GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00001723
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Oryza sativa - many cultivars
Trait State in Taxon B
Oryza sativa - many cultivars
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
rice
Synonyms
rice; red rice; Oryza sativa L.
Rank
species
Lineage
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ytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B
Latin Name
Common Name
rice
Synonyms
rice; red rice; Oryza sativa L.
Rank
species
Lineage
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ytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
HD1
Synonyms
Hd1; SE1; OsHd1; Os06g0275000; LOC_Os06g16370; P0038C05.23; P0676F10.34
String
Sequence Similarities
Belongs to the CONSTANS family.
GO - Molecular Function
GO:0003700 : DNA-binding transcription factor activity
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GO - Biological Process
GO:0030154 : cell differentiation
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GO - Cellular Component
Presumptive Null
Molecular Type
Aberration Type
Deletion Size
1-9 bp
Molecular Details of the Mutation
1bp deletion at position 321 ; presumptive protein truncated
Experimental Evidence
Authors
Takahashi Y; Teshima KM; Yokoi S; Innan H; Shimamoto K
Abstract
Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of flowering time in cultivated rice are not known. We used a core collection of 64 rice cultivars that represent the genetic diversity of 332 accessions from around the world and studied the expression levels and polymorphisms of 6 genes in the short-day flowering pathway. The RNA levels of Heading date 3a (Hd3a), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of Hd3a expression. Functional and nonfunctional alleles of Hd1 are associated with early and late flowering, respectively, suggesting that Hd1 is a major determinant of variation in flowering time of cultivated rice. We also found that the type of Hd3a promoter and the level of Ehd1 expression contribute to the diversity in flowering time and Hd3a expression level. We evaluated the contributions of these 3 factors by a statistical analysis using a simple linear model, and the results supported our experimental observations.
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