GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00001779
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Oryza sativa - non-fragrant
Trait State in Taxon B
Oryza sativa - fragrant - variety from India, Sri Lanka and Nepal
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?
No
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
Katak Tara; Suwanda Al; UPRB28 Basmati Bahar; Basmati
GENOTYPIC CHANGE
Generic Gene Name
BADH2
Synonyms
fgr; BADH2; OsBADH2; OsJ_27367; LOC_Os08g32870; Os08g0424500; OSJNBa0056L09.30; P0456B03.101
Sequence Similarities
Belongs to the aldehyde dehydrogenase family.
UniProtKB
Oryza sativa subsp. japonica
GenebankID or UniProtKB
Presumptive Null
Yes
Molecular Type
Aberration Type
Insertion Size
1-9 bp
Molecular Details of the Mutation
1-bp insertion (G) in exon 14
Experimental Evidence
Authors
Kovach MJ; Calingacion MN; Fitzgerald MA; McCouch SR
Abstract
Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (BADH2) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the BADH2 gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the badh2.1 allele within the Japonica varietal group and demonstrate the introgression of this allele from Japonica to Indica. Basmati-like accessions were nearly identical to the ancestral Japonica haplotype across a 5.3-Mb region flanking BADH2 regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the Japonica gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the Indica varietal group.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
9
COMMENTS
@Parallelism
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