GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00001572
Main curator
Prigent
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Rice japonica variety with large grain
Trait State in Taxon B
Rice japonica variety with small grain
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
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
Rice japonica variety with large grain
Taxon B
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
Rice japonica variety with small grain
GENOTYPIC CHANGE
Generic Gene Name
SPL13
Synonyms
GLW7; SPL13; Os07g0505200; LOC_Os07g32170; P0430F03.47
Sequence Similarities
-
GO - Biological Process
-
GO - Cellular Component
UniProtKB
Oryza sativa subsp. japonica
GenebankID or UniProtKB
Presumptive Null
No
Molecular Type
Aberration Type
Insertion Size
1-9 bp
Molecular Details of the Mutation
a CACTTC tandem repeat sequence in the 5' UTR is causing reduced expression
Experimental Evidence
Authors
Si L; Chen J; Huang X; Gong H; Luo J; Hou Q; Zhou T; Lu T; et al. ... show more
Abstract
Although genetic diversity has a cardinal role in domestication, abundant natural allelic variations across the rice genome that cause agronomically important differences between diverse varieties have not been fully explored. Here we implement an approach integrating genome-wide association testing with functional analysis on grain size in a diverse rice population. We report that a major quantitative trait locus, GLW7, encoding the plant-specific transcription factor OsSPL13, positively regulates cell size in the grain hull, resulting in enhanced rice grain length and yield. We determine that a tandem-repeat sequence in the 5' UTR of OsSPL13 alters its expression by affecting transcription and translation and that high expression of OsSPL13 is associated with large grains in tropical japonica rice. Further analysis indicates that the large-grain allele of GLW7 in tropical japonica rice was introgressed from indica varieties under artificial selection. Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data.
Additional References
RELATED GEPHE
Related Haplotypes
No matches found.
COMMENTS
@Introgression - Non-null mutation. Large-grain haplotype in japonica varieties was probably introgressed from indica varieties
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