Gene - Detail

Detail of Gene

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Basic Information
CGSNL Gene Symbol PHYB
Gene Symbol Synonym phyB, PHYB1, OsPHYB, OsphyB, OsYHB, YHB, OsPHYB/OsYHB
Gene Name Synonym PhytochromeB, Phytochrome B
Allele phyb, osphyB, phyB-1, phyB-2, phyB-3, phyB-4, phyB-5, phyB-6
Chromosome No. 3
Explanation A2XFW2 (indica), Q10MG9 (japonica). AB109892 (Japonica). JN594127-JN594211 (O. sativa and other wild rice species). CL523988 (phyB-6). MT460250 - MT460374. a rice ortholog of Arabidopsis gene for circadian clock component. NCBI Gene Expression Omnibus with an accession number GSE36320. GO:2000028: regulation of photoperiodism, flowering.
Trait Class Biochemical character
Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Vegetative organ - Leaf
Vegetative organ - Culm
Vegetative organ - Root
Coloration - Chlorophyll
cDNA Accession No. AK071993
MSU ID LOC_Os03g19590.1
RAP ID Os03g0309200
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
Link map Classical linkage map
Ahn H.R., Kim Y.J., Lim Y.J., Duan S., Eom S.H., Jung K.H.
Plants (Basel) 2021  10(1) 
Key Genes in the Melatonin Biosynthesis Pathway with Circadian Rhythm Are Associated with Various Abiotic Stresses.
Liang L., Zhang Z., Cheng N., Liu H., Song S., Hu Y., Zhou X., Zhang J., Xing Y.
Plant Cell Environ. 2021  44(3)  842-855
The transcriptional repressor OsPRR73 links circadian clock and photoperiod pathway to control heading date in rice.
Cui Y., Wang J., Feng L., Liu S., Li J., Qiao W., Song Y., Zhang Z., Cheng Y., Zhang L., Zheng X., Yang Q.
Front Plant Sci 2020  11  864
A Combination of Long-Day Suppressor Genes Contributes to the Northward Expansion of Rice.
Hu W., Figueroa-Balderas R., Chi-Ham C., Lagarias J.C.
Plant Direct 2020  4(4)  e00210
Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B.
Xie C., Zhang G., An L., Chen X., Fang R.
Planta 2019  250(1)  105-114
Phytochrome-interacting factor-like protein OsPIL15 integrates light and gravitropism to regulate tiller angle in rice.
Cui Y., Zhu M., Xu Z., Xu Q.
Theor. Appl. Genet. 2019  132(6)  1887-1896
Assessment of the effect of ten heading time genes on reproductive transition and yield components in rice using a CRISPR/Cas9 system.
Mao C., Lu S., Lv B., Zhang B., Shen J., He J., Luo L., Xi D., Chen X., Ming F.
Plant Physiol. 2017  174(3)  1747-1763
A Rice NAC Transcription Factor Promotes leaf senescence via ABA Biosynthesis.
Yoo Y.H., Nalini Chandran AK., Park J.C., Gho Y.S., Lee S.W., An G., Jung K.H.
Front Plant Sci 2017  8  580
OsPhyB-Mediating Novel Regulatory Pathway for drought tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.
Sheng P., Wu F., Tan J., Zhang H., Ma W., Chen L., Wang J., Wang J., Zhu S., Guo X., Wang J., Zhang X., Cheng Z., Bao Y., Wu C., Liu X., Wan J.
Plant Mol. Biol. 2016  92(1-2)  209-22
A CONSTANS-like transcriptional activator, OsCOL13, functions as a negative regulator of flowering downstream of OsphyB and upstream of Ehd1 in rice.
Cordeiro A.M., Figueiredo D.D., Tepperman J., Borba A.R., Lourenço T., Abreu I.A., Ouwerkerk P.B., Quail P.H., Margarida Oliveira M., Saibo N.J.
Biochim. Biophys. Acta 2016  1859(2)  393-404
Rice Phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of Phytochrome B.
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.
Matsuzaki J., Kawahara Y., Izawa T.
Plant Cell 2015  27(3)  633-48
Punctual Transcriptional Regulation by the Rice Circadian Clock under Fluctuating Field Conditions.
Gao H., Jin M., Zheng X.M., Chen J., Yuan D., Xin Y., Wang M., Huang D., Zhang Z., Zhou K., Sheng P., Ma J., Ma W., Deng H., Jiang L., Liu S., Wang H., Wu C., Yuan L., Wan J.
Proc. Natl. Acad. Sci. U.S.A. 2014   
Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice.
Yang Y., Peng Q., Chen G.X., Li X.H., Wu C.Y.
Mol Plant 2013  6(1)  202-15
OsELF3 is Involved in Circadian Clock Regulation for Promoting Flowering under Long-Day Conditions in Rice.
Zhao,D.-S., Zhang,C.-Q., Gu,M.-H. and Liu,Q.-Q.
Zuo Wu Xue Bao 2013  39(10)  1799-1805
Genetic and Expression Anaylses of Ef7-1, a Novel Ef7 Allele, in Rice
Hirose F., Inagaki N., Takano M.
Plant Signal Behav 2013  8(3) 
Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots.
Huang,C.L., Hung,C.Y., Chiang,Y.C., Hwang,C.C., Hsu,T.W., Huang,C.C., Hung,K.H., Tsai,K.C., Wang,K.H., Osada,N., Schaal,B.A. and Chiang,T.Y.
Plant J. 2012  70(5)  769-782
Footprints of natural and artificial selection for photoperiod pathway genes in Oryza
Ishikawa R. , Aoki M. , Kurotani K. , Yokoi S. , Shinomura T. , Takano M. , Shimamoto K.
Mol. Genet. Genomics 2011  285(6)  461-70
Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice.
Lee Y.-S., Jeong D.-H., Lee D.-Y., Yi J., Ryu C.-H., Kim S.L., Jeong H.J., Choi S.C., Jin P., Yang J., Cho L.-H., Choi H., An G.
Plant Journal 2010  63(1)  18-30
OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB.
Takano M,Inagaki N,Xie X,Kiyota S,Baba-Kasai A,Tanabata T,Shinomura T
Proc. Natl. Acad. Sci. U.S.A. 2009  106(34)  14705-10
Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice.
Komiya R., Yokoi S., Shimamoto K.
Development 2009  136(20)  3443-50
A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice.
Pareek A, Singh A, Kumar M, Kushwaha HR, Lynn AM, Singla-Pareek SL.
Plant Physiol. 2006  142(2)  380-97
Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis.
Ishikawa R., Tamaki S., Yokoi S., Inagaki N., Shinomura T., Takano M., Shimamoto K.
Plant Cell 2005  17(12)  3326-36
Suppression of the floral activator Hd3a is the principal cause of the night break effect in rice.
Takano,M., Inagaki,N., Xie,X., Yuzurihara,N., Hihara,F., Ishizuka,T., Yano,M., Nishimura,M., Miyao,A., Hirochika,H. and Shinomura,T.
Plant Cell 2005  17(12)  3311-3325
Distinct and cooperative functions of phytochromes a, B, and C in the control of deetiolation and flowering in rice.
Basu,D., Dehesh,K., Schneider-Poetsch,H.J., Harrington,S.E., McCouch,S.R. and Quail,P.H.
Plant Mol. Biol. 2000  44(1)  27-42
Rice PHYC gene: structure, expression, map position and evolution.
Mathews,S. and Sharrock,R.A.
Mol. Biol. Evol. 1996  13(8)  1141-1150
The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms.
Dehesh,K., Tepperman,J., Christensen,A.H. and Quail,P.H.
Mol. Gen. Genet. 1991  225(2)  305-313
phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots.
TextPresso Search Search textpresso for PHYB ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID -
Gene Ontology chloroplast organization( GO:0009658 )
response to deep water( GO:0030912 )
photoreceptor activity( GO:0009881 )
response to red light( GO:0010114 )
photomorphogenesis( GO:0009640 )
two-component sensor activity( GO:0000155 )
protein-chromophore linkage( GO:0018298 )
protein homodimerization activity( GO:0042803 )
protein-tetrapyrrole linkage( GO:0017006 )
ATP binding( GO:0005524 )
G-protein coupled photoreceptor activity( GO:0008020 )
membrane( GO:0016020 )
peptidyl-histidine phosphorylation( GO:0018106 )
transcription( GO:0006350 )
regulation of transcription, DNA-dependent( GO:0006355 )
sensory perception( GO:0007600 )
red, far-red light phototransduction( GO:0009585 )
circadian rhythm( GO:0007623 )
photoperiodism, flowering( GO:0048573 )
regulation of chlorophyll biosynthetic process( GO:0010380 )
response to water deprivation( GO:0009414 )
hydrogen peroxide catabolic process( GO:0042744 )
Trait Ontology days to heading( TO:0000137 )
chlorophyll content( TO:0000495 )
chlorophyll ratio( TO:0000298 )
leaf color( TO:0000326 )
flowering time( TO:0002616 )
drought tolerance( TO:0000276 )
hydrogen peroxide content( TO:0000605 )
stomatal frequency( TO:0000566 )
filled grain number( TO:0000447 )
seed set percent( TO:0000455 )
red light sensitivity( TO:0000158 )
leaf length( TO:0000135 )
seminal root length( TO:0000586 )
crown root number( TO:0002685 )
root shape( TO:0002710 )
submergence tolerance( TO:0000524 )
tiller number( TO:0000346 )
chloroplast development trait( TO:0002715 )
plant height( TO:0000207 )
Plant Ontology -
Related Strains
Phenotype images
Last updated
Jan 12, 2022