Microarray of barley genes in wheat-barley chromosome addition lines
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PROVIDER: PRJNA148947 | ENA |
REPOSITORIES: ENA
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Project description:Transcript levels of barley genes were examined in the wheat-barley chromosome addition lines having one of six barley chromomes, 2H, 3H, 4H, 5H, 6H and 7H. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Seungho Cho. The equivalent experiment is BB8 at PLEXdb.]
2011-11-22 | GSE33415 | GEO
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels.
2011-12-08 | GSE28023 | GEO
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
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels. Gene expression levels of each barley chromosome addition line of common wheat were compared to that of common wheat. Total RNA samples were isolated from the 2-week-old seedling leaves. The experiments were replicated three times for each addition line using independent samples.
2011-12-08 | E-GEOD-28023 | biostudies-arrayexpress
Project description:Transcript levels of barley genes were examined in the wheat-barley chromosome addition lines having one of six barley chromomes, 2H, 3H, 4H, 5H, 6H and 7H. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Seungho Cho. The equivalent experiment is BB8 at PLEXdb.] genotype: chr2H(3-replications); genotype: chr2HL(3-replications); genotype: chr3H(3-replications); genotype: chr4H(3-replications); genotype: chr5H(3-replications); genotype: chr6H(3-replications); genotype: chr6HL(3-replications); genotype: chr6HS(3-replications); genotype: chr7H(3-replications); genotype: Betzes(3-replications); genotype: Chinese Spring(3-replications)
2011-11-22 | E-GEOD-33415 | biostudies-arrayexpress
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
Project description:Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines
| PRJNA149141 | ENA
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.
2010-12-02 | E-TABM-1011 | biostudies-arrayexpress
Project description:Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affecting the flowering heads (or spikes). A FHB resistance locus has been identified on the chromosome 7E of the wild wheat relative Thinopyrum elongatum (Th.e.). That chromosome (7E) or a long arm fragment of it (7EL) have been transferred as additions in the wheat background 'Chinese Spring' (CS). The two addition lines are resistant to FHB while 'Chinese Spring' is moderately susceptible to it. The mechanism of resistance is not known. The analysis of this work is published in the Canadian Journal of Plant Pathology (Wang et al, 2010).
2010-06-15 | GSE21386 | GEO
Project description:Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affecting the flowering heads (or spikes). A FHB resistance locus has been identified on the chromosome 7E of the wild wheat relative Thinopyrum elongatum (Th.e.). That chromosome (7E) or a long arm fragment of it (7EL) have been transferred as additions in the wheat background 'Chinese Spring' (CS). The two addition lines are resistant to FHB while 'Chinese Spring' is moderately susceptible to it. The mechanism of resistance is not known. The analysis of this work is published in the Canadian Journal of Plant Pathology (Wang et al, 2010). We used the wheat microarray to determine the global expression profil in inoculated spikelets of the addition and parental lines, after water or Fg treatment, with samplings at 2 and 4 days after inoculation (DAI).
2010-06-23 | E-GEOD-21386 | biostudies-arrayexpress