GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00000078
Main curator
Martin
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Oryza sativa indica - Kasalath
Trait State in Taxon B
Oryza sativa japonica - Nipponbare
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
Oryza sativa indica - Kasalath
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
Oryza sativa japonica - Nipponbare
GENOTYPIC CHANGE
Generic Gene Name
SSII-3
Synonyms
ALK; SSS2A; SSII-3; Os06g0229800; LOC_Os06g12450; P0525F01.23
Sequence Similarities
Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.
UniProtKB
Oryza sativa subsp. japonica
GenebankID or UniProtKB
Mutation #1
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
4 epistatic amino-acid substitutions - Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath versus Asp-88 and Ser-604 in japonica cultivars Nipponbare and Kinmaze SSIIa - Val-737 and Leu-781 in indica SSIIa versus Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa.
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid Glu Asp 88
Authors
Umemoto T; Yano M; Satoh H; Shomura A; Nakamura Y
Abstract
The present investigation revealed that the alk and gel(t) genes, which cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinisation in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties. The segregation pattern of the profile for amylopectin chain-length, which was distinguished by enrichment in short chains of DP<==11 and depletion in intermediate-size chains of 12<==DP<==24 in japonica as compared with indica, was exactly the same as those of the above physico-chemical properties of starch granules, and the gene was designated as acl(t). Gene-mapping analysis showed that the starch synthase IIa ( SSIIa) gene is located at the alk locus on chromosome 6 in the rice genome. These results lead us to the possibility that different alleles of the SSIIa gene are responsible for differences in amylopectin structure between the two varieties, in that SSIIa plays a distinct role in the elongation of short chains within clusters (A+B(1) chains) of amylopectin. It is proposed that the activity of SSIIa in japonica rice is reduced in amount or functional capacity relative to the activity of this enzyme in indica rice. This, in turn, would explain why starch from japonica rice has a lower gelatinisation temperature than starch from indica rice and is more susceptible to disintegration in alkali or urea. The evidence for this hypothesis is that the alk(t), gel(t), acl(t) and SSIIa genes all map to the same locus.
Mutation #2
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
4 epistatic amino-acid substitutions - Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath versus Asp-88 and Ser-604 in japonica cultivars Nipponbare and Kinmaze SSIIa - Val-737 and Leu-781 in indica SSIIa versus Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa.
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid Gly Ser 604
Authors
Umemoto T; Yano M; Satoh H; Shomura A; Nakamura Y
Abstract
The present investigation revealed that the alk and gel(t) genes, which cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinisation in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties. The segregation pattern of the profile for amylopectin chain-length, which was distinguished by enrichment in short chains of DP<==11 and depletion in intermediate-size chains of 12<==DP<==24 in japonica as compared with indica, was exactly the same as those of the above physico-chemical properties of starch granules, and the gene was designated as acl(t). Gene-mapping analysis showed that the starch synthase IIa ( SSIIa) gene is located at the alk locus on chromosome 6 in the rice genome. These results lead us to the possibility that different alleles of the SSIIa gene are responsible for differences in amylopectin structure between the two varieties, in that SSIIa plays a distinct role in the elongation of short chains within clusters (A+B(1) chains) of amylopectin. It is proposed that the activity of SSIIa in japonica rice is reduced in amount or functional capacity relative to the activity of this enzyme in indica rice. This, in turn, would explain why starch from japonica rice has a lower gelatinisation temperature than starch from indica rice and is more susceptible to disintegration in alkali or urea. The evidence for this hypothesis is that the alk(t), gel(t), acl(t) and SSIIa genes all map to the same locus.
Mutation #3
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
4 epistatic amino-acid substitutions - Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath versus Asp-88 and Ser-604 in japonica cultivars Nipponbare and Kinmaze SSIIa - Val-737 and Leu-781 in indica SSIIa versus Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa.
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid Val Met 737
Authors
Umemoto T; Yano M; Satoh H; Shomura A; Nakamura Y
Abstract
The present investigation revealed that the alk and gel(t) genes, which cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinisation in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties. The segregation pattern of the profile for amylopectin chain-length, which was distinguished by enrichment in short chains of DP<==11 and depletion in intermediate-size chains of 12<==DP<==24 in japonica as compared with indica, was exactly the same as those of the above physico-chemical properties of starch granules, and the gene was designated as acl(t). Gene-mapping analysis showed that the starch synthase IIa ( SSIIa) gene is located at the alk locus on chromosome 6 in the rice genome. These results lead us to the possibility that different alleles of the SSIIa gene are responsible for differences in amylopectin structure between the two varieties, in that SSIIa plays a distinct role in the elongation of short chains within clusters (A+B(1) chains) of amylopectin. It is proposed that the activity of SSIIa in japonica rice is reduced in amount or functional capacity relative to the activity of this enzyme in indica rice. This, in turn, would explain why starch from japonica rice has a lower gelatinisation temperature than starch from indica rice and is more susceptible to disintegration in alkali or urea. The evidence for this hypothesis is that the alk(t), gel(t), acl(t) and SSIIa genes all map to the same locus.
Mutation #4
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
4 epistatic amino-acid substitutions - Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath versus Asp-88 and Ser-604 in japonica cultivars Nipponbare and Kinmaze SSIIa - Val-737 and Leu-781 in indica SSIIa versus Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa.
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid Leu Phe 781
Authors
Umemoto T; Yano M; Satoh H; Shomura A; Nakamura Y
Abstract
The present investigation revealed that the alk and gel(t) genes, which cause the differences between a japonica rice variety Nipponbare and an indica rice variety Kasalath in terms of the disintegration of endosperm starch granules in alkali solution and their gelatinisation in a 4 M urea solution, respectively, cosegregated in backcross inbred lines derived from a cross between the two varieties. The segregation pattern of the profile for amylopectin chain-length, which was distinguished by enrichment in short chains of DP<==11 and depletion in intermediate-size chains of 12<==DP<==24 in japonica as compared with indica, was exactly the same as those of the above physico-chemical properties of starch granules, and the gene was designated as acl(t). Gene-mapping analysis showed that the starch synthase IIa ( SSIIa) gene is located at the alk locus on chromosome 6 in the rice genome. These results lead us to the possibility that different alleles of the SSIIa gene are responsible for differences in amylopectin structure between the two varieties, in that SSIIa plays a distinct role in the elongation of short chains within clusters (A+B(1) chains) of amylopectin. It is proposed that the activity of SSIIa in japonica rice is reduced in amount or functional capacity relative to the activity of this enzyme in indica rice. This, in turn, would explain why starch from japonica rice has a lower gelatinisation temperature than starch from indica rice and is more susceptible to disintegration in alkali or urea. The evidence for this hypothesis is that the alk(t), gel(t), acl(t) and SSIIa genes all map to the same locus.
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
@Epistasis @SeveralMutationsWithEffect
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