GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00000493
Main curator
Martin
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Hordeum vulgare - Saffron
Trait State in Taxon B
Hordeum vulgare - Retriever
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Common Name
-
Synonyms
barley; Hordeum vulgare L.; Horedum vulgare
Rank
species
Lineage
Show more ... yta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
Hordeum vulgare - Saffron
Taxon B
Common Name
-
Synonyms
barley; Hordeum vulgare L.; Horedum vulgare
Rank
species
Lineage
Show more ... yta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
Hordeum vulgare - Retriever
GENOTYPIC CHANGE
Generic Gene Name
bHLH1
Synonyms
-
String
-
Sequence Similarities
-
GO - Biological Process
-
GO - Cellular Component
-
UniProtKB
Hordeum vulgare subsp. vulgare
GenebankID or UniProtKB
Presumptive Null
Yes
Molecular Type
Aberration Type
Deletion Size
10-99 bp
Molecular Details of the Mutation
16bp deletion resulting in premature stop codon
Experimental Evidence
Authors
Cockram J; White J; Zuluaga DL; Smith D; Comadran J; Macaulay M; Luo Z; Kearsey MJ; et al. ... show more
Abstract
Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
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