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Detail of Gene

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Basic Information
CGSNL Gene Symbol HD5
Gene Symbol Synonym Hd5(t)*, Hd5, qHD5, HAP3H, OsHAP3H, NF-YB, CBF-A, DTH8 , qHD5(t)*, Ghd8, Ghd8/DTH8, Lhd1, NF-YB11, OsNF-YB11, NFYB11, LH8, DTH8/Ghd8, RH8, DTH8/Ghd8/LHD1, CAR8, DTH8/Ghd8/ OsHAP3H, EF8, OsEF8
CGSNL Gene Name Heading date (QTL)-5(t)
Gene Name Synonym Heading date (QTL)-5(t), Heading date 5, HAP3H SUBUNIT OF CCAAT-BOX BINDING COMPLEX, days to heading8, days to heading on chromosome 8, NUCLEAR FACTOR-Y subunit B11, NUCLEAR FACTOR-Y subunit NF-YB11, rice heterosis 8, "GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8", Carbon Assimilation Rate 8, NF-YB subunit 11, NF-YB family 11, early flowering 8
Allele ghd8, dth8, dth8-2, Ghd8NIP, Ghd8ZS97, Ghd8MH63, Ghd8-9311, Ghd8ACC10, Ghd8i, Ghd8j
Chromosome No. 8
Explanation AB693200-AB693204. AB288039. HM775396, HM775397. MT500364 - MT500499. Os08g0174500 which encodes a histone-like CCAAT-box binding transcription factor suggested that the ORF would be tentatively referred to as the first strong candidate gene for qHY-8, a pleiotropic QTL for heading date and yield-related traits. Also this ORF was annotated in RiceGAAS as the candidate gene of Hd5, a gene controlling heading date in rice. Protein Data Bank under PDB:7C9O (DNA-bound HD1CCT/GHD8/OsNF-YC2) and PDB:7C9P (GHD8/OsNF-YC2).
Trait Class Vegetative organ - Culm
Reproductive organ - Heading date
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
cDNA Accession No. CT837794
MSU ID LOC_Os08g07740.1
RAP ID Os08g0174500
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
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.
Xiong Y., Zhang C., Zhou H., Sun W., Wang P., Wang D., Qiu X., Ali J., Yu S.
Rice (N Y) 2021  14(1)  97
Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice.
Fujino K., Ikegaya T.
Breed. Sci. 2020  70(2)  193-199
A novel genotype DATTO5 developed using the five genes exhibits the fastest heading date designed 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.
Shen C., Liu H., Guan Z., Yan J., Zheng T., Yan W., Wu C., Zhang Q., Yin P., Xing Y.
Plant Cell 2020  32(11)  3469-3484
Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering.
Yang X., Wang J., Dai Z., Zhao X., Miao X., Shi Z.
Rice (N Y) 2019  12(1)  40
miR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways.
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.
Cai M., Chen S., Wu M., Zheng T., Zhou L., Li C., Zhang H., Wang J., Xu X., Chai J., Ren Y., Guo X., Zhang X., Lei C., Cheng Z., Wang J., Jiang L., Zhai H., Wang H., Zhu S., Wan J.
Plant Cell Rep. 2019  38(5)  521-532
Early heading 7 interacts with DTH8, and regulates flowering time in rice.
Na-Hyun Shin, Do Thi Trang, Woo-Jong Hong, Kang K., Chuluuntsetseg J., Joon-Kwan Moon, Yo-Han Yoo, Ki-Hong Jung, Soo-Cheul Yoo
Int J Mol Sci 2019  21(1) 
Rice Senescence-Induced Receptor-Like Kinase (<i>OsSRLK</i>) Is Involved in Phytohormone-Mediated Chlorophyll Degradation.
Kim S.R., Torollo G., Yoon M.R., Kwak J., Lee C.K., Prahalada G.D., Choi I.R., Yeo U.S., Jeong O.Y., Jena K.K., Lee J.S.
Front Plant Sci 2018  9  1827
Loss-of-Function Alleles of <i>Heading date 1</i> (<i>Hd1</i>) Are Associated With Adaptation of Temperate <i>Japonica</i> Rice Plants to the Tropical Region.
Jiang D., Chen W., Dong J., Li J., Yang F., Wu Z., Zhou H., Wang W., Zhuang C.
J. Exp. Bot. 2018  69(7)  1533-1543
Overexpression of miR164b-resistant OsNAC2 improves plant architecture and grain yield in rice.
Hong Y., Zhang Y., Sinumporn S., Yu N., Zhan X., Shen X., Chen D., Yu P., Wu W., Liu Q., Cao Z., Zhao C., Cheng S., Cao L.
