Os06g0275000

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Annotated Information

Hd-1 is Se-1. Hd-1 is regulated by photoperiod. Hd-1 affects the heading period of rice. The allele of Hd-1 from Kasalath is nonsensitive to photoperiod, but promotes heading.

Function

The quantity of Hd1 mRNA is not affected by the time of light. Maybe, there is dual function in Hd-1: Hd-1 keeps heading period in advance in the condition of short photoperiod. Hd-1 delays heading period in the condition of long photoperiod.（Yano et al. 2000） Hd1 may be one of selective genes when human being was taming wild rice. Genes relating to flowering period affect the traits of plant type. Hd1 and Ehd can discrease the number of spikelet, without affecting flowering period. Hd3a and RFT1, genes of flowering hormone, have up-regulated expression in leaives when the strain of Hd1 and Ehd1 is in the conversion period of bloom. Further results show that Hd1 and\or Ehd1 lead to the up regulation of genes similar to Terminal Flower 1 in apical meristem when spikelet is developing and keep the expression of genes related to forming spikelet in advance. In conclusion, Hd1 and Ehd1 regulate the devolopment of spikelet by affecting genes of flowering hormone and then affect the produce of rice.（Endo-Higashi et al. 2011）

Expression

There are 1557bp in Hd1 cDNA, containing two exons. The production of the gene includes 395 amino acids. The Zinc finger domain in the protein belongs to CO family. The allele of Hd1 in Nipponbare and Kasalath are different in structure. There is a 2bp missing in the 2ed exon in the allele of Hd1 in Nipponbare, resulting to an early terminator. The lenth of Hd1 protein in Kasalath is shorter than Nipponbare's, because of the missing of C terminal. The quantity of Hd1 mRNA is not affected by the time of light. Maybe, there is dual function in Hd-1: Hd-1 keeps heading period in advance in the condition of short photoperiod. Hd-1 delays heading period in the condition of long photoperiod.（Yano et al. 2000) Chuanqing Sun，Daoxi Xie, and Zongxiu Sun studed how the interaction of photoperiod and temperture affects the heading period of rice. They reported one early heading mutant gaining from tissue culture. They inspected the heading period of flower11 and the mutant under different photoperiod and temperature. linkage analysis showed that the relationship between the mutation and Hd1 is coseparation. Sequence analysis showed the mutation includes 2 insertion and some single-base substitution, resulting to a sharp decrease of the mRNA expression of the mutation. At the same time, they analyzed the expression mode of Hd1 and Hd3a, under different photoperiod and temperature. The analysis indicated the expression mode of Hd1 mRNA is same under different photoperiod and temperature. The mode is high expression in dark and low in light. Otherwise, it is a slightly high expression of Hd1 in long-day condition and low temperature. The expression of Hd3a is always very low in low temperature, no matter in long-day or short-day condition. All of these results indicate that the inhibition of Hd3a results to late leading in long-day condition and low temperature.（Luan et al. 2009）

Evolution

There are 2 main QTLs, namely Hd-1 and Hd-2. There are 3 minor QTLs, namely Hd-3, Hd-4, and Hd-5. All of these 5 QTLs account for 84% of the phenotype mutation. Hd-1 accounts for 67%, locusing in the middle of the 6th chromosome, linkaging with R1679.（Yano et al., 1997) The relationship between Hd-1 and C235 is coseparation.（Yamamoto et al. 1997) The sequencing map of Hd-1 in Nipponbare locus in 9335536 - 9337360 (Rice Genome Annotation Project) In long-day condition, Hd-1 has epistasis over Hd-2; In short-day condition, the epistasis misses. The alleles of Hd-1 and Hd-2 in Nipponbare have epistasis over the allele of Hd-3 in Kasalath. The phenomenon implies the allele of Hd-3 in Kasalath is nonsensitive to photoperiod, but sensitive to the photoperiod reaction of the alleles of Hd-1 and Hd-2 in Nipponbare.（Lin et al. 2000） You can also add sub-section(s) at will. NCBI GeneBank：AB041837, AB041838, AB041839, AB041840, AB041841, AB041842, AP003044 RAP-DB：Os06g0275000

Labs working on this gene

China Agricultural University. Tsinghua University. China National Rice Research Institute.

References

1. Chao-Li Huang;Cheng-Yu Hung;Yu-Chung Chiang;Chi-Chuan Hwang;Tsai-Wen Hsu;Chi-Chun Huang;Kuo-Hsiang Hung;Kun-Chan Tsai;Kuo-Hsiung Wang;Naoki Osada;Barbara Anna Schaal;Tzen-Yuh Chiang

 Footprints of natural and artificial selection for photoperiod pathway genes in Oryza
 The Plant Journal, 2012, 70(5): 769-782

2. Zhen-Hua Zhang;Kai Wang;Liang Guo;Yu-Jun Zhu;Ye-Yang Fan;Shi-Hua Cheng;Jie-Yun Zhuang

 Pleiotropism of the Photoperiod-Insensitive Allele of Hd1 on Heading Date, Plant Height and Yield Traits in Rice
 PLoS ONE, 2012, 7(12): e52538

3. Yasuyuki Takahashi;Ko Shimamoto

 Heading date 1 (Hd1), an ortholog of Arabidopsis CONSTANS, is a possible target of human selection during domestication to diversify flowering times of cultivated rice
 Genes & Genetic Systems, 2011, 86(3): 175-182

4. Naokuni Endo-Higashi;Takeshi Izawa

 Flowering Time Genes Heading date 1 and Early heading date 1 Together Control Panicle Development in Rice
 Plant and Cell Physiology, 2011, 52(6): 1083-1094

5. Ryo Ishikawa;Mayumi Aoki;Ken-ichi Kurotani;Shuji Yokoi;Tomoko Shinomura;Makoto Takano;Ko Shimamoto

 Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice
 Molecular Genetics and Genomics, 2011, 285(6): 461-470

6. Weijiang Luan;Huizhe Chen;Yaping Fu;Huamin Si;Wen Peng;Susheng Song;Wenzhen Liu;Guocheng Hu;Zongxiu Sun;Daoxin Xie;Chuanqing Sun

 The Effect of the Crosstalk between Photoperiod and Temperature on the Heading-Date in Rice
 PLoS ONE, 2009, 4(6): e5891

7. Yasuyuki Takahashi;Kosuke M. Teshima;Shuji Yokoi;Hideki Innan;Ko Shimamoto

 Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice
 Proceedings of the National Academy of Sciences, 2009, 106(11): 4555-4560

8. Masahiro Yano;Yuichi Katayose;Motoyuki Ashikari;Utako Yamanouchi;Lisa Monna;Takuichi Fuse;Tomoya Baba;Kimiko Yamamoto;Yosuke Umehara;Yoshiaki Nagamura;and Takuji Sasaki

 Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS
 The Plant Cell, 2000, 12(12): 2473-2484

9. H. X. Lin;T. Yamamoto;T. Sasaki3 and M. Yano

 Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines
 Theoretical and Applied Genetics, 2000, 101(7): 1021-1028

10. T. Yamamoto;Y. Kuboki;S. Y. Lin;T. Sasaki and M. Yano

 Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors
 Theoretical and Applied Genetics, 1998, 97(1-2): 37-44

11. M. Yano;Y. Harushima;Y. Nagamura;N. Kurata;Y. Minobe and T. Sasaki

 Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map
 Theoretical and Applied Genetics, 1997, 95(7): 1025-1032