GEPHE SUMMARY
Print
Gephebase Gene
Entry Status
Published
GepheID
GP00001637
Main curator
Prigent
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Japonica rice Nipponbare
Trait State in Taxon B
Japonica rice Koshihikari
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
rice
Synonyms
rice; red rice; Oryza sativa L.
Rank
species
Lineage
Show more ...
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?
Yes
Taxon A Description
Japonica rice Nipponbare
Taxon B
Latin Name
Common Name
Japanese rice
Synonyms
Oryza sativa (japonica cultivar-group); Oryza sativa subsp. japonica; Japanese rice; Japonica rice; Oryza sativa (japonica culticar-group); Oryza sativa japonica; Oryza sativa ssp. japonica
Rank
no rank
Lineage
Show more ...
hyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
Japonica rice Koshihikari
GENOTYPIC CHANGE
Generic Gene Name
HD16
Synonyms
CKI; EL1; Hd16; OsJ_12923; Os03g0793500; LOC_Os03g57940; OSJNBb0060J21.12
String
Sequence Similarities
Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily.
GO - Molecular Function
GO:0005524 : ATP binding
... show more
GO - Biological Process
GO:0009908 : flower development
... show more
GO - Cellular Component
GO:0005737 : cytoplasm
... show more
UniProtKB
Oryza sativa subsp. japonica
Oryza sativa subsp. japonica
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
G991A p.Ala331Thr in the serine/threonine kinase domain leading to non-functional protein
Experimental Evidence
Taxon A | Taxon B | Position | |
---|---|---|---|
Codon | - | - | - |
Amino-acid | - | - | - |
Main Reference
Authors
Kwon CT; Yoo SC; Koo BH; Cho SH; Park JW; Zhang Z; Li J; Li Z; et al.
... show more
Abstract
Natural variation in heading-date genes enables rice, a short-day (SD) plant, to flower early under long-day (LD) conditions at high latitudes. Through analysis of heading-date quantitative trait loci (QTL) with F7 recombinant inbred lines from the cross of early heading 'H143' and late heading 'Milyang23 (M23)', we found a minor-effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/CKI in H143 and Koshihikari are non-functional. In F7:9 heterogeneous inbred family-near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD-dependent flowering repressor, down-regulating Ehd1 expression. In the world rice collection, two types of non-functional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions.
© 2013 John Wiley & Sons Ltd.
© 2013 John Wiley & Sons Ltd.
Additional References
RELATED GEPHE
EXTERNAL LINKS
COMMENTS
@GxE Non-functional variants are associated with cultivars of high latitudes
YOUR FEEDBACK is welcome!