Plant J. 2018   
Premature leaf senescence 3, encoding a methyltransferase, is required for melatonin biosynthesis in rice.
Wang A., Shu X., Niu X., Zhao W., Ai P., Li P., Zheng A.
PLoS ONE 2018  13(10)  e0202309
Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection.
Gong R., Cao H., Zhang J., Xie K., Wang D., Yu S.
Plant J. 2018  94(1)  32-47
Divergent functions of the GAGA-binding transcription factor family in rice.
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.
Yanga W., Lub Z., Xionga Y., Yaoa J.
The Crop Journal 2017  5(1)  21-31
Genome-wide identification and co-expression network analysis of the OsNF-Y gene family in rice
Goretti D., Martignago D., Landini M., Brambilla V., Gómez-Ariza J., Gnesutta N., Galbiati F., Collani S., Takagi H., Terauchi R., Mantovani R., Fornara F.
PLoS Genet. 2017  13(1)  e1006530
Transcriptional and Post-transcriptional Mechanisms Limit HEADING DATE 1 (Hd1) Function to Adapt Rice to High Latitudes.
Zhu S., Wang J., Cai M., Zhang H., Wu F., Xu Y., Li C., Cheng Z., Zhang X., Guo X., Sheng P., Wu M., Wang J., Lei C., Wang J., Zhao Z., Wu C., Wang H., Wan J.
J. Exp. Bot. 2017  68(3)  553-568
The OsHAPL1-DTH8-Hd1 complex functions as the transcription regulator to repress heading date in rice.
Adachi S., Yoshikawa K., Yamanouchi U., Tanabata T., Sun J., Ookawa T., Yamamoto T., Sage R.F., Hirasawa T., Yonemaru J.
Front Plant Sci 2017  8  60
Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag leaf nitrogen content, stomatal conductance and Photosynthesis in Rice.
Du A., Tian W., Wei M., Yan W., He H., Zhou D., Huang X., Li S., Ouyang X.
Mol Plant 2017  10(7)  948-961
The DTH8-Hd1 module Mediates Day-Length-Dependent Regulation of Rice Flowering.
Li Q., Yan W., Chen H., Tan C., Han Z., Yao W., Li G., Yuan M., Xing Y.
J. Exp. Bot. 2016  67(6)  1759-68
Duplication of OsHAP family genes and their association with heading date in rice.
Huang X., Yang S., Gong J., Zhao Q., Feng Q., Zhan Q., Zhao Y., Li W., Cheng B., Xia J., Chen N., Huang T., Zhang L., Fan D., Chen J., Zhou C., Lu Y., Weng Q., Han B.
Nature 2016  537(7622)  629-633
Genomic architecture of heterosis for yield traits in rice.
Du Y., He W., Deng C., Chen X., Gou L., Zhu F., Guo W., Zhang J., Wang T.
PLoS ONE 2016  11(3)  e0150458
Flowering-Related RING Protein 1 (FRRP1) Regulates flowering time and Yield Potential by Affecting histone H2B Monoubiquitination in Rice (Oryza Sativa).
Hwang Y.H., Kim S.K., Lee K.C., Chung Y.S., Lee J.H., Kim J.K.
Plant Cell Rep. 2016  35(4)  857-65
Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time.
Li D., Huang Z., Song S., Xin Y., Mao D., Lv Q., Zhou M., Tian D., Tang M., Wu Q., Liu X., Chen T., Song X., Fu X., Zhao B., Liang C., Li A., Liu G., Li S., Hu S., Cao X., Yu J., Yuan L., Chen C., Zhu L.
Proc. Natl. Acad. Sci. U.S.A. 2016  113(41)  E6026-E6035
Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.
Kim S.K., Park H.Y., Jang Y.H., Lee K.C., Chung Y.S., Lee J.H., Kim J.K.
Planta 2015   
OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice.
Chen J., Li X., Cheng C., Wang Y., Qin M., Zhu H., Zeng R., Fu X., Liu Z., Zhang G.
Sci Rep 2014  4  4263
Characterization of epistatic interaction of QTLs LH8 and EH3 controlling heading date in rice.
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.
Ikeda M., Miura K., Aya K., Kitano H., Matsuoka M.
Curr. Opin. Plant Biol. 2013  16(2)  213-20
Genes offering the potential for designing yield-related traits in rice.
Fujino K., Yamanouchi U., Yano M.
Theor. Appl. Genet. 2013  126(3)  611-8
Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation.
