Pale-green durum wheat mutant under terminal drought stress condition
Ontology highlight
ABSTRACT:
ORGANISM(S): Triticum turgidum Triticum aestivum
PROVIDER: GSE47090 | GEO | 2016/05/09
SECONDARY ACCESSION(S): PRJNA203539
REPOSITORIES: GEO
Similar Datasets
Project description:Durum wheat is an important cereal crop grown mainly in semi-arid environments (e.g. Mediterranean regions) characterized by water scarcity and high temperatures often occurring at the same time. This work reports on a transcriptomic analysis carried out on two durum wheat cultivars (Cappelli and Ofanto) characterized by different water use efficiency (WUE), grown to booting stage and subjected to a combination of drought and heat stresses, a situation similar to the experience of a crop grown in Mediterranean environments and exposed to a terminal heat/drought stress. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, alessio. The equivalent experiment is TA47 at PLEXdb.]
2016-03-22 | GSE45563 | GEO
Project description:To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10) lacks the distal part (43%) of the long arm of chromosome 5A. Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA23 at PLEXdb.]
2011-08-31 | GSE31759 | GEO
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.
2015-10-01 | GSE69339 | GEO
Project description:A global, systems-based study of the transcriptome response of three drought resistant durum wheat genotypes to water stress. Two parents of a mapping population (Lahn x Cham 1) and a recombinant inbred line (RIL2219), selected for their drought resistance in multiyear field trials, were subjected to controlled time series water stress and samples taken over a six day period to study flag leaf gene expression in parallel with physiological measurements. The aim was to dissect the responses to water stress in an attempt to identify molecular and physiological properties defining stress resistance and thus to build knowledge to accelerate the breeding effort.
2014-09-29 | E-MTAB-2410 | biostudies-arrayexpress
Project description:To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10) lacks the distal part (43%) of the long arm of chromosome 5A. Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA23 at PLEXdb.] genotype: Creso - stress condition: Control(3-replications); genotype: Creso - stress condition: Mild stress(3-replications); genotype: Creso - stress condition: Severe stress(3-replications); genotype: CS - stress condition: Control(3-replications); genotype: CS - stress condition: Mild stress(3-replications); genotype: CS - stress condition: Severe stress(3-replications); genotype: CS-5AL - stress condition: Control(3-replications); genotype: CS-5AL - stress condition: Mild stress(3-replications); genotype: CS-5AL - stress condition: Severe stress(3-replications)
2011-08-30 | E-GEOD-31759 | biostudies-arrayexpress
Project description:Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in germination time-course and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly has revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provides the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for superior breeding germplasm and/or varieties.
2020-02-04 | GSE143454 | GEO
Project description:Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.
2020-08-20 | GSE152973 | GEO
Project description:Barley cv. Morex inoculated with Fusarium graminearum (isolate Butte 86) or water (mock). Sampled at 24, 48, 72, 96 and 144 hours after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jayanand Boddu. The equivalent experiment is BB9 at PLEXdb.]
2011-11-22 | GSE33407 | GEO
Project description:Six months old seed grown under well-watered greenhouse conditions were used in the current study. The seedlings of the two wild emmer wheat genotypes were vernalized on a moist germination paper (Hofman Manufacturing, Inc, Jefferson, OR, USA) for three weeks in the dark at 4oC, followed by three days acclimation at 24oC. Seedlings were then transplanted into 5L pots containing a mixture of pure quartz sand and peat (4:1 v/v), supplemented with a slow release fertilizer (2 g/L, Osmocote® Standard 14-14-14, Scotts-Sierra Horticulture, Marysville, OH, USA) and by a weekly application of 100 ml/pot of 0.5X Murashigi and Skoog growth solution (Sigma Chemical Co., St Louis, MO, USA). Pots were placed in a screen-house under natural winter conditions (December to February; 5-18°C) in Haifa, Israel (Mt. Carmel; 35o01′ E, 32o45′ N; 480 m above sea level) for 10 weeks and irrigated daily by a drip irrigation system. Three weeks prior to application of terminal drought stress, the pots were transferred to a controlled environment greenhouse (22/18 oC; 12 h day/12 h night) in order to prevent rainfall during the drought experiment. Five pots per genotype served as biological replicates, plants of three pots of each genotype/treatment were used for transcriptome study whereas two additional pots were used for quantitative PCR analysis (altogether five biological replicated of were used for quantitative real time PCR). Three individual plants were grown in each pot, one plant was used for measurements of leaf relative water content (RWC) (Barrs and Weatherley 1968), whereas the other two plants were used for sampling of flag leaf tissue for RNA extraction. Terminal drought stress (D) was applied at inflorescence emergence stage (Zadoks 50-60), (Zadoks et al. 1974), after emergence of 1-2 spikes in all biological replicates of both genotypes. The time from transplanting to inflorescence emergence stage was not significantly different between genotypes (70 days in the S genotype and 72 days in the R genotype). Drought stress application initiated after irrigation with excess amount of water in order to assure that all pots start the experiment at the same soil water capacity. Drought stress was imposed by withholding water for eight days until stress symptoms (i.e. leaf rolling and wilting symptoms) were visible in plants of both genotypes. Stress symptoms were more visible in the S genotype, however, leaf relative water content (RWC), measured after eight days of drought stress was low but was not significantly different between the two genotypes (49.68%±1.48 in the R genotype and 53.34%±1.83 in the S genotype). The well-watered control (C) plants were irrigated daily by ample amount of water. Flag leaf tissues of drought-stressed plants and well-watered control plants were harvested, immediately frozen in liquid nitrogen, and stored at -80ºC for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Krugman Tamar. The equivalent experiment is TA33 at PLEXdb.]
2011-08-31 | GSE31762 | GEO
Project description:Water-deficit stress negatively affects wheat yield and quality. Abiotic stress on the parental plants during reproduction could have transgenerational effects on the progenies. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in the progenies. Parental water-deficit stress had positive impacts on the progenies in certain traits like harvest index and protein content in given genotype. Small RNA-seq identified 1739 conserved and 774 novel microRNAs (miRNAs). Transcriptome-seq characterised the expression of 66,559 genes while degradome-seq profiled the miRNA-guided mRNA cleavage dynamics. Differentially expressed miRNAs and genes were identified, with significant regulatory patterns subject to trans- and inter- generational stress. Integrated analysis based on the three omics revealed the significant biological interactions between stress-responsive miRNA and targets, with possible contributions towards transgenerational stress tolerance via pathways such as hormone signalling and nutrient metabolism. Our study provides the first confirmation of the transgenerational effects of water-deficit stress in durum wheat. New insights gained on the molecular level indicate that key miRNA-mRNA modules are potential candidates in transgenerational stress improvement.
2021-02-03 | GSE162008 | GEO