GEPHE SUMMARY Print
Gephebase Gene
B2
Entry Status
Published
GepheID
GP00002058
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
yellow bulb
Trait State in Taxon B
white bulb - recessive allele
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
onion
Synonyms
onion; Allium cepa L.
Rank
species
Lineage
Show more ... reptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Amaryllidaceae; Allioideae; Allieae; Allium
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B
Latin Name
Common Name
onion
Synonyms
onion; Allium cepa L.
Rank
species
Lineage
Show more ... reptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Amaryllidaceae; Allioideae; Allieae; Allium
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
-
Synonyms
-
String
-
Sequence Similarities
-
GO - Molecular Function
-
GO - Biological Process
-
GO - Cellular Component
-
UniProtKB
GenebankID or UniProtKB
Presumptive Null
Yes
Molecular Type
Aberration Type
Insertion Size
100-999 bp
Molecular Details of the Mutation
577-bp insertion of a transposable element named AcWHITE in the 5′ upstream region of the white allele of B2. A 8-bp target site duplication (GTTATA AC) and a 7-bp terminal inverted repeat (CAAGGTT) were identified at both ends of this insertion - no SNP detected in the coding region
Experimental Evidence
Authors
Jo C; Kim S
Abstract
A DNA transposon was found in the gene encoding a bHLH transcription factor. Genotypes of the marker tagging this DNA transposon perfectly co-segregated with color phenotypes in large F populations A combined approach of bulked segregant analysis and RNA-Seq was used to isolate causal gene for C locus controlling white bulb color in onions (Allium cepa L.). A total of 114 contigs containing homozygous single nucleotide polymorphisms (SNPs) between white and yellow bulked RNAs were identified. Four of them showed high homologies with loci clustered in the middle of chromosome 5. SNPs in 34 contigs were confirmed by sequencing of PCR products. One of these contigs showed perfect linkage to the C locus in F populations consisting of 2491 individuals. However, genotypes of molecular marker tagging this contig were inconsistent with color phenotypes of diverse breeding lines. A total of 146 contigs showed differential expression between yellow and white bulks. Among them, transcription levels of B2 gene encoding a bHLH transcription factor were significantly reduced in white RNA bulk and F individuals, although there was no SNP in the coding region. Phylogenetic analysis showed that onion B2 was orthologous to bHLH-coding genes regulating anthocyanin biosynthesis pathway in other plant species. Promoter regions of B2 gene were obtained by genome walking and a 577-bp non-autonomous DNA transposon designated as AcWHITE was found in the white allele. Molecular marker tagging AcWHITE showed perfect linkage with the C locus. Marker genotypes of the white allele were detected in some white accessions. However, none of tested red or yellow onions contained AcWHITE insertion, implying that B2 gene was likely to be a casual gene for the C locus.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
COMMENTS
@TE @&-No-UniProtKB-curated
YOUR FEEDBACK is welcome!