Gao Z.Y., Zhao S.C., He W.M., Guo L.B., Peng Y.L., Wang J.J., Guo X.S., Zhang X.M., Rao Y.C., Zhang C., Dong G.J., Zheng F.Y., Lu C.X., Hu J., Zhou Q., Liu H.J., Wu H.Y., Xu J., Ni P.X., Zeng D.L., Liu D.H., Tian P., Gong L.H., Ye C., Zhang G.H., Wang J., Tian F.K., Xue D.W., Liao Y., Zhu L., Chen M.S., Li J.Y., Cheng S.H., Zhang G.Y., Wang J., Qian Q.
Proc. Natl. Acad. Sci. U.S.A. 2013  110(35)  14492-7
Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.
Hori K., Ogiso-Tanaka E., Matsubara K., Yamanouchi U., Ebana K., Yano M.
Plant J. 2013  76(1)  36-46
Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response.
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.
Dai X., Ding Y., Tan L., Fu Y., Liu F., Zhu Z., Sun X., Sun X., Gu P., Cai H., Sun C.
J Integr Plant Biol 2012  54(10)  790-9
LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).
Petroni K., Roderick W Kumimoto, Gnesutta N., Calvenzani V., Fornari M., Tonelli C., Ben F Holt, Mantovani R.
Plant Cell 2012  24(12)  4777-92
The promiscuous life of plant NUCLEAR FACTOR Y transcription factors.
Cai H.Y., Diao S., He Y.G., Zhang L.P., Liu S.J., Zhu Y.G., Zhang Z.H.
Euphytica 2012  184  109-118
Genetic and physical mapping of qHY-8, a pleiotropic QTL for heading date and yield-related traits in rice
Shibaya T., Nonoue Y., Ono N., Yamanouchi U., Hori K., Yano M.
Theor. Appl. Genet. 2011  123(7)  1133-43
Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions.
Miura K., Ashikari M., Matsuoka M.
Trends Plant Sci. 2011  16(6)  319-26
The role of QTLs in the breeding of high-yielding 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.
Yan W.H., Wang P., Chen H.X., Zhou H.J., Li Q.P., Wang C.R., Ding Z.H., Zhang Y.S., Yu S.B., Xing Y.Z., Zhang Q.F.
Molecular plant 2011  4  319-330
A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice
Wei X., Xu J., Guo H., Jiang L., Chen S., Yu C., Zhou Z., Hu P., Zhai H., Wan J.
Plant Physiol. 2010  153(4)  1747-1758
DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously.
Thirumurugan,T., Ito,Y., Kubo,T., Serizawa,A. and Kurata,N.
Mol. Genet. Genomics 2008  279(3)  279-289
Identification, characterization and interaction of HAP family genes in rice
Nonoue,Y., Fujino,K., Hirayama,Y., Yamanouchi,U., Lin,S.Y. and Yano,M.
Theor. Appl. Genet. 2008  116(5)  715-722
Detection of quantitative trait loci controlling extremely early heading in rice
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'.
Lin, H., Z.W. Liang, T. Sasaki and M. Yano
Breeding Science 2003  53  51-59
Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice.
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.
Yano, M., Y. Harushima, Y. Nagamura, N. Kurata, Y. Minobe and T. Sasaki
Theor. Appl. Genet. 1997  95  1025-1032.
Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map.
TextPresso Search Search textpresso for HD5 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID -
Gene Ontology photosynthesis( GO:0015979 )
regulation of stomatal movement( GO:0010119 )
nucleus( GO:0005634 )
cytoplasm( GO:0005737 )
transcription( GO:0006350 )
regulation of transcription, DNA-dependent( GO:0006355 )
photoperiodism( GO:0009648 )
sequence-specific DNA binding( GO:0043565 )
photoperiodism, flowering( GO:0048573 )
negative regulation of short-day photoperiodism, flowering( GO:0048577 )
negative regulation of long-day photoperiodism, flowering( GO:0048579 )
regulation of photoperiodism, flowering( GO:2000028 )
defense response to fungus( GO:0050832 )
Trait Ontology leaf nitrogen content( TO:0000543 )
stomatal conductance( TO:0000522 )
days to heading( TO:0000137 )
plant height( TO:0000207 )
grain number( TO:0002759 )
inflorescence branching( TO:0000050 )
flowering time( TO:0002616 )
grain yield( TO:0000396 )
fungal disease resistance( TO:0000439 )
panicle number( TO:0000152 )
filled grain number( TO:0000447 )
1000-dehulled grain weight( TO:0000592 )
Plant Ontology -
Related Strains
Phenotype images
Last updated
Aug 22, 2022