Project description:A comparative RNA-Seq analysis was done in root and shoot of Najran wheat cultivar between plants grown under two conditions: control (0 mM NaCl) and salt treatment (200 mM NaCl). The current study revealed differentially expressed genes and various associated biological pathways involved in plant responses to salt stress between the two conditions in the root and shoot plant tissues, providing important insights into the molecular mechanisms underlying salt tolerance in wheat.
Project description:Study of gene expression under no salt condition from total leaf RNA and gene expression after five days of salt stress in 150mM NaCl from total leaf RNA of PcINO1 and OsINO1 introgressed IR-64 transgenic rice lines.
2019-11-01 | GSE122850 | GEO
Project description:RNA-Seq of ZM05 under Cd stress
Project description:Root traits are significant targets for breeding stress-resilient and high-yielding wheat genotypes under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research. We performed transcriptome analysis of thirty bread wheat cultivars using RNA-seq to investigate the diversity and expression of root system architecture (RSA) related transcripts. We examined the expression patterns of these transcripts in both root and leaf tissues and found that various transcripts are root-specific which could be manipulated for desirable root traits.The presented RNA-seq datasets provide valueable source for identification of genes involved in various biological processes under varying climatic conditions.
2023-06-29 | GSE235844 | GEO
Project description:Comparative RNA-seq of Wheat plants grown under salt stress (200 mM NaCl) conditions
Project description:Purpose: To characterize the functional implication of autophagy in the wheat response to stress, the key genes contributing in mediated salt tolerance of wheat seedlings through 3-MA were identified in normal or salt stress conditions in the presence or absence of added 3-MA by the transcriptome profiles. Methods: Four days after NaCl and 3-MA treatment, the roots and the third leaves were collected respectively with every 10 of them being mixed as one biological replicate for each treatment. Every treatment had four biological replicates. The wheat root and leaves mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The RNA-Seq data had high quality and reliable results were obtained from the transcriptome assembly. A high correlation between biological replicates was observed for all treatments, which indicated that the four biological replicates were reliable in this study. Based on the principal component analysis (PCA), a clear separation between the NaCl-treated group and controls could be observed. The Q30 percentage (sequences with sequencing error rate lower than 0.1%) was over 94%, and the average GC content of the RNA-seq reads was 55.46%. After removing the adaptor and low-quality sequence, each library received 68310810-83844286 clean reads. These clean reads were mapped to the reference genome with match ratios in the range of 93.6%-95.9%, and 120744 genes predicted from the genome were found to be expressed (with FPKM > 0), including 25180 annotated genes in wheat genome. 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings. Conclusions: 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings.
Project description:Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. Yield loss in durum wheat can be exacerbated due to minimal rainfall in the early reproductive stages of development during Spring in Australia. This study describes genotypic differences in the miRNAome between water deficit tolerant/sensitive durum, using flag leaf and developing head tissue, and more specifically identifies miRNAs associated with water deficit stress. Results: Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes (Tamaroi, Yawa, EGA Bellaroi, Tjilkuri), with or without water deficit stress. Illumina sequencing and subsequent analysis detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of the abundance of sequencing reads revealed 66 conserved miRNAs and five novel miRNA hairpins showing differential expression under water deficit stress. During stress, several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes studied. Several miRNAs were also identified to have different abundance in the flag leaf compared to the developing head regardless of treatment. Predicted mRNA targets from four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development. Conclusion: For the first time, we present a comprehensive study of the miRNA transcriptome of flag leaf and developing head tissues in different durum genotypes under water deficit stress. The identification of differentially expressed miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotype-specific physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs identified, and their interaction with mRNA targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:RNA-seq of leaves in Platostoma palustre under Cd stress
Project description:Stress events have transgenerational effects that influence plant growth in the subsequent generation. In Mediterranean regions, water-deficit and heat (WH) stress is a frequent issue that negatively affects crop yield and quality. Nitrogen (N) is an essential plant macronutrient and often a yield-limiting factor for crops. Here, the response of durum wheat seedlings to N starvation under the transgenerational effects of WH stress were investigated in two genotypes. Both genotypes showed significant reduction in seedling height, leaf number, shoot and root weight (fresh and dry), primary root length and chlorophyll content under N starvation stress. However, in the WH stress-tolerant genotype, the reduction rate of most traits were lower in progeny from the stressed parents than progeny from the control parents. Small RNA sequencing identified 1,534 microRNAs in different treatment groups. Differentially expressed microRNAs (DEMs) were characterized subject to N starvation, parental stress and genotype factors, with their target genes identified in silico. GO and KEGG enrichment analyses revealed the biological functions associated with DEM-target modules in stress adaptation processes, which could contribute to the phenotypic differences observed in two genotypes. The study provides the first evidence of the transgenerational effects of WH stress on N starvation response in durum wheat.