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

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References

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Structured Information

Gene Name	Os06g0275000
Description	Hd1
Version	NM_001063913.1 GI:115467557 GeneID:4340746
Length	2194 bp
Definition	Oryza sativa Japonica Group Os06g0275000, complete gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Chromosome 6
Location	Chromosome 6:9335377..9337570
Sequence Coding Region	9335536..9336363,9337001..9337360
Expression	GEO Profiles:Os06g0275000
Genome Context	<gbrowseImage1> name=NC_008399:9335377..9337570 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008399:9335377..9337570 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atgaattataattttggtggcaacgtgttcgaccaggaggttggagttggaggcgaaggaggaggaggaggagaggggagcggctgcccatgggcgcggccgtgcgacgggtgccgcgcggcgccgagcgtggtgtactgccgcgcggacgcggcgtacctgtgcgcgtcgtgcgacgcgcgggtgcacgcggccaaccgcgtggcgtcccgccacgagcgcgtgcgggtgtgcgaggcctgcgagcgcgccccggccgcgctcgcgtgccgcgccgacgccgccgcgctgtgcgtggcgtgcgacgtgcaggtgcactccgcgaacccgctcccggccatcaccatcccggccacctccgtcctcgctgaggcggtggtggccaccgccaccgtcctcggcgacaaggacgaggaggtggactcttggcttctcctctccaaagattccgacaacaacaacaacaataacaacaacaacgacaacgacaataacgacaacaacaacagcaacagcagcaacaacggcatgtattttggtgaagtcgatgagtactttgatcttgtcgggtacaattcgtactacgacaaccgcatcgaaaacaaccaagatcggcagtatgggatgcatgaacagcaagagcagcagcagcagcagcaggagatgcaaaaggagtttgcagagaaggaagggagcgagtgtgtggtaccttcacagatcacaatgctgagtgagcagcagcatagtggttatggagttgtgggagcagaccaggccgcctccatgaccgccggcgtcagtgcttacacagattccatcagcaacagcatatctttctcatcaatggaggcgggtatagtaccagacagcacggtgatagatatgccaaattccagaatcctgacacctgctggagcaatcaatctcttctcaggtccctcgcttcagatgtcccttcacttcagctccatggacagggaggccagggtgctcaggtacagggagaagaagaaggccaggaagtttgagaagacaatacgttatgaaacaagaaaggcgtatgcagaggcacgaccccggatcaagggccgtttcgccaagagatcagatgtgcagatcgaagtggaccagatgttctccactgcagctctatctgacggtagctatggtactgttccatggttctga</cdnaseq>
Protein Sequence	<aaseq>MNYNFGGNVFDQEVGVGGEGGGGGEGSGCPWARPCDGCRAAPSV VYCRADAAYLCASCDARVHAANRVASRHERVRVCEACERAPAALACRADAAALCVACD VQVHSANPLPAITIPATSVLAEAVVATATVLGDKDEEVDSWLLLSKDSDNNNNNNNNN DNDNNDNNNSNSSNNGMYFGEVDEYFDLVGYNSYYDNRIENNQDRQYGMHEQQEQQQQ QQEMQKEFAEKEGSECVVPSQITMLSEQQHSGYGVVGADQAASMTAGVSAYTDSISNS ISFSSMEAGIVPDSTVIDMPNSRILTPAGAINLFSGPSLQMSLHFSSMDREARVLRYR EKKKARKFEKTIRYETRKAYAEARPRIKGRFAKRSDVQIEVDQMFSTAALSDGSYGTV PWF</aaseq>
Gene Sequence	<dnaseqindica>160..987#1625..1984#caaaattccacaagagccatgcgaggtagaggaacaggagaagacgcatacacacacgacacatagagagagaggacaaacacaatagcttggatcgatagacttgtccatgtggtgcaagctaaagctactactaccacaagcaaggctacttcgttcatgaattataattttggtggcaacgtgttcgaccaggaggttggagttggaggcgaaggaggaggaggaggagaggggagcggctgcccatgggcgcggccgtgcgacgggtgccgcgcggcgccgagcgtggtgtactgccgcgcggacgcggcgtacctgtgcgcgtcgtgcgacgcgcgggtgcacgcggccaaccgcgtggcgtcccgccacgagcgcgtgcgggtgtgcgaggcctgcgagcgcgccccggccgcgctcgcgtgccgcgccgacgccgccgcgctgtgcgtggcgtgcgacgtgcaggtgcactccgcgaacccgctcccggccatcaccatcccggccacctccgtcctcgctgaggcggtggtggccaccgccaccgtcctcggcgacaaggacgaggaggtggactcttggcttctcctctccaaagattccgacaacaacaacaacaataacaacaacaacgacaacgacaataacgacaacaacaacagcaacagcagcaacaacggcatgtattttggtgaagtcgatgagtactttgatcttgtcgggtacaattcgtactacgacaaccgcatcgaaaacaaccaagatcggcagtatgggatgcatgaacagcaagagcagcagcagcagcagcaggagatgcaaaaggagtttgcagagaaggaagggagcgagtgtgtggtaccttcacagatcacaatgctgagtgagcagcagcatagtggttatggagttgtgggagcagaccaggccgcctccatgaccgccggcgtcagtgcttacacagattccatcagcaacagcgtgagttcatctattactagctgcaactatttttttttcagagaatgaacatctattactgttgttagttagttgttactacatgccacgttgtcaatgttttagagttcatactagtacttttgagtggaaaaacattctccaaacaaaagctactgtctaacaaaatgaagggataaataaacagatctcaacaagaaaacaaagatacttttctacttccaagctgcgatctttaggctgattaaatggaaccgataaaaaaaatactttaaagaaaagtacacaattgatctttaggcagaccagttgactacttcctgtatttctaagcatatacgatccatgctaactcactaattgaaaagaagtgagtttgttaaccttttatgtacacagcaatcaccacacgaaagacctcatgaaaagtaggataagtgtaagtgtaattcatattttatcccagtgcataaatttaaaatatcttacttttgcgacagtaaaaaagatattggaagtttttcttatgtatgtaaaattaaattaagcccatctatatatcattgcagggtctctgacacctgcaatctccttatgattcgcatatttcagtgaccatttgccgattccatctcagatatctttctcatcaatggaggcgggtatagtaccagacagcacggtgatagatatgccaaattccagaatcctgacacctgctggagcaatcaatctcttctcaggtccctcgcttcagatgtcccttcacttcagctccatggacagggaggccagggtgctcaggtacagggagaagaagaaggccaggaagtttgagaagacaatacgttatgaaacaagaaaggcgtatgcagaggcacgaccccggatcaagggccgtttcgccaagagatcagatgtgcagatcgaagtggaccagatgttctccactgcagctctatctgacggtagctatggtactgttccatggttctgatgggactcatgagacgctatcttataggcatatatatggggacttactgagtagcaataacatcgatccagtgggagtagttctagacaatctgtgttatgaataatagtgtgttgtttgcgacttaaaattgatcaagtaccttagctttttaaagttttgctttgtaatttccggatagcagatatatattgttggtacttgctcagt</dnaseqindica>
External Link(s)	NCBI Gene:Os06g0275000, RefSeq:Os06g0275000