113(3)  509-517
Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.).
D.T. Li, S.S. Zhu, L. Jiang and J.M. Wan
RGN 2005  22  20-22
Mapping for a new locus causing hybrid sterility in a China landrace (Oryza sativa L.).
Nori Kurata, Kazumaru Miyoshi, Ken-Ichi Nonomura, Yukiko Yamazaki and Yukihiro Ito
Plant Cell Physiol. 2005  46(1)  48-62
Rice Mutants and Genes Related to Organ Development , Morphogenesis and Physiological Traits
Wan, J. and H. Ikehashi
Euphytica 1997  94  151-161.
Identification of two types of differentiation in cultivated rice (Oryza sativa L.) detected by polymorphism of isozymes and hybrid sterility.
Malik, S.S. and G.S. Khush
RGN 1996  13  121-124.
Identification of wide compatibility varieties (WCV's) and tagging of WC gene with isozyme markers.
Wan, J. and H. Ikehashi
Breeding Science 1996  46  167-172.
Evidence for mutational origin of hybrid sterility genes in rice (Oryza sativa L.).
Ikehashi, H. and J. Wan
Rice Genetics III. IRRI, Manila, Philippines. 1996    404-408.
Differentiation of alleles at seven loci for hybrid sterility in cultivated rice (Oryza sativa L.).
Wan, J. and H. Ikehashi
RGN 1996  13  110-114.
List of hybrid sterility gene loci (HSGLi) in cultivated rice (Oryza sativa L.).
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.).
Causse, M.A., T.M. Fulton, Y.G. Cho, S.N. Ahn, J. Chunwongse, K. Wu, J. Xiao, Z. Yu, P.C. Ronald, S.E. Harrington, G. Second, S.R. McCouch and S.D. Tanksley
Genetics 1994  138  1251-1274.
Saturated molecular map of the rice genome based on an interspecific backcross population.
Wan, J., S. Yanagihara, H. Kato and H. Ikehashi
Japan. J. Breed. 1993  43  507-516.
Multiple alleles at a new locus causing hybrid sterility between a Korean Indica variety and Javanica variety in rice (Oryza sativa L.).
Yanagihara, S., H. Ikehashi, H. Araki and K. Maruyama
Japan. J. Breed. 1992  42  15-21.
Difference in recombination frequency between chromogen (C) and waxy (wx) genes in Japonica and Indica rice (Oryza sativa L.) by using Japonica lines with a wide compatibility gene (S-5n).
Liu, A., Q. Zhang and H. Li
RGN 1992  9  135-136.
Location of a gene for wide-compatibility in the RFLP linkage map.
Ikehashi, H., H. Araki and S. Yanagihara
Rice Genetics. II. IRRI, Manila, Philippines. 1991    33-43.
Screening and analysis of wide compatibility loci in wide crosses of rice.
Ikehashi, H. and H. Araki
Rice Genetics. IRRI, Manila, Philippines. 1986    119-130.
Genetics of F1 sterility in remote crosses of rice.
Ikehashi, H. and H. Araki
Japan. J. Breed. 1984  34(Suppl. 2)  226-227.
Multiple alleles in linkage group I of rice for spikelet sterility in distant crosses.
TextPresso Search Search textpresso for S5 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID GR:0060812
Gene Ontology aspartic-type endopeptidase activity( GO:0004190 )
cytoplasm( GO:0005737 )
cell wall( GO:0005618 )
mitochondrion( GO:0005739 )
megasporogenesis( GO:0009554 )
proteolysis( GO:0006508 )
multicellular organismal development( GO:0007275 )
embryo sac development( GO:0009553 )
Trait Ontology female sterility( TO:0000358 )
male sterility( TO:0000437 )
f1-hybrid incompatibility( TO:0000042 )
embryosac abortion( TO:0000416 )
spikelet fertility( TO:0000180 )
Plant Ontology female archesporial cell( PO:0006015 )
plant ovule( PO:0020003 )
nucellus( PO:0020020 )
integument( PO:0020021 )
flower( PO:0009046 )
megasporocyte( PO:0000431 )
megaspore( PO:0020019 )
Related Strains
Stocks for Genes 4
F Lines 1
Phenotype images
Last updated
Dec 27, 2017