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Title: Transcription profiling by array of wheat and barley to anchor physical and genetic maps in wheat using a barley array      
dateReleased:
12-02-2010
description:
Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. However, we recently constructed the first physical map of a wheat chromosome (3B). But gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridized to a barley Agilent 15K expression microarray. This led to the identification of 738 barley genes with a homolog on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-TABM-1011
refinement:
raw
dateSubmitted:
06-02-2010
keywords:
functional genomics
dateModified:
05-02-2014
creators:
Pete Hedley
availability:
available
types:
gene expression
name:
reference
ID:
A-MEXP-1533
name:
SCRI Hordeum vulgare 15k v2 col 82 row 192
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-TABM-1011/E-TABM-1011.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-TABM-1011/E-TABM-1011.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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