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Oryza sativa gene "DU1" (GR:0060261) | Species | Oryza sativa (Rice) [ GR_tax:013681 ] | ||||||
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| Accession | GR:0060261 | ||||||
| Gene Symbol | DU1 | ||||||
| Gene Name | DULL ENDOSPERM 1 | ||||||
| Synonyms (6) |
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| E.C. Numbers (0) | |||||||
| Pathway Reactions (0) | |||||||
| Chromosome No. | 10 | ||||||
| Gene Type | CDS (Protein coding) | ||||||
| Has Phenotype | yes | ||||||
| Description | "Dull" mutation lowers amylose content in endosperm (2.0-5.7% in mutant lines, 15.7% in original cv. Kinmaze). Grains have intermediate degree of translucence but character is expressed only when grains are dry (unlike floury mutants). I2-KI staining is intermediate between Kinmaze (blue) and waxy (brown). Dull endosperm mutants have closely packed squarish endosperm cells that are compactly filled with compound starch granules like those of waxy mutants. Endosperm cell surface is more uneven than Kinmaze but less than that of waxy mutants. Du1, encodes for Prp1, a member of the pre-mRNA processing protein family. It is expressed mainly in panicles and affects the starch biosynthesis by regulating the pre-mRNA splicing of Waxy gene (Wx, GR:0061010) and expression of other key genes involved in starch biosynthesis. It acts upstream of Wx gene in starch biosynthesis process. As reported by Zeng et al. (2007), the non-synonymous SNP mutation (G/A) in du1 at position 1742b in the first exon of cDNA results in the substitution of Serine (S) by Asparagine (N) at amino acid position position 581. This substitution was found to be present in the TPR7 (tetratric peptide repeat) domain at the C-terminal and may affect its interaction with other proteins leading to functional inefficiency (not a total loss of function). Du1 has about 73% identity with the Du1L (Dull 1 like; GR:0101268) gene located on chromosome-1. |
Germplasm (3) Sequences (4) | Protein |
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| Nucleotide (DNA) |
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Gene-To-Gene Interactions (0)
Gene Interactions (1) | # | Gene-1 | Gene-1 object | Mode of action | Gene-2 | Gene-2 object | Evidence | Evidence code | Comment |
|---|---|---|---|---|---|---|---|---|
| 1 | DU1 | protein | down-regulates | WX1 | RNA | Zeng-D et al., 2007 | IGI | regulates the pre-mRNA splicing of Waxy (Wx) transcript |
Map Positions (2) | Map Type | Map Set | Name | Map | Position | Ext. Links | |||
|---|---|---|---|---|---|---|---|---|
| Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 10 | 18,938,237-18,942,831bp | View Comparative Map | |||
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| Map Type | Map Set | Name | Map | Position | Ext. Links | |||
|---|---|---|---|---|---|---|---|---|
| Genetic | JRGP RFLP 2000 | BNL6.32 | 10 | 51.8-54.8cM | View Comparative Map | |||
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Gene Map Positions (2) | Map Position [ View in Marker DB ] | |||||
|---|---|---|---|---|---|
| # | Map Set Name | Linkage Group | Start Position | Stop Position | CMap Feature Acc |
| 1 | JRGP RFLP 2000 | 10 | 51.8 cM | 54.8 cM | jrgp-2000-10-ip1 |
| 2 | Rice japonica MSU6 | Chr. 10 | 18938237 bp | 18942831 bp | grjp2009a-10-GR:0060261 |
Associated Ontologies (18) | Trait | amylose content (TO:0000196) |
| Plant Structure | root (PO:0009005), stem (PO:0009047), inflorescence (PO:0009049), endosperm (PO:0009089), leaf lamina (PO:0020039), leaf sheath (PO:0020104) |
| Plant Growth and Development Stage | whole plant fruit ripening complete stage (PO:0007038) |
| Cereal Plant Growth Stage | 09-mature grain stage (GRO:0007045), 6.1-flowering stage (GRO:0007151) |
| Cellular Component | intracellular (GO:0005622), amyloplast starch grain (GO:0009568) |
| Biological Process | mRNA splicing, via spliceosome (GO:0000398), polysaccharide metabolic process (GO:0005976), RNA processing (GO:0006396), starch biosynthetic process (GO:0019252) |
| Environment | Magnaporthe grisea (EO:0007226), unknown environment (EO:0007403) |
Associated QTL (0)
Database Cross-References (1) Literature (14) Images (3) 1.
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1. Phenotypes of dull endosperm are affected by low temperature treatments (middle row) and no effects for both glutinous (wx) (top row) and normal endosperms (bottom row). Three temperature conditions are; 26-18°C, 26-20°C and 28-24°C for noon and night (from left to right). (Photo courtesy H. Kikuchi). |
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2. Chalky endosperms due to du1 gene (on two from left). (Photo courtesy H. Satoh) |
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3. Opaque grains caused by low amylose content in endosperm, similar to waxy (glutinous) rice phenotype. The top row is brown rice, the middle row is milled rice, and the bottom row is reaction to I2-KI solution. From left to right, the first is normal, the second is du-1, the third is du-2, the forth is du-3, the fifth is du-4, the sixth is du-5. |
SNPs (15) | Chr | Start | Stop | Exp | Num. SNP Positions | |
|---|---|---|---|---|---|
| chr10 | 18,938,237 | 18,942,831 | ~160K SNPs x 20 accessions (McNally 2... | 4 | Search for SNPs |
| chr10 | 18,938,237 | 18,942,831 | '1536 chip' - 1311 SNPs x 395 rice ac... | 0 | |
| chr10 | 18,938,237 | 18,942,831 | Huang X, et al, Nat Genetics 2010 Nov... | 5 | Search for SNPs |
| chr10 | 18,938,237 | 18,942,831 | RiceDiversity 44K SNP assay, 34 trait... | 5 | Search for SNPs |
| chr10 | 18,938,237 | 18,942,831 | RiceDiversity 44K SNP assay, 34 trait... | 1 | Search for SNPs |
