Species | Oryza sativa (Rice) [ GR_tax:013681 ] | ||||||||||||
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Accession | GR:0060894 | ||||||||||||
Gene Symbol | SK2 | ||||||||||||
Gene Name | SCENTED KERNEL 2 | ||||||||||||
Synonyms (11) |
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E.C. Numbers (1) | 1.2.1.8 | ||||||||||||
Pathway Reactions (6) |
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Chromosome No. | 8 | ||||||||||||
Gene Type | CDS (Protein coding) | ||||||||||||
Has Phenotype | yes | ||||||||||||
Description | sk1 also called as fgr is linked to one of the most important traits in rice, i.e. fragrance. This trait has undergone human selection during domestication. The fragrance of basmati and jasmine rice is associated with the presence of 2-acetyl-1-pyrroline. sk1 encodes for betaine aldehyde dehydrogenase (BAD). Compared to the non-fragrant genotypes, the accumulation of 2-acetyl-1-pyrroline in fragrant rice genotypes is due to the loss of BAD activity. The allele in fragrant genotypes has a mutation introducing a stop codon upstream of key amino acid sequences conserved in other BADs. Another fragrance related gene called BAD1 is present on chromosome 4. The loss of function of SK1 does not affect the growth of fragrant rice genotypes. |
Protein |
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Nucleotide (DNA) |
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 8 | 20,377,081-20,383,348bp | View Comparative Map | |||
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Genetic | IGCN 1998 | BNL6.32 | 8 | 85.1-114.6cM | View Comparative Map | |||
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JRGP RFLP 2000 | BNL6.32 | 8 | 71.7-72.2cM | View Comparative Map | ||||
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KRGRP 1998 | BNL6.32 | 8 | 78.6-104.1cM | View Comparative Map | ||||
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Map Position [ View in Marker DB ] | |||||
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# | Map Set Name | Linkage Group | Start Position | Stop Position | CMap Feature Acc |
1 | IGCN 1998 | 8 | 85.1 cM | 114.6 cM | igcn-1998-8_GR:0060894 |
2 | KRGRP 1998 | 8 | 78.6 cM | 104.1 cM | krgrp-1998-8_GR:0060894 |
3 | JRGP RFLP 2000 | 8 | 71.7 cM | 72.2 cM | jrgp-rflp-2000-8_GR:0060894 |
4 | Rice japonica MSU6 | Chr. 8 | 20377081 bp | 20383348 bp | grjp2009a-8-GR:0060894 |
Trait | aroma (TO:0000087) |
Plant Structure | whole plant (PO:0000003), seed (PO:0009010), plant structure (PO:0009011) |
Plant Growth and Development Stage | whole plant development stage (PO:0007033), whole plant fruit ripening complete stage (PO:0007038), plant structure development stage (PO:0009012) |
Cellular Component | peroxisome (GO:0005777) |
Molecular Function | betaine-aldehyde dehydrogenase activity (GO:0008802) |
Biological Process | response to stress (GO:0006950), phenylpropanoid metabolic process (GO:0009698), glycine betaine biosynthetic process (GO:0031456) |
Chr | Start | Stop | Exp | Num. SNP Positions | |
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chr8 | 20,377,081 | 20,383,348 | ~160K SNPs x 20 accessions (McNally 2... | 0 | |
chr8 | 20,377,081 | 20,383,348 | '1536 chip' - 1311 SNPs x 395 rice ac... | 0 | |
chr8 | 20,377,081 | 20,383,348 | Huang X, et al, Nat Genetics 2010 Nov... | 9 | Search for SNPs |
chr8 | 20,377,081 | 20,383,348 | RiceDiversity 44K SNP assay, 34 trait... | 9 | Search for SNPs |
chr8 | 20,377,081 | 20,383,348 | RiceDiversity 44K SNP assay, 34 trait... | 0 |