QTL Accession ID | CQO1 |
---|---|
Species | Oryza sativa (Rice) [ GR_tax:013681 ] |
Trait Symbol | COLDTL |
Trait Name | cold tolerance |
Published Symbol | ctb-1 |
Trait Synonym(s) |
ctol low temperature resistance |
Trait Category | Abiotic stress |
Chromosome | 4 |
Comments | The QTL was identified in the NIL derived from 12 recombinants in a segregating population BT4 derived from a single plant heterozygous for introgression on Chr4. This plant was derived from a BC2 population of a cross between Syo6 and Kirara397. Syo6 contains introgressed segments on chr3 and chr4 from BC1F5 lines derived from the cross Kirara397/Norin-PL8//Kirara397. Norin-PL8 and Kirara397 are cold-tolerant and cold-sensitive varieties respectively. MAPL97 used for interval mapping and StatView 5.0 was used for analysis of variance between marker classes. The trait cold tolerance was assayed by using the cool-water irrigation method. After the seed ripening stage, the cold tolerance was evaluated on the basis of mean seed fertility. The experiment was carried out both in the field and green house. The QTL is closely associated with the QTL for large anther length (QTL accession:CQO2) present in the same region. The gene OsAOX1a for terminal alternative oxidase (Gramene Protein Accession: O82807) was mapped in the same region of the QTL. The sequencing of the gene product and western blot analyses revealed a single nucleotide polymorphism (SNP) or allelic variation for the gene OsAOX1a among the parents Kirara397 and Norin-PL8. The Kirara397 allele accries a base subsitution at position 297 in codon AAG (Lys71). It is replaced by T in codon AAT (Asn71) in Norin-PL8. The western blot analyses revealed a 32 kDa and 34kDa bands for OsAOX1a in Kirara397 and Norin-PL8 respectively. There is another gene OsAOX1b for terminal alternative oxidase (Gramene Protein Accession: O82766) which also maps in the same region as that for OsAOX1a (Gramene curation). The study involving OsAOX1a also suggests that OsAOX1b neither the protein or its transcripts were detected, thus suggesting a strong correlation between the QTL and the gene OsAOX1a. |
Map Type | Map Set | Name | Map | Position | Ext. Links | |||
---|---|---|---|---|---|---|---|---|
Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 4 | 31,276,528-32,772,351 bp | View Comparative Map | |||
|
Map Type | Map Set | Name | Map | Position | Ext. Links | |||
---|---|---|---|---|---|---|---|---|
QTL | JRGP Nip/Kas F2 QTL 2000 | BNL6.32 | 4 | 106.5-113.2 cM | View Comparative Map | |||
|
Name | Chromosome | Start | Stop |
---|---|---|---|
CQO1 | 4 | 106.5 | 113.2 |
Term Type | Term | Evidence |
---|---|---|
Trait Ontology | (TO:0000303) | Saito-K et al., 2001 (IAGP) Abe-F et al., 2002 (IAGP) |
Plant Structure | (PO:0009049) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
(PO:0009066) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
|
(PO:0000003) | Gramene curators, 2007 (IC) | |
(PO:0009011) | Gramene curators, 2007 (IC) | |
Plant Growth and Development Stage | (PO:0007134) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
(PO:0007041) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
|
(PO:0007033) | Gramene curators, 2007 (IC) | |
(PO:0009012) | Gramene curators, 2007 (IC) | |
Growth Stage | (GRO:0007001) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
Environment | (EO:0007174) | Gramene curators, 2007 (IC) |
Species Ontology | (GR_tax:013681) | Saito-K et al., 2001 (SM) Abe-F et al., 2002 (SM) |
Chr | Start | Stop | Exp | Num. SNP Positions | |
---|---|---|---|---|---|
chr4 | 31,276,528 | 32,772,351 | ~160K SNPs x 20 accessions (McNally 2... | 756 | Search for SNPs |
chr4 | 31,276,528 | 32,772,351 | '1536 chip' - 1311 SNPs x 395 rice ac... | 10 | Search for SNPs |
chr4 | 31,276,528 | 32,772,351 | Huang X, et al, Nat Genetics 2010 Nov... | 5,636 | Search for SNPs |
chr4 | 31,276,528 | 32,772,351 | RiceDiversity 44K SNP assay, 34 trait... | 5,636 | Search for SNPs |
chr4 | 31,276,528 | 32,772,351 | RiceDiversity 44K SNP assay, 34 trait... | 211 | Search for SNPs |