Project description:One day cold (14 and 19 °C) and hydrogen peroxide (H2O2) treatment of wheat (Triticum aestivum ssp. aestivum L.) variety Chinese Spring and two chromosome 5A substitution lines of Chinese Spring, Chinese Spring(T. ae. ssp. aestivum L. Cheyenne 5A) and Chinese Spring(T. ae. ssp. spelta L. 5A).
Project description:One day cold treatment of wheat (Triticum aestivum L.) lines Chinese Spring, Cheyenne and two 5A chromosome substitution lines of Chinese Spring, Chinese Spring(Cheyenne 5A) and Chinese Spring(Spelta 5A)
Project description:We monitored the transcriptomic response of roots and leaves of Triticum aestivum (cv Chinese Spring) at 2 months following the root inoculation by Azospirillum brasilense sp245 or Burkholderia graminis C4D1M. Plants were grown in pot containing a solid substrate (sand+soil) and 3 plants per pot, conditions in triplicates, in greenhouse conditions, and inoculated at seedling stage with OD 1 washed bacterial culture.
Project description:We monitored by RNAseq the transcriptomic response of roots and leaves of Triticum aestivum cv chinese Spring during a long term interaction with Funneliformis mossae (2 months) with or without a pathogen infection by infiltration of Xanthomonas translucens CFBP 2054. The control condition of roots and leaves wheat without mycorhizal fungi is in E-MTAB-5891 (material produced simultaneously and treated at the same time).
Project description:This study aimed at decrypting the transcriptomic response of 2 months-old grown tender wheat (cv Chinese Spring) to a the Xanthomonas translucens pathogen infection by infiltration. The response was monitored by RNAseq 24h post leaf clipping. Triticum aestivum cv. Chinese Spring plants were maintained in a growth chamber with cycles of 12 h of light at 21C and 50% relative humidity (RH) and 12 h of dark at 21C and 50% RH. Leaves of 49 days-old plants were infiltrated with a bacterial suspension in water with an optical density at 600 nm (OD600) of 0.5 using a needleless syringe. Plants inoculated with water were used as controls. For transcriptomic and proteomic analyses, leaves and root tissues were harvested 1 day post-inoculation (dpi), when symptoms were not visible yet. Three biological replicates per treatment were performed, and each with pooled leaves from two independent plants per replicate. The files per conditions and replicates are:Sample 1 Root tissue with 3 replicates: CONTROL * control condition for roots (wheat without pathogen infection): 3 replicates: 1.1R,1.2R, 1.3R * control condition for leaves (wheat without pathogen infection): 3 replicates1.1L,1.2L, 1.3L * Wheat Roots infected by Xanthomonas translucens: 3 replicates: 5.1R, 5.2R, 5.3R * Wheat Leaves infected by Xanthomonas translucens: 3 replicates: 5.1L, 5.2L, 5.3L
Project description:A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.
Project description:We report a time series RNA-seq experiment involving two isolates of Puccinia graminis separately infecting Triticum aestivum cv. Morocco points post inoculation
