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Comparative genomic hybridization by array of barley chromosome arms to assign locations to genes

ABSTRACT: Assigning barley chromosome arm locations to genes using microarrays. DNA from flow sorted chromosome arms of barley cv Betzes were hybridised to custom Agilent barley 44k microarrays to determine gene content.

ORGANISM(S): Hordeum vulgare

SUBMITTER: Pete Hedley

PROVIDER: E-TABM-1063 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

Project description:We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Hatice Bilgic. The equivalent experiment is BB55 at PLEXdb.]

2011-11-22 | GSE33400 | GEO

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

Project description:We utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese SpringM-bM-^@M-^SBetzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Hatice Bilgic. The equivalent experiment is BB55 at PLEXdb.] genotype: CS (Chinese Spring)(3-replications); genotype: Betzes(3-replications); genotype: 1HS(3-replications); genotype: 2HS(3-replications); genotype: 3HS(3-replications); genotype: 3HL(3-replications); genotype: 4HS(3-replications); genotype: 4HL(3-replications); genotype: 5HS(3-replications); genotype: 5HL(3-replications); genotype: 7HS(3-replications); genotype: 7HL(3-replications)

2011-11-22 | E-GEOD-33400 | biostudies-arrayexpress

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

Project description:Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines

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Transcription profiling by array of wheat and barley to anchor physical and genetic maps in wheat using a barley array

Project 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.

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