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Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica Nipponbare and the india variety Kasalath.

Annotated Information


Figure a.jpg

Hd6 encodes the α subunit of protein kinase CK2. Hd6 was involved in photoperiod sensitivity, and the Kasalath allele increases days-to-heading under natural and long-day conditions but not under short-day conditions (Takahashi et al., 2001).

Casein kinase II (CK2) is a protein kinase with an evolutionarily conserved function as a circadian clock component in several organisms, including the long-day plant Arabidopsis (Arabidopsis thaliana). The circadian clock component CIRCADIAN CLOCK ASSOCIATED1(CCA1) is a CK2 target in Arabidopsis, where it influences photoperiodic flowering. In rice (Oryza sativa), a short-day plant, Heading date6(Hd6) encodes CK2α subunit that delays flowering time under long-day conditions. Control of flowering time in rice by the Hd6 CK2α subunit requires a functional Hd1 gene (an Arabidopsis CONSTANS ortholog) and is independent of the circadian clock mechanism. Findings from overexpressing the dominant negative CK2 allele in rice support the independence of CK2 function from the circadian clock. This lack of control of the circadian clock by Hd6 CK2 might be due to the presence of glutamate in OsLHY (a CCA1 ortholog in rice) instead of the serine at the corresponding CK2 target site in CCA1. However, this glutamate is critical for the control of the OsPRR1 gene (a rice ortholog of the Arabidopsis TOC1/PRR1 gene) by OsLHY for regulation of the circadian clock. The other conserved CK2 target sites in OsLHY conferred robust rhythmic expression of OsLHY-LUC under diurnal conditions. These findings imply that the role of CK2 in flowering-time regulation in higher plants has diversified during evolution(Ogiso et al., 2010).

"Casein Kinase II (Jacob P. Turowec,2012)"
Figure c.jpg
  • Hd6 Delays Flowering by Repressing FT-Like Genes under LD Conditions

Researchers analyzed the expression patterns of flowering-time genes in Nipponbare, a nearly isogenic line of Hd6 , and in lines overexpressing Hd6 under LD conditions. Consistent with the delayed flowering phenotype, the overexpression of Hd6 repressed expression of Hd3a and RFT1 (another FT ortholog; Komiya et al., 2008) but had no effect on the expression profile of Hd1. To further confirm this genetic interaction, they analyzed the expression of Hd1, Hd3a, and RFT1 in an Hd1 nonfunctional background [NIL(Hd1) and NIL(Hd1,6)]. Hd3a and RFT1 were not dramatically repressed by Hd6 in the Hd1 nonfunctional background under LD conditions, although there seemed to be some Hd3a repression by Hd6 in the hd1 background. These results suggested that Hd6 modulates Hd1 repressor activity mainly by posttranslational modification(Ogiso et al., 2010).


  • Characterization of Hd6.

The left figure shows the location of Hd6 in chromosome 3. The table shows days to heading in NIL(Hd6) and Nipponbare under different day lengths. There was a significant difference in photoperiod sensitivity between NIL(Hd6) and Nipponbare at 13.5-hr day length, suggesting that Hd6 was the locus controlling photoperiod sensitivity and that the Kasalath allele enhanced photoperiod sensitivity(Yamamoto T et al., 2000)

Figure g.jpgTable a.jpg

Figure d.jpg
  • Hd6 Requires Functional Hd1 for Flowering Repression under LD Conditions

To elucidate the molecular function of Hd6, researcher examined flowering time in rice with functional, nonfunctional, or overexpressed Hd6 alleles (including nearly isogenic lines and transgenic lines) under LD and SD conditions. Under LD conditions, Hd6 delayed flowering time in a dose-dependent manner. This Hd6-induced delay required the presence of a functional Hd1 allele. A 30-min extension of the LD photoperiod caused a synergistic delay in flowering through the interaction of Hd6 with Hd1; therefore, Hd6 can enhance Hd1 floral repression activity under LD conditions. The time of flowering under SD conditions was also examined in plants with these Hd6-related alleles; the results suggested that Hd6 plays a critical role in Hd1 activity.

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  • Overexpression of a Dominant-Negative Form of Hd6 Causes Early Flowering under LD Conditions

By a genome-wide homology search in the Rice Annotation Project Database, researchers found four genes with very high levels of identity to CK2α subunit genes in the rice genome. Expression analysis revealed that, of the four CK2α genes, functional Hd6(OsCKA2-1) and OsCKA2-2 were the two main ones expressed in various tissues of rice. they used Hd6Tik, theTimekeeper (Tik) mutant form of Hd6, a dominant-negative CK2α allele that was originally identified in Drosophila (Akten et al., 2003; Moreno-Romero et al., 2008), to elucidate the role of CK2 in rice. Overexpression of the dominant-negative form of Hd6 resulted in early flowering equivalent to that observed in plants with Hd1-defective alleles under LD conditions. Some of the Hd6Tik lines failed to thrive in the T1 generation, especially under SD conditions, suggesting that CK2 has pleiotropic functions in rice, as recently found in Arabidopsis by the use of transgenic lines carrying a dominant-negative mutation in a CK2α allele and an antisense construct (Lee et al., 1999; Smith et al., 2008).

  • Hd6 Has Protein Kinase Activity But Does Not Phosphorylate Hd1 in Vitro

To confirm the protein kinase activity of Hd6, researchers measured the CK2 activity of the Hd6 recombinant protein (rHd6; Sugano et al., 1998). Hd6 was expressed as a glutathione S-transferase(GST) fusion protein and isolated it from GST by thrombin treatment of the purified fusion protein bound to glutathione agarose beads. Then the CK2 activity of the isolated rHd6 was measured . Purified rHd6 had nearly the same CK2 activity as a control human CK2α. To investigate Hd1 phosphorylation, GST fusion Hd1 protein was purified as above and its potential as an Hd6 substrate was characterized in vitro. Hd1 was not phosphorylated by rHd6 in vitro. The observation that flowering regulation by Hd6 required Hd1 and that Hd1 was not a direct Hd6 target suggests that Hd6 protein phosphorylates an unknown flowering repressor target that works together with Hd1(Ogiso et al., 2010).


Figure e.jpg

Differences in mean values for days to heading in nine genotype classes of F2 segregants derived from the cross combination between NIL(Hd2) and NIL(Hd6) under field. conditions.Each genotype is represented by the two nearest marker loci (C728 for Hd2 and R2311 for Hd6). N, H, and K indicate homozygosity for the Nipponbare allele, heterozygosity, and homozygosity for the Kasalath allele, respectively.

Knowledge Extension

  • Relationship between Hd6 and previously reported genes (QTL and classical mutants)

Some QTL on rice chromosome 3 controlling heading date have already been reported (LIet al. 1995; H. X. LINet al. 1995; XIAO et al.1995, 1996, 1998; S. Y. LINet al. 1998; XIONGet al. 1999). Most were identified by using RFLP markers developed at Cornell University (CAUSSEet al. 1994). HARUSHIMA et al.(1998) clarified the direction of the chromosome arms in a high-density linkage map from the Japanese Rice Genome Research Program by using RFLP markers that had been used to define the direction in the Cornell linkage map (SINGHet al. 1996). Based on the comparison of these two linkage maps, Hd6 might be at the same locus as both dth3-2and dth3.1 reported by XIAO et al. (1995, 1998). To confirm this possibility, common molecular markers must be used to map both QTL. Including the major photoperiod sensitivity gene reported previously, there are now no more reported genes on the long arm of chromosome 3(Yamamoto et al., 2000).

Labs working on this gene

  • Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba,Japan.
  • Bio-oriented Technology Research Advancement Institution, Omiya, Japan.
  • Department of Molecular Genetics, National Institute of Agrobiological Resources, Tsukuba, Japan.
  • National Institute of Agrobiological Sciences, Tsukuba, Japan


1. Eri Ogiso;Yuji Takahashi;Takuji Sasaki;Masahiro Yano;Takeshi Izawa.,(2010) The Role of Casein Kinase II in Flowering Time Regulation Has Diversified during Evolution. Plant Physiology, 152(2): 808-820.

2. Yuji Takahashi;Ayahiko Shomura;Takuji Sasaki;and Masahiro Yano.,(2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. Proceedings of the National Academy of Sciences, 98(14): 7922-7927.

3. Toshio Yamamoto; Hongxuan Lin; Takuji Sasaki and Masahiro Yano.,(2000) Identification of Heading Date Quantitative Trait Locus Hd6 and Characterization of Its Epistatic Interactions With Hd2 in Rice Using Advanced Backcross Progeny. Genetics, 154(2): 885-891.

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Structured Information