HD16 (HEADING DATE16) : Os03g0793500


Locus ID: Os03g0793500
Transcript ID: Os03t0793500-01 (chr03:32999502-33006898)
Description: Casein kinase I, Photoperiodic control of flowering time, Long-day repression
RAP-DB Gene symbol: HD16, Hd16, EL1, CK1
RAP-DB Gene name: HEADING DATE 16, EARLY FLOWERING 1, Early flowering1, Casein Kinase I
Gene Ontolgy: protein kinase activity (GO:0004672)
protein serine/threonine kinase activity (GO:0004674)
ATP binding (GO:0005524)
protein phosphorylation (GO:0006468)
Links: TASUKE (for RAP-DB), GBrowse


CGSNL Gene symbol: HD16
Oryzabase Gene symbol: Hd16, EL1, CK1, Hd16/CKI, Hd16/EL1
Oryzabase Gene name: EARLY FLOWERING 1, Early flowering1, Casein Kinase I
Gene Ontolgy: protein kinase activity (GO:0004672)
protein serine/threonine kinase activity (GO:0004674)
ATP binding (GO:0005524)
protein phosphorylation (GO:0006468)
photoperiodism (GO:0009648)
photoperiodism, flowering (GO:0048573)
regulation of photoperiodism, flowering (GO:2000028)
Trait Ontolgy: days to heading (TO:0000137)
flowering time (TO:0002616)
Plant Ontolgy: -
Links: Oryzabase

Gene information from literatures

Gene function

  • Hd16 encodes a casein kinase-I protein. One non-synonymous substitution in Hd16 results in decreased photoperiod sensitivity in rice. Hd16 is involved in a genetic control pathway for photoperiodic flowering under LD conditions that includes Hd1, Ghd7, DTH8 and Hd2. Hd16 plays a role in the phosphorylation of Ghd7, thereby enhancing the function of Ghd7, downregulating the transcription of Ehd1 and other downstream genes, such as Hd3a and RFT1, and obviously delaying flowering. Hd16 is not likely to be associated with circadian clock regulation (PMID:23789941).

Functional variations

Representative variations
#Var Cultivar 1 Cultivar 2 Positions (protein or transcript) Description References
V1 NPB Koshihikari g.33002789G>A
Photoperiod sensitivity of Nipponbare was greater than that of Koshihikari PMID:23789941
  • The japonica rice cultivars Nipponbare and Koshihikari differ in their flowering time and in the response of their flowering to the photoperiod. The number of days to flowering of Nipponbare increase more than that of Koshihikari under LD conditions. The photoperiod sensitivity of Nipponbare is greater than that of Koshihikari. The cultivar Koshihikari contains a non-synonymous substitution of Ala331Thr (V1), which confers strongly reduced kinase activity of HD16, and results in decreased photoperiod sensitivity compared to the cultivar Nipponbare. Based on the pedigree of Koshihikari, it is likely that the non-synonymous substitution originated from an old japonica cultivar: Moritawase. (PMID:23789941).

Gene expression

  • Expression pattern analysis by quantitative real-time RT–PCR (qRT–PCR) showed that EL1 (HD16) was transcribed in various tissues, including root, stem, leaf, seedling, and ripened seeds. Although EL1 was expressed at relatively low levels in flowers, it was specifically transcribed at stage 2 during floral development (PMID:20400938).
  • The mRNA level of Hd16 itself showed no clear difference between Nipponbare and N-NIL(Hd16), and little or no diurnal change under either SD or LD conditions (PMID:23789941).
  • Hd16 negatively regulated the transcription of Ehd1, Hd3a and RFT1 under LD conditions. No clear difference was observed in mRNA levels between Nipponbare and N-NIL(Hd16) for OsLHY, OsGI, OsPRR1, DTH8, Ghd7 and Hd1 under SD and LD conditions. In contrast, the mRNA level of Ehd1 was significantly higher in N-NIL(Hd16) than in Nipponbare under LD conditions. Likewise, the mRNA levels of Hd3a and RFT1 were also significantly higher in N-NIL(Hd16) under LD conditions, whereas the reverse was true under SD conditions (PMID:23789941).


  • Dai C et al. 2010 Rice early flowering1, a CKI, phosphorylates DELLA protein SLR1 to negatively regulate gibberellin signalling. EMBO J. PMID:20400938
  • Hori K et al. 2013 Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant J. PMID:23789941