GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00001542
Main curator
Prigent
PHENOTYPIC CHANGE
Trait #1
Trait Category
Trait
Trait State in Taxon A
Nipponbare japonica (NPB) cultivar
Trait State in Taxon B
Ping13 (P13) indica variety with superior grain length and appearance quality (decreased chalkiness & larger starch granules)
Trait #2
Trait Category
Trait
Trait State in Taxon A
-
Trait State in Taxon B
-
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?
Yes
Taxon A Description
Nipponbare japonica (NPB) cultivar
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
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
Ping13 (P13) indica variety with superior grain length and appearance quality (decreased chalkiness & larger starch granules)
GENOTYPIC CHANGE
Generic Gene Name
Os07g0603400
Synonyms
OsJ_25030; OSNPB_070603400
String
-
Sequence Similarities
-
GO - Molecular Function
-
GO - Biological Process
-
GO - Cellular Component
-
UniProtKB
Oryza sativa subsp. japonica
Oryza sativa subsp. japonica
Mutation #1
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsense
Molecular Details of the Mutation
first null mutation resulting in a truncated protein of a negative regulator of GL7 in long-grain varieties - GAA>TAA (Fig S15 - the stop codon has not been highlighted)
Experimental Evidence
Taxon A | Taxon B | Position | |
---|---|---|---|
Codon | GAA | TAA | - |
Amino-acid | Glu | STP | - |
Main Reference
Authors
Wang Y; Xiong G; Hu J; Jiang L; Yu H; Xu J; Fang Y; Zeng L; et al.
... show more
Abstract
Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits. Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.
Additional References
Mutation #2
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsense
Molecular Details of the Mutation
second null mutation resulting in a truncated protein of a negative regulator of GL7 in long-grain varieties - TGG>TAG (Fig S15 - this second stop codon has been highlighted)
Experimental Evidence
Taxon A | Taxon B | Position | |
---|---|---|---|
Codon | TGG | TAG | - |
Amino-acid | Trp | STP | - |
Main Reference
Authors
Wang Y; Xiong G; Hu J; Jiang L; Yu H; Xu J; Fang Y; Zeng L; et al.
... show more
Abstract
Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits. Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.
Additional References
RELATED GEPHE
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
same allele found in Oryza rufipogon indicating that this natural variation could be an ancient event
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