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Detail of Gene

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Basic Information
CGSNL Gene Symbol HD6
Gene Symbol Synonym Hd6(t)*, OSCKA2, OsCKA2, CKA2, OsCKA2-1, CKA2-1, Hd6/CK2alpha, CK2alpha
Gene Name Synonym Heading date (QTL)-6(t), Heading date-6, Heading date6, casein kinase II alpha subunit, CK2alpha subunit 1, Casein Kinase 2alpha
Chromosome No. 3
Explanation Under long day (13.5hr) treatment, this QTL introduced from Kasalath to Nipponbare increased the days to heading. Hd6 has an epistatic effect with Hd2. This is homoeologous to wheat vernalization gene vrn-A1 on chromosome 5A. AB036785, AB036786, AB036787, AB036788. MT453303 - MT453434. HD6 is likely to be E3. PO:0000230; inflorescence meristem ; PO:0009049; inflorescence ; PO:0009013; meristem ; PO:0006318; floret (sensu Poaceae) ; PO:0009010; seed. GRO:0007048; 04-stem elongation stage ; GRO:0007044; 06-heading stage ; GRO:0007045; 09-mature grain stage. LOC_Os03g55389.
Trait Class Reproductive organ - Heading date
cDNA Accession No. CT837832
MSU ID LOC_Os03g55389.1
RAP ID Os03g0762000
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 map Classical linkage map
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.
Yano K., Yamamoto E., Aya K., Takeuchi H., Lo P.C., Hu L., Yamasaki M., Yoshida S., Kitano H., Hirano K., Matsuoka M.
Nat. Genet. 2016  48(8)  927-34
Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice.
Kwon C.T., Koo B.H., Kim D., Yoo S.C., Paek N.C.
Mol. Cells 2014   
Casein Kinases I and 2alpha Phosphorylate Oryza Sativa Pseudo-Response Regulator 37 (OsPRR37) in Photoperiodic Flowering in Rice.
Ogiso-Tanaka E., Matsubara K., Yamamoto S., Nonoue Y., Wu J., Fujisawa H., Ishikubo H., Tanaka T., Ando T., Matsumoto T., Yano M.
PLoS ONE 2013  8(10)  e75959
Natural Variation of the RICE FLOWERING LOCUS T 1 Contributes to flowering time Divergence in Rice.
Ebana K,Shibaya T,Wu J,Matsubara K,Kanamori H,Yamane H,Yamanouchi U,Mizubayashi T,Kono I,Shomura A,Ito S,Ando T,Hori K,Matsumoto T,Yano M
Theor. Appl. Genet. 2011  122(6)  1199-210
Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars.
Ogiso E,Takahashi Y,Sasaki T,Yano M,Izawa T
Plant Physiol. 2010  152(2)  808-20
The role of casein kinase II in flowering time regulation has diversified during evolution.
Matsubara,K., Kono,I., Hori,K., Nonoue,Y., Ono,N., Shomura,A., Mizubayashi,T., Yamamoto,S., Yamanouchi,U., Shirasawa,K., Nishio,T. and Yano,M.
Theor. Appl. Genet. 2008  117(6)  935-945
Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars
Uga Y, Nonoue Y, Liang ZW, Lin HX, Yamamoto S, Yamanouchi U, Yano M.
Theor. Appl. Genet. 2007  114  1457-66
Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar 'Nona Bokra'.
Nakagawa, H., J. Yamagishi, N. Miyamoto, M. Motoyama, M. Yano and K. Nemoto
Theor. Appl. Genet. 2005  110 (4)  778-786
Flowering response of rice to photoperiod and temperature: a QTL analysis using a phenological model.
Takahashi,Y., Shomura,A., Sasaki,T. and Yano,M.
Proc. Natl. Acad. Sci. U.S.A. 2001  98(14)  7922-7927
Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2.
Yano, M., Kojima, S., Takahashi, Y, Lin, H. and Sasaki, T.
Plant Physiol. 2001  127  1425-1429
Genetic control of flowering time in rice, a short-day plant.
Yamamoto, T., H. Lin, T. Sasaki and M. Yano
Genetics 2000  154  885-891
Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny.
Sharma, R.N., B.S. Gill, T. Sasaki, G. Galiba, J. Sutka, D.A. Laurie and J.W. Snape
Theor. Appl. Genet. 1998  97  103-109
Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time.
Yamamoto, T., M. Yano, S.Y. Lin and T. Sasaki
Breeding Science 1996  46(Suppl. 2)  59
Hd-6, a newly detected quantitative trait locus conferring heading date in rice as revealed by analysis of backcross progenies.
TextPresso Search Search textpresso for HD6 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID GR:0060444
Gene Ontology transcription factor activity( GO:0003700 )
protein tyrosine kinase activity( GO:0004713 )
protein amino acid phosphorylation( GO:0006468 )
inflorescence development( GO:0010229 )
protein kinase activity( GO:0004672 )
protein serine/threonine kinase activity( GO:0004674 )
ATP binding( GO:0005524 )
photoperiodism( GO:0009648 )
negative regulation of long-day photoperiodism, flowering( GO:0048579 )
Trait Ontology days to heading( TO:0000137 )
days to maturity( TO:0000469 )
photoperiod sensitivity( TO:0000229 )
flowering time( TO:0002616 )
Plant Ontology inflorescence meristem( PO:0000230 )
spikelet floret( PO:0009082 )
seed( PO:0009010 )
portion of meristem tissue( PO:0009013 )
inflorescence( PO:0009049 )
Related Strains
Phenotype images
Last updated
Sep 16, 2020