RNA-Seq from wheat-Th. elongatum translocation line Zhongke 1878
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ABSTRACT:
PROVIDER: PRJNA720120 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To screen the transcripts from Th. elongatum 7EL, we inoculated the spikes of translocation line Zhongke 1878 with Fusarium graminearum. We performed full-length transcriptome sequencing after 96 hours. To detect the expression level, we performed RNA-Seq on Zhongke 1878 after 12h, 24h, 48h and 96h.
2021-04-07 | GSE171576 | GEO
Project description:The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum.
2015-09-14 | GSE70797 | GEO
Project description:The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum. Expression profiling of inoculated rachis from CS and CS-7EL heads sampled at 4 days after inoculation. Inoculation of all developed spikelets on each head at mid-anthesis was done with either water or F. graminearum strain DAOM 180378. Three biological replicates were done for each treatment, and 10 to 12 heads were inoculated per biological replicate.
2015-09-14 | E-GEOD-70797 | 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:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.
2016-04-02 | GSE63752 | 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
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).
2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress
Project description: Not available
| S-EPMC5790049 | biostudies-literature
Project description:Triticum aestivum/Dasypyrum villosum translocation line Assembly
| PRJNA700793 | ENA
Project description:Five RNA samples were used. The RNA source material was from wheat cytogenetic stocks from Dr. Adam Lukaszewski, University of California, Riverside. The lines used for this study are Pavon, Pavon Dt1BL, 1RS.1BL, 1B+5 and T-1 wheat samples. whole seedling minus starchy endosperm. Equal portions of RNA from unstressed and 48 hr drought-stressed seedling were combined to make one RNA sample. The person who produced the RNA was Prasanna R. Bhat in the TJ Close lab at University of California, Riverside. Everything downstream of RNA production was done at the UC Irvine DNA and Protein Microarray Facility (Denis Heck, manager) by Sriti Misra. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Prasanna Bhat. The equivalent experiment is TA10 at PLEXdb.] genetic line: Pavon(2-replications); genetic line: Pavon Dt1BL(2-replications); genetic line: 1RS.1BL(2-replications); genetic line: T-1(2-replications); genetic line: 1B+5(2-replications)
2011-08-30 | E-GEOD-31754 | biostudies-arrayexpress