GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00002070
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Oryza sativa
Trait State in Taxon B
Oryza sativa - glutinous - Oragamochi and Hidekomochi cultivars
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?
No
Taxon B
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 B an Infraspecies?
Yes
Taxon B Description
Oragamochi and Hidekomochi cultivars
GENOTYPIC CHANGE
Generic Gene Name
waxy
Synonyms
GBSSI
String
-
Sequence Similarities
Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.
UniProtKB
Setaria italica
GenebankID or UniProtKB
Presumptive Null
Yes
Molecular Type
Aberration Type
Insertion Size
1-10 kb
Molecular Details of the Mutation
insertion of 7764 bp in the ninth exon of the wx gene. Transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and the deduced amino acid sequence of the transcript lacks a motif important for GBSS. The 7,764-bp insertion is a retrotransposon-like sequence with long terminal repeats; a primer binding site and a polypurine tract
Experimental Evidence
Authors
Hori Y; Fujimoto R; Sato Y; Nishio T
Abstract
DNA polymorphism of the Wx gene in glutinous rice cultivars was investigated by PCR-RF-SSCP and heteroduplex cleavage analysis using Brassica petiole extract, and the nucleotide sequence variations were identified. Most japonica-type glutinous rice was found to have a 23-bp duplication in the second exon, which causes loss of the function of granule-bound starch synthase (GBSS) encoded by the Wx gene. Without the 23-bp duplication, there was an insertion of 7,764 bp in the ninth exon of the wx allele of 'Oragamochi'. Expression analysis of the wx allele using RT-PCR and Northern blot analysis revealed that transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and that the deduced amino acid sequence of the transcript lacks a motif important for GBSS. Therefore, this insertion was considered to be the cause of the glutinous trait of 'Oragamochi'. This 7,764-bp insertion had long terminal repeats, a primer binding site, and a polypurine tract, but no sequence homologous with gag and pol, suggesting that it is a non-autonomous element. Furthermore, it had a structure similar to Dasheng and may be a member of Dasheng.
Additional References
RELATED GEPHE
Related Genes
Related Haplotypes
2
EXTERNAL LINKS
COMMENTS
@TE
YOUR FEEDBACK is welcome!