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Oryza sativa QTL "CQE38" (chlorophyll ratio)
| QTL Accession ID | CQE38 |
|---|---|
| Species | Oryza sativa (Rice) [ GR_tax:013681 ] |
| Trait Symbol | CHLRO |
| Trait Name | chlorophyll ratio |
| Published Symbol | |
| Trait Synonym(s) | |
| Trait Category | Biochemical |
| Chromosome | 5 |
| Comments | The ratio of Chl-a to Chl-b (Chl a:b) were analyzed at 5 days after heading. Assay is an indicator of relative amounts of photosystem I or II. The means of ten replications per line were used in the data analysis. Phenotypic effect contributed by Nipponbare allele. Chromosomal locations of putative QTLs were determined by single-factor analysis (one-way ANOVA) with the general linear model procedure of QGENE. Two-way ANOVAs for epistatic interaction were also carried out with QGENE at Pd0.01 threshold. The tests were done only with marker loci linked to QTLs with a single-factor P of d0.01 to reduce the likelihood of committing a type-I error. |
Map Positions (2)
| Map Type | Map Set | Name | Map | Position | Ext. Links | |||
|---|---|---|---|---|---|---|---|---|
| Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 5 | 139,187-3,344,572 bp | View Comparative Map | |||
|
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| Map Type | Map Set | Name | Map | Position | Ext. Links | |||
|---|---|---|---|---|---|---|---|---|
| QTL | JRGP Nip/Kas F2 QTL 2000 | BNL6.32 | 5 | 3-27.7 cM | View Comparative Map | |||
|
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QTL DB Map Position (1)
| Name | Chromosome | Start | Stop |
|---|---|---|---|
| CQE38 | 5 | 3 | 27.7 |
Associated Markers (48)
Associated Genes (0)
Associated Ontologies (9)
| Term Type | Term | Evidence |
|---|---|---|
| Trait Ontology | (TO:0000298) | Ishimaru-K et al., 2001 (IAGP) |
| Plant Structure | (PO:0020103) | Ishimaru-K et al., 2001 (SM) |
| (PO:0009025) | Gramene curators, 2007 (IC) | |
| Plant Growth and Development Stage | (PO:0007134) | Ishimaru-K et al., 2001 (SM) |
| (PO:0007041) | Ishimaru-K et al., 2001 (SM) | |
| (PO:0007130) | Gramene curators, 2007 (IC) | |
| Growth Stage | (GRO:0007139) | Ishimaru-K et al., 2001 (SM) |
| Environment | (EO:0007403) | Gramene curators, 2007 (IC) |
| Species Ontology | (GR_tax:013681) | Ishimaru-K et al., 2001 (SM) |
Database Cross-References (1)
SNPs (14,622)
| Chr | Start | Stop | Exp | Num. SNP Positions | |
|---|---|---|---|---|---|
| chr5 | 139,187 | 3,344,572 | ~160K SNPs x 20 accessions (McNally 2... | 1,908 | Search for SNPs |
| chr5 | 139,187 | 3,344,572 | '1536 chip' - 1311 SNPs x 395 rice ac... | 18 | Search for SNPs |
| chr5 | 139,187 | 3,344,572 | Huang X, et al, Nat Genetics 2010 Nov... | 6,120 | Search for SNPs |
| chr5 | 139,187 | 3,344,572 | RiceDiversity 44K SNP assay, 34 trait... | 6,120 | Search for SNPs |
| chr5 | 139,187 | 3,344,572 | RiceDiversity 44K SNP assay, 34 trait... | 456 | Search for SNPs